Gene expression profile algorithm and test for likelihood of recurrence of colorectal cancer and response to chemotherapy

Information

  • Patent Grant
  • 10179936
  • Patent Number
    10,179,936
  • Date Filed
    Friday, April 30, 2010
    14 years ago
  • Date Issued
    Tuesday, January 15, 2019
    5 years ago
Abstract
Algorithm-based molecular assays that involve measurement of expression levels of prognostic and/or predictive genes, or co-expressed genes thereof, from a biological sample obtained from a cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of recurrence of colorectal cancer and/or the likelihood of a beneficial response to chemotherapy for the patient are provided herein. Methods of analysis of gene expression values of prognostic and/or predictive genes, as well as methods of identifying gene expression-tumor region ratios, tumor-associated stromal surface area, and gene cliques, i.e. genes that co-express with a validated biomarker and thus may be substituted for that biomarker in an assay, are also provided.
Description
TECHNICAL FIELD

The present disclosure relates to molecular diagnostic assays that provide information concerning prognosis and prediction of response to chemotherapy in colorectal cancer patients. The present disclosure also provides methods of identifying genes that co-express with one or more biomarker genes.


INTRODUCTION

Colorectal cancer is the third most common malignant neoplasm worldwide, and the second leading cause of cancer-related mortality in the United States and the European Union. It is estimated that there will be approximately 150,000 new cases diagnosed each year in the United States, with about 65% of these being diagnosed as stage II/III colorectal cancer, as discussed below.


Clinical diagnosis of colorectal cancer generally involves evaluating the progression status of the cancer using standard classification criteria. Two classification systems have been widely used in colorectal cancer, the modified Duke's (or Astler-Coller) staging systems and more recently TNM staging as developed by the American Joint Committee on Cancer. Estimates of recurrence risk and treatment decisions in colorectal cancer are currently based primarily on tumor stage.


A series of trials carried out during the 1980's demonstrated that postoperative adjuvant therapy with fluorouracil (“5-FU”) and levamisole or leucovorin (“LV”) led to a significant survival benefit for colon cancer patients. However, the benefits of adjuvant therapy are not enjoyed equally by all patients. For example, adjuvant 5-FU/LV chemotherapy has been shown to benefit a relatively small (˜3%) but statistically significant subset of patients with stage II colon cancer, while the addition of oxaliplatin significantly improved overall DFS with no survival benefit seen in with stage II disease. (See, R. Gray et al., Lancet 370:2020-29 (2007), T. Andre, et al., N Engl J Med (2004), J. Kuebler, et al, J Clin Oncol (2007).) Moreover, significant neurotoxicity and GI toxicity is common and toxic deaths (0.5% in published studies) are well documented in other randomized trials.


These results underline the importance of identifying prognostic and predictive tests which better define for individual patients their likelihood of recurrence and/or magnitude of benefit that they can expect from adjuvant chemotherapy. Under current guidelines, many patients who would be cured by surgery are unnecessarily given adjuvant therapy, while other patients who would benefit from such therapy do not receive it.


SUMMARY

Algorithm-based molecular assays that involve measurement of expression levels of prognostic and/or predictive genes, or co-expressed genes thereof, from a biological sample obtained from a cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of recurrence of colorectal cancer (Recurrence Score or RS) and/or the likelihood of a beneficial response to chemotherapy (Treatment Score or TS) for the patient are provided herein. Methods of analysis of gene expression values of prognostic and/or predictive genes, as well as methods of identifying gene cliques, i.e. genes that co-express with a validated biomarker and exhibit correlation of expression with the validated biomarker, and thus may be substituted for that biomarker in an assay, are also provided. One skilled in the art would recognize that such substitutions may impact the algorithm, for example the risk profile and weighting of the gene groups may need to be adjusted.


In exemplary embodiments, expression levels of a gene from gene subsets comprising a stromal group and a cell cycle group may be used to calculate a Recurrence Score (RS). The stromal group includes at least one of the following: BGN, FAP, INHBA, or a gene that that co-expresses with BGN, FAP, or INHBA. The cell cycle group includes at least one of the following: MYBL2, Ki-67, cMYC, MAD2L1, or a gene that co-expresses with MYBL2, Ki-67, cMYC, or MAD2L1. In other exemplary embodiments, the stromal gene is BGN and the cell cycle gene is Ki-67.


In exemplary embodiments, gene expression levels of one or more genes from additional gene subsets may be measured and used to calculate the RS, including a cell signaling group, and angiogenesis group, and/or an apoptosis group. The cell signaling group includes GADD45B and genes that co-express with GADD45B. The apoptosis group includes BIK and genes that co-express with BIK. The angiogenesis group includes EFNB2 and genes that co-express with EFNB2. The calculation may be performed on a computer programmed to execute the RS algorithm.


In exemplary embodiments, the method can further include measuring expression levels of predictive genes in a tumor sample obtained from the patient; and calculating a Treatment Score (TS) for the patient using measured gene expression levels, wherein the TS is calculated by assigning the measured expression levels to gene subsets of a TS algorithm, wherein the gene subsets comprise at least one gene each from an MSI group, an apoptosis group, and a stromal group. Calculation of the TS may be performed on a computer programmed to execute the TS algorithm. In exemplary embodiments, a benefit score for the patient based on the RS and the TS may be calculated. In exemplary embodiments, the MSI group can include AXIN2 and genes that co-express with AXIN2. In exemplary embodiments, the apoptosis group can include BIK and genes that co-express with BIK. In exemplary embodiments, the stromal group can include EFNB2 and genes that co-express with EFNB2. In exemplary embodiments, the gene subsets can further include a transcription factor group, where, e.g., the transcription factor group comprises RUNX1 and genes that co-express with RUNX1. In exemplary embodiments, the gene subsets can further include a cell cycle group, where, e.g., the cell cycle group includes MAD2L1 and HSPE1, and genes that co-express with MAD2L1 and HSPE1. In exemplary embodiments, the at least one gene from the gene subsets may be replaced by a substitute gene from the group consisting of RANBP2, BUB1, TOP2A, C20_ORF1, CENPF, STK15, AURKB, HIF1A, UBE2C, and MSH2, and genes that co-express with RANBP2, BUB1, TOP2A, C20_ORF1, CENPF, STK15, AURKB, HIF1A, UBE2C, and MSH2.


In exemplary embodiments, the expression level for each gene subset may be weighted according to a contribution of the gene subset to risk of recurrence and/or response to chemotherapy.


The present disclosure provides methods to analyze gene expression taking into account variability of expression of certain gene subsets within particular regions of the tumor. In exemplary embodiments, this method may be incorporated into a RS algorithm. For example, the gene expression levels for the stromal group may be calculated as a ratio of stromal gene expression values per stroma unit area of a colorectal tumor. Similarly, gene expression levels for the cell cycle group may be calculated as a ratio of cell cycle expression values per epithelial unit area of the colorectal tumor.


The present disclosure provides methods to estimate likelihood of colon cancer recurrence based on analysis of measurements of the surface area of the tumor-associated stroma in a colon tumor sample obtained from a patient. In exemplary embodiments, this method may be incorporated into a RS algorithm.


The present disclosure provides methods to use a threshold value for expression values used in an algorithm-based gene expression analysis, which methods involve measuring an expression level of a gene in a tissue section obtained from a patient; and comparing the measured expression level to a threshold value for said gene; wherein if the threshold value is less than the expression level of said gene, the expression value is used in an expression algorithm, and wherein if the expression level of said gene is greater than or equal to the threshold value, the expression level is used in an expression algorithm.


In exemplary embodiments, the threshold value is based on a Ct value. The threshold value can be, for example, one or more from those listed in Table 3.


The present disclosure provides gene expression analysis methods to identify a gene that is co-expressed with a target gene which methods involve normalizing microarray gene expression data for cancer tumor samples based on array probes; calculating a correlation coefficient based on gene expression levels for every unique pair of array probes; determining significant probe pairs, wherein significant probe pairs are a target gene probe and an array probe with a correlation co-efficient greater than a significant threshold value; mapping the target gene to its corresponding target gene probe, selecting a candidate probe set, wherein each candidate probe is part of a significant probe pair; and identifying a gene associated with each candidate probe; wherein said gene associated with each candidate probe is a co-expressed gene.


The present disclosure also provides methods of assessing gene expression, the method comprising measuring a normalized expression level of a gene in a cancer tumor sample obtained from a patient calculating a ratio of normalized expression of the gene to a tissue unit area in the colorectal sample, wherein the tissue unit area is a tumor-associated stroma unit area or a tumor epithelial unit area; and calculating a recurrence score (RS) or a treatment score (TS) for the patient using the ratio. In related embodiments, the gene is a stromal group gene. In related embodiments, the tissue unit area is a tumor-associated stroma unit area. In further related embodiments, the gene is a cell cycle group gene. In related embodiments, the tissue unit area is a tumor epithelial unit area unit area.


The present disclosure provides methods of determining a prognosis for a cancer patient, comprising measuring a stromal area of a tumor sample obtained from the cancer patient to obtain a Stromal Risk Score, wherein increased stromal area of the tumor sample is positively correlated with an increased risk of recurrence of cancer for said cancer patient, and generating a report based on the Stromal Risk Score. In related embodiments, the tumor sample is a colorectal cancer tumor.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 is a set of graphs providing hazard ratio estimates and 95% confidence intervals for gene expression from univariate Cox PH regression models of recurrence-free interval (RFI) in NSABP C-01/02 patients and CCF patients for the 65 genes that were significantly related to RFI in both studies.



FIG. 2 is a series of graphs providing hazard ratio estimates and 95% confidence intervals for gene expression from univariate Cox PH regression models of RFI in C-01/02/04/06 and CCF patients for 48 gene significantly related to RFI in both surgery only and surgery plus FU-based chemotherapy.



FIG. 3a is a graph illustrating Kaplan-Meier estimates of recurrence-free interval Stage II patients treated with surgery only, by tertile of recurrence score.



FIG. 3b is a graph illustrating Kaplan-Meier estimates of recurrence-free interval Stage III patients treated with surgery only, by tertile of recurrence score.



FIG. 4a provides a graph and a table illustrating a risk profile and recurrence scores (RS) for recurrence in Stage II colon cancer patients.



FIG. 4b provides a graph and a table illustrating a risk profile and recurrence scores (RS) for recurrence in Stage III colon cancer, surgery only patients.



FIG. 5 is a graph providing a chemotherapy benefit plot for Stage II patients.



FIG. 6 provides a collection of graphs illustrating thresholding analysis for BGN, FAP and INHBA.



FIG. 7 provides a collection of graphs illustrating thresholding analysis for cMYC, Ki-67 and MYBL2.



FIG. 8 provides a collection of graphs illustrating thresholding analysis for GADD45B.



FIG. 9 provides a collection of graphs illustrating thresholding analysis for EFNB2, RUNX1 and BIK.



FIG. 10 provides a collection of graphs illustrating thresholding analysis for MAD2L1, HSPE1 and AXIN2.



FIG. 11 is a schematic illustrating seeding of gene cliques.



FIG. 12 is a Kaplan Meier curve demonstrating group risk from the QUASAR Stage II colon cancer patients treated with surgery alone.



FIG. 13 is a risk profile plot (by Kaplan Meier curve) for risk of recurrence at five years and recurrence scores.



FIG. 14 is a graph showing stromal group score (SGS) and cell cycle group score (CCGS) in tumor-associated stroma and tumor luminal areas.



FIG. 15 is a graph showing results of analysis of stromal group score in tumor-associated stroma in six patients.



FIG. 16 is a graph showing results of analysis of variability of stromal group and cell cycle group scores, GADD45B, and RS between tumor sections taken from 11 patient blocks.



FIG. 17 is a graph showing the range of performance for multi-gene recurrence score models across all colon cancer studies



FIG. 18: Performance of two gene model including a Stromal group gene (BGN) and Cell cycle group gene (Ki-67)



FIG. 19: Performance of three gene model including a Stromal group gene (BGN), a Cell cycle group gene (Ki-67) and an Apoptosis group gene (BIK)



FIG. 20: Comparative performance of ten-gene prognostic model (RS2) vs. seven-gene prognostic model (RS) in surgery-alone patients from the QUASAR study



FIG. 21 is a variability plot for natural logarithm of stroma area for 444 colon cancer patients.



FIG. 22 is a Kaplan-Meier plot for stage II colon cancer patients stratified by stroma risk group.



FIG. 23 is a Kaplan-Meier plot for stage III colon cancer patients stratified by stroma risk group.



FIG. 24 provides Kaplan-Meier estimates for stage II colon cancer patients stratified by stroma risk group and recurrence score risk group.



FIG. 25 provides Kaplan-Meier survival curves for stage III colon cancer patients stratified by stroma risk group and recurrence score risk group.



FIG. 26 is a graph showing the effects of diluting RNA concentration on (non-normalized) gene expression (Ct) measurements of Ki-67.





DETAILED DESCRIPTION

Definitions


Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York, N.Y. 1994), and March, Advanced Organic Chemistry Reactions, Mechanisms and Structure 4th ed., John Wiley & Sons (New York, N.Y. 1992), provide one skilled in the art with a general guide to many of the terms used in the present application.


One skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention. Indeed, the present invention is in no way limited to the methods and materials described herein. For purposes of the invention, the following terms are defined below.


The terms “tumor” and “lesion” as used herein, refer to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues.


The terms “cancer” and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Examples of cancer in the present disclosure include cancer of the gastrointestinal tract, such as invasive colorectal cancer or Dukes B (stage II) or Dukes C (stage III) colorectal cancer.


The “pathology” of cancer includes all phenomena that compromise the well-being of the patient. This includes, without limitation, abnormal or uncontrollable cell growth, metastasis, interference with the normal functioning of neighboring cells, release of cytokines or other secretory products at abnormal levels, suppression or aggravation of inflammatory or immunological response, neoplasia, premalignancy, malignancy, invasion of surrounding or distant tissues or organs, such as lymph nodes, etc.


As used herein, the terms “colon cancer” and “colorectal cancer” are used interchangeably and in the broadest sense and refer to (1) all stages and all forms of cancer arising from epithelial cells of the large intestine and/or rectum and/or (2) all stages and all forms of cancer affecting the lining of the large intestine and/or rectum. In the staging systems used for classification of colorectal cancer, the colon and rectum are treated as one organ.


According to the tumor, node, metastasis (TNM) staging system of the American Joint Committee on Cancer (AJCC) (Greene et al. (eds.), AJCC Cancer Staging Manual. 6th Ed. New York, N.Y.: Springer; 2002), the various stages of colorectal cancer are defined as follows:


Tumor: T1: tumor invades submucosal T2: tumor invades muscularis propria; T3: tumor invades through the muscularis propria into the subserose, or into the pericolic or perirectal tissues; T4: tumor directly invades other organs or structures, and/or perforates.


Node: NO: no regional lymph node metastasis; N1: metastasis in 1 to 3 regional lymph nodes; N2: metastasis in 4 or more regional lymph nodes.


Metastasis: M0: mp distant metastasis; M1: distant metastasis present.


Stage groupings: Stage I: T1 NO MO; T2 NO MO; Stage II: T3 NO MO; T4 NO MO; Stage III: any T, N1-2; MO; Stage IV: any T, any N, M1.


According to the Modified Duke Staging System, the various stages of colorectal cancer are defined as follows:


Stage A: the tumor penetrates into the mucosa of the bowel wall but not further. Stage B: tumor penetrates into and through the muscularis propria of the bowel wall; Stage C: tumor penetrates into but not through muscularis propria of the bowel wall, there is pathologic evidence of colorectal cancer in the lymph nodes; or tumor penetrates into and through the muscularis propria of the bowel wall, there is pathologic evidence of cancer in the lymph nodes; Stage D: tumor has spread beyond the confines of the lymph nodes, into other organs, such as the liver, lung or bone.


Prognostic factors are those variables related to the natural history of colorectal cancer, which influence the recurrence rates and outcome of patients once they have developed colorectal cancer. Clinical parameters that have been associated with a worse prognosis include, for example, lymph node involvement, and high grade tumors. Prognostic factors are frequently used to categorize patients into subgroups with different baseline relapse risks.


The term “prognosis” is used herein to refer to the prediction of the likelihood that a cancer patient will have a cancer-attributable death or progression, including recurrence, metastatic spread, and drug resistance, of a neoplastic disease, such as colon cancer.


The term “prognostic gene” is used herein to refer to a gene, the expression of which is correlated, positively or negatively, with a likelihood of cancer recurrence in a cancer patient treated with the standard of care. A gene may be both a prognostic and predictive gene, depending on the correlation of the gene expression level with the corresponding endpoint. For example, using a Cox proportional hazards model, if a gene is only prognostic, its hazard ratio (HR) does not change when measured in patients treated with the standard of care or in patients treated with a new intervention.


The term “prediction” is used herein to refer to the likelihood that a cancer patient will have a particular clinical response to treatment, whether positive (“beneficial response”) or negative, following surgical removal of the primary tumor. For example, treatment could include chemotherapy.


The predictive methods of the present invention can be used clinically to make treatment decisions by choosing the most appropriate treatment modalities for any particular patient. The predictive methods of the present disclosure are valuable tools in predicting if a patient is likely to respond favorably (“beneficial response”) to a treatment regimen, such as chemotherapy, surgical intervention, or both. Prediction may include prognostic factors.


The terms “predictive gene” and “response indicator gene” are used interchangeably herein to refer to a gene, the expression level of which is correlated, positively or negatively, with likelihood of beneficial response to treatment with chemotherapy. A gene may be both a prognostic and predictive gene, and vice versa, depending on the correlation of the gene expression level with the corresponding endpoint (e.g., likelihood of survival without recurrence, likelihood of beneficial response to chemotherapy). A predictive gene can be identified using a Cox proportional hazards model to study the interaction effect between gene expression levels from patients treated with treatment A compared to patients who did not receive treatment A (but may have received standard of care, e.g. treatment B). The hazard ratio (HR) for a predictive gene will change when measured in untreated/standard of care patients versus patients treated with treatment A.


As used herein, the term “expression level” as applied to a gene refers to the normalized level of a gene product, e.g. the normalized value determined for the RNA expression level of a gene or for the polypeptide expression level of a gene.


The term “gene product” or “expression product” are used herein to refer to the RNA transcription products (transcripts) of the gene, including mRNA, and the polypeptide translation products of such RNA transcripts. A gene product can be, for example, an unspliced RNA, an mRNA, a splice variant mRNA, a microRNA, a fragmented RNA, a polypeptide, a post-translationally modified polypeptide, a splice variant polypeptide, etc.


The term “RNA transcript” as used herein refers to the RNA transcription products of a gene, including, for example, mRNA, an unspliced RNA, a splice variant mRNA, a microRNA, and a fragmented RNA.


Unless indicated otherwise, each gene name used herein corresponds to the Official Symbol assigned to the gene and provided by Entrez Gene (URL: www.ncbi.nlm.nih.gov/sites/entrez) as of the filing date of this application.


The terms “correlated” and “associated” are used interchangeably herein to refer to a strength of association between two measurements (or measured entities). The disclosure provides genes and gene subsets, the expression levels of which are associated with a particular outcome measure, such as for example between the expression level of a gene and the likelihood of beneficial response to treatment with a drug or microsatellite instability (MSI) phenotype status. For example, the increased expression level of a gene may be positively correlated (positively associated) with an increased likelihood of good clinical outcome for the patient, such as an increased likelihood of long-term survival without recurrence of the cancer and/or beneficial response to a chemotherapy, and the like. Such a positive correlation may be demonstrated statistically in various ways, e.g. by a low hazard ratio. In another example, the increased expression level of a gene may be negatively correlated (negatively associated) with an increased likelihood of good clinical outcome for the patient. In that case, for example, the patient may have a decreased likelihood of long-term survival without recurrence of the cancer and/or beneficial response to a chemotherapy, and the like. Such a negative correlation indicates that the patient likely has a poor prognosis or will respond poorly to a chemotherapy, and this may be demonstrated statistically in various ways, e.g., a high hazard ratio. “Correlated” is also used herein to refer to a strength of association between the expression levels of two different genes, such that expression level of a first gene can be substituted with an expression level of a second gene in a given algorithm in view of their correlation of expression. Such “correlated expression” of two genes that are substitutable in an algorithm usually gene expression levels that are positively correlated with one another, e.g., if increased expression of a first gene is positively correlated with an outcome (e.g., increased likelihood of good clinical outcome), then the second gene that is co-expressed and exhibits correlated expression with the first gene is also positively correlated with the same outcome.


A “positive clinical outcome” and “beneficial response” can be assessed using any endpoint indicating a benefit to the patient, including, without limitation, (1) inhibition, to some extent, of tumor growth, including slowing down and complete growth arrest; (2) reduction in the number of tumor cells; (3) reduction in tumor size; (4) inhibition (i.e., reduction, slowing down or complete stopping) of tumor cell infiltration into adjacent peripheral organs and/or tissues; (5) inhibition of metastasis; (6) enhancement of anti-tumor immune response, possibly resulting in regression or rejection of the tumor; (7) relief, to some extent, of one or more symptoms associated with the tumor; (8) increase in the length of survival following treatment; and/or (9) decreased mortality at a given point of time following treatment. Positive clinical response may also be expressed in terms of various measures of clinical outcome. Positive clinical outcome can also be considered in the context of an individual's outcome relative to an outcome of a population of patients having a comparable clinical diagnosis, and can be assessed using various endpoints such as an increase in the duration of Recurrence-Free interval (RFI), an increase in the time of survival as compared to Overall Survival (OS) in a population, an increase in the time of Disease-Free Survival (DFS), an increase in the duration of Distant Recurrence-Free Interval (DRFI), and the like. An increase in the likelihood of positive clinical response corresponds to a decrease in the likelihood of cancer recurrence.


The term “risk classification” means a level of risk (or likelihood) that a subject will experience a particular clinical outcome. A subject may be classified into a risk group or classified at a level of risk based on the methods of the present disclosure, e.g. high, medium, or low risk. A “risk group” is a group of subjects or individuals with a similar level of risk for a particular clinical outcome.


The term “long-term” survival is used herein to refer to survival for a particular time period, e.g., for at least 3 years, more preferably for at least 5 years.


The term “Recurrence-Free Interval (RFI)” is used herein to refer to the time (in years) from randomization to first colon cancer recurrence or death due to recurrence of colorectal cancer.


The term “Overall Survival (OS)” is used herein to refer to the time (in years) from randomization to death from any cause.


The term “Disease-Free Survival (DFS)” is used herein to refer to the time (in years) from randomization to first colon cancer recurrence or death from any cause.


The term “Distant Recurrence-Free Interval (DRFI)” is used herein to refer to the time (in years) from surgery to the first anatomically distant cancer recurrence.


The calculation of the measures listed above in practice may vary from study to study depending on the definition of events to be either censored or not considered.


The term “tumor-associated stroma unit area” (or “sua”) is used herein to refer to a measurement of the tumor-associated stroma area surrounding a tumor. Stroma is the framework or matrix of an organ providing support to the epithelia which includes components such as blood vessels, connective tissues and lymphoid cells. In the colon, tumor-associated stroma is interposed between normal stroma, epithelia, smooth muscle and malignant epithelial cells.


The term “tumor epithelial unit area” (or “cua”) is used herein to refer to a measurement of the epithelial area of a tumor which comprises cancerous (e.g., malignant) epithelial cells. In the colon, the tumor associated epithelia cells are glandular in form, genomically clonal and are referred to as the adenocarcinoma.


The term “stromal area” as used herein, refers to the surface area of colon tumor-associated stroma in a biological sample obtained from a patient sample. The stromal area may be measured by any suitable method, such as by micrometer, or standard or digital microscopic assessment of a Hematoxylin and Eosin (H&E) section.


The term “Stromal Risk,” as used herein, refers to an estimate of recurrence risk of a patient with colon cancer based on stromal area. The amount of stromal area in a colon cancer tumor obtained from a patient is associated with the risk of recurrence of colon cancer for that patient. The greater the amount of stromal area present, the greater the risk of colon cancer recurrence. This estimate may be, for example, provided in the form of a Stromal Risk Score or Group that reflects the likelihood that a colon cancer patient will have a recurrence, such as a numeric range, descriptive categories (low, intermediate, high), etc.


The term “microarray” refers to an ordered arrangement of hybridizable array elements, e.g. oligonucleotide or polynucleotide probes, on a substrate.


The term “polynucleotide,” when used in singular or plural, generally refers to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. Thus, for instance, polynucleotides as defined herein include, without limitation, single- and double-stranded DNA, DNA including single- and double-stranded regions, single- and double-stranded RNA, and RNA including single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or include single- and double-stranded regions. In addition, the term “polynucleotide” as used herein refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules. The regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules. One of the molecules of a triple-helical region often is an oligonucleotide. The term “polynucleotide” specifically includes cDNAs. The term includes DNAs (including cDNAs) and RNAs that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons, are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritiated bases, are included within the term “polynucleotides” as defined herein. In general, the term “polynucleotide” embraces all chemically, enzymatically and/or metabolically modified forms of unmodified polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells.


The term “oligonucleotide” refers to a relatively short polynucleotide, including, without limitation, single-stranded deoxyribonucleotides, single- or double-stranded ribonucleotides, RNArDNA hybrids and double-stranded DNAs. Oligonucleotides, such as single-stranded DNA probe oligonucleotides, are often synthesized by chemical methods, for example using automated oligonucleotide synthesizers that are commercially available. However, oligonucleotides can be made by a variety of other methods, including in vitro recombinant DNA-mediated techniques and by expression of DNAs in cells and organisms.


As used herein, the term “expression level” as applied to a gene refers to the level of the expression product of a gene, e.g. the normalized value determined for the RNA expression product of a gene or for the polypeptide expression level of a gene.


The term “Ct” as used herein refers to threshold cycle, the cycle number in quantitative polymerase chain reaction (qPCR) at which the fluorescence generated within a reaction well exceeds the defined threshold, i.e. the point during the reaction at which a sufficient number of amplicons have accumulated to meet the defined threshold.


The terms “threshold” or “thresholding” refer to a procedure used to account for non-linear relationships between gene expression measurements and clinical response as well as to further reduce variation in reported patient scores. When thresholding is applied, all measurements below or above a threshold are set to that threshold value. Non-linear relationship between gene expression and outcome could be examined using smoothers or cubic splines to model gene expression in Cox PH regression on recurrence free interval or logistic regression on recurrence status. Variation in reported patient scores could be examined as a function of variability in gene expression at the limit of quantitation and/or detection for a particular gene.


As used herein, the term “amplicon,” refers to pieces of DNA that have been synthesized using amplification techniquest, such as polymerase chain reactions (PCR) and ligase chain reactions.


“Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to re-anneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).


“Stringent conditions” or “high stringency conditions”, as defined herein, typically: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium citrate) and 50% formamide, followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C.


“Moderately stringent conditions” may be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent that those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.


The terms “splicing” and “RNA splicing” are used interchangeably and refer to RNA processing that removes introns and joins exons to produce mature mRNA with continuous coding sequence that moves into the cytoplasm of an eukaryotic cell.


As used herein, the term “exon” refers to any segment of an interrupted gene that is represented in the mature RNA product. As used herein, the term “intron” refers to any segment of DNA that is transcribed but removed from within the transcript by splicing together the exons on either side of it. “Intronic RNA” refers to mRNA derived from an intronic region of DNA. Operationally, exonic sequences occur in the mRNA sequence of a gene as defined by Ref. SEQ ID numbers. Operationally, intron sequences are the intervening sequences within the genomic DNA of a gene.


The term “co-expressed”, as used herein, refers to a statistical correlation between the expression level of one gene and the expression level of another gene. Pairwise co-expression may be calculated by various methods known in the art, e.g., by calculating Pearson correlation coefficients or Spearman correlation coefficients. Co-expressed gene cliques may also be identified using a graph theory. An analysis of co-expression may be calculated using normalized expression data.


A “computer-based system” refers to a system of hardware, software, and data storage medium used to analyze information. The minimum hardware of a patient computer-based system comprises a central processing unit (CPU), and hardware for data input, data output (e.g., display), and data storage. An ordinarily skilled artisan can readily appreciate that any currently available computer-based systems and/or components thereof are suitable for use in connection with the methods of the present disclosure. The data storage medium may comprise any manufacture comprising a recording of the present information as described above, or a memory access device that can access such a manufacture.


To “record” data, programming or other information on a computer readable medium refers to a process for storing information, using any such methods as known in the art. Any convenient data storage structure may be chosen, based on the means used to access the stored information. A variety of data processor programs and formats can be used for storage, e.g. word processing text file, database format, etc.


A “processor” or “computing means” references any hardware and/or software combination that will perform the functions required of it. For example, a suitable processor may be a programmable digital microprocessor such as available in the form of an electronic controller, mainframe, server or personal computer (desktop or portable). Where the processor is programmable, suitable programming can be communicated from a remote location to the processor, or previously saved in a computer program product (such as a portable or fixed computer readable storage medium, whether magnetic, optical or solid state device based). For example, a magnetic medium or optical disk may carry the programming, and can be read by a suitable reader communicating with each processor at its corresponding station.


As used herein, the term “surgery” applies to surgical methods undertaken for removal of cancerous tissue, including resection, laparotomy, colectomy (with or without lymphadenectomy), ablative therapy, endoscopic removal, excision, dissection, and tumor biopsy/removal. The tumor tissue or sections used for gene expression analysis may have been obtained from any of these methods.


As used herein, “graph theory” refers to a field of study in Computer Science and Mathematics in which situations are represented by a diagram containing a set of points and lines connecting some of those points. The diagram is referred to as a “graph”, and the points and lines referred to as “vertices” and “edges” of the graph. In terms of gene co-expression analysis, a gene (or its equivalent identifier, e.g. an array probe) may be represented as a node or vertex in the graph. If the measures of similarity (e.g., correlation coefficient, mutual information, alternating conditional expectation) between two genes is higher than a significant threshold, the two genes are said to be co-expressed and an edge will be drawn in the graph. When co-expressed edges for all possible gene pairs for a given study have been drawn, all maximal cliques are computed. The resulting maximal clique is defined as a gene clique. A gene clique is a computed co-expressed gene group that meets predefined criteria.


As used herein, the terms “gene clique” and “clique” refer to a subgraph of a graph in which every vertex is connected by an edge to every other vertex of the subgraph.


As used herein, a “maximal clique” is a clique in which no other vertex can be added and still be a clique.


Reference to “markers for prediction of response” with reference to 5-fluorouracil (5-FU), and like expressions, encompass within their meaning response to treatment comprising 5-FU as monotherapy, or in combination with other agents, or as prodrugs, or together with local therapies such as surgery and radiation, or as adjuvant or neoadjuvant chemotherapy, or as part of a multimodal approach to the treatment of neoplastic disease.


As used herein, the terms “5-FU-based therapy”, “5-FU based treatment”, and “5-FU therapy” are used interchangeably to refer to encompass administration of 5-FU or a prodrug thereof and further encompasses administration of 5-FU combination or 5-FU combination therapy.


“5-FU combination” or “5-FU combination therapy” refers to a combination of 5-FU and another agent. A number of agents have been combined with 5-FU to enhance the cytotoxic activity through biochemical modulation. Addition of exogenous folate in the form of 5-formyl-tetrahydrofolate (leucovorin) sustains inhibition of thymidylate synthase. Methotrexate, by inhibiting purine synthesis and increasing cellular pools of certain substrates for reactivity with 5-FU, enhances the activation of 5-FU. The combination of cisplatin and 5-FU increases the antitumor activity of 5-FU. Oxaliplatin is commonly used with 5-FU and leucovorin for treating colorectal cancer, and it may inhibit catabolism of 5-FU, perhaps by inhibiting dihydropyrimidine dehydrogenase (the enzyme that is responsible for the catabolism of 5-FU), and may also inhibit expression of thymidylate synthase. The combination of 5-FU and irinotecan, a topoisomerase-1 inhibitor, is a treatment that combines 5-FU with an agent that has a different mechanism of action. Eniluracil, which is an inactivator of dihydropyrimidine dehydrogenase, leads to another strategy for improving the efficacy of 5-FU.


“5-FU prodrug” refers to drugs that, following administration to a patient, provide for activity of 5-FU. A number of 5-FU prodrugs have been developed. For example, capecitabine (N4-pentoxycarbonyl-5′-deoxy-5-fluorcytidine) is an orally administered agent that is approved by the FDA for certain treatments including colorectal cancer. Another fluoropyrimidine that acts as a prodrug for 5-FU is florafur.


Algorithm-Based Methods and Gene Subsets


The present disclosure provides an algorithm-based molecular diagnostic assay for determining an expected clinical outcome (prognostic) and/or the likelihood that a patient with cancer will have a clinically beneficial response to chemotherapy (predictive). For example, the expression levels of the prognostic genes may be used to calculate a likelihood of colorectal cancer recurrence. The expression levels of the predictive genes, and in some cases the predictive and prognostic genes, may be used to calculate the likelihood that a patient with colorectal cancer will have a clinically beneficial response to chemotherapy. The cancer can be, for example, Stage II and/or Stage III colorectal cancer. The chemotherapy can be, for example, a 5-FU-based chemotherapy.


The present disclosure provides methods to classify a tumor based on the likelihood of cancer recurrence for a patient. The likelihood of recurrence is calculated based on expression levels of prognostic genes from particular gene subsets, wherein gene subsets include at least one gene each from a stromal group and a cell cycle group. Prognostic gene subsets may also include at least one gene from a cell signaling group, an apoptosis group, and/or a transcription factor group.


The present disclosure provides methods of classifying a tumor according to the likelihood that a patient with cancer will have a beneficial response to chemotherapy based on expression levels of predictive genes. The likelihood of a beneficial response is calculated based on expression levels of predictive genes from particular gene subsets, wherein the gene subsets include at least one gene from each of a stromal group, an apoptosis group, and a MSI group. Predictive gene subsets can also include at least one gene from a transcription factor group and/or a cell cycle group.


The gene subset identified herein as the “stromal group” includes genes that are synthesized predominantly by stromal cells and are involved in stromal response and genes that co-express with stromal group genes. “Stromal cells” are defined herein as connective tissue cells that make up the support structure of biological tissues. Stromal cells include fibroblasts, immune cells, pericytes, endothelial cells, and inflammatory cells. “Stromal response” refers to a desmoplastic response of the host tissues at the site of a primary tumor or invasion. See, e.g., E. Rubin, J. Farber, Pathology, 985-986 (2nd Ed. 1994). The stromal group includes, for example, BGN, FAP, INHBA, and genes that are co-expressed with BGN, FAP, or INHBA, wherein a gene is said to be co-expressed with a stromal gene when the expression level of the gene exhibits a Pearson correlation coefficient greater than or equal to 0.6. For example, the stromal group includes the genes and/or gene cliques shown in Tables 4, 5 and 6 (provided in specification just prior to claims). The combination of genes used from within the stromal group can vary with the method of analysis for which expression is to be evaluated. For example, the stromal group for classifying a tumor according to the likelihood of colorectal cancer recurrence includes BGN, FAP and INHBA. The gene subset herein identified as the “cell cycle group” includes genes that are involved with cell cycle functions and genes that co-express with cell cycle group genes. “Cell cycle functions” are defined herein as cell proliferation and cell cycle control, e.g. checkpoint/G1 to S phase transition. The cell cycle group thus includes genes that (1) are involved in biological pathways associated with cell cycle functions; and (2) co-express with Ki-67, cMYC, MYBL2, MAD2L1, or HSPE1, with a Pearson correlation coefficient greater than or equal to 0.4. Exemplary co-expressed genes and/or gene cliques for Ki-67, cMYC, MYBL2, MAD2L1, and HSPE1 are provided in Tables 5 and 6. The combination of genes used from within the cell cycle group can vary with the method of analysis for which expression is to be evaluated. For example, the cell cycle group for classifying a tumor according to the likelihood of colorectal cancer recurrence includes Ki-67, cMYC, MYBL2, MAD2L1, and HSPE1. The cell cycle group for classifying a tumor according to likelihood that a patient will have a beneficial response to chemotherapy includes MAD2L1 and HSPE1.


This specification discloses data demonstrating that genes associated with the stroma of a tumor are associated with an increased risk of recurrence, whereas cell cycle genes are correlated with a decreased risk of recurrence. In addition, the present disclosure provides prognostic and predictive methods that take into account the observation that expression levels for certain genes vary with respect to the regions of a tumor.


Specifically, the present disclosure provides evidence that there are higher expression levels of (1) the stromal genes in the tumor-associated stroma; and (2) the cell cycle genes in the luminal part of the tumor. The ratios of expression levels to tumor region areas vary from patient to patient. This ratio of expression between tumor-associated stroma and the luminal part of the tumor can be exploited in the prognostic and predictive methods disclosed herein.


In exemplary embodiments, expression values of stromal genes may be calculated using stromal gene expression per stroma unit area, and expression values of cell cycle genes may be calculated using cell cycle gene expression per epithelial unit area. Thus, the area of the tumor-associated stroma and the area of the tumor-luminal regions may be taken into account by the prognostic and predictive algorithms in order to increase reproducibility and accuracy of RFI prediction and prediction of response to therapy, respectively. One skilled in the art would recognize that there are many conventional methods available to capture percent stroma and percent epithelia. For example, such ratios could be obtained by examining the H&E slide immediately adjacent to the tissue sections to be analyzed. This could be performed by either a pathologist (to get a gross measurement) or by digital image analysis (to obtain a more precise measurement).


In addition, the present disclosure provides evidence that measurement of the stroma area has prognostic value to colon cancer patients. Specifically, the stromal surface area of the tumor-associate stromal region of a tumor is positively correlated with increase risk of recurrence. This risk of recurrence may be reported in the form of a Stromal Risk score, or combined with risk information obtained from other sources, such as a Recurrence Score


The gene subset herein identified as the “angiogenesis group” includes genes that regulate new blood capillary formation or that otherwise participate in “wound healing.” The angiogenesis group includes genes that (1) are involved in biological pathways associated with wound healing functions; and (2) co-express with EFNB2 with a Peason correlation coefficient greater than or equal to 0.6.


The gene subset defined herein as the “apoptosis group” includes genes which are involved in apoptosis functions and genes that co-express with apoptosis group genes. “Apoptosis functions” are defined herein as a series of cellular signaling intended to positively or negatively induce apoptosis, or programmed cell death. The apoptosis group includes BIK and genes that co-express with BIK with a Pearson correlation coefficient greater than or equal to 0.6. The gene subset defined herein as the “cell signaling group” includes genes which are involved with signaling pathways impacting cell growth and apoptosis and genes that co-express with cell signaling group genes. The cell signaling group includes GADD45B and genes that co-express with GADD45B, with a Pearson correlation coefficient greater than or equal to 0.6. Exemplary genes that co-express with GADD45B are provided in Tables 4 and 5. Table 4 provides genes for which expression is highly correlated with validated prognostic and/or predictive genes (by rank and Pearson co-expression co-efficient). Table 5 provides the results of identification of genes through gene module/clique analysis of validated gene biomarkers.


The gene subset herein defined as the “transcription factor group” includes genes which are involved with transcription factor functions and genes that co-express with transcription factor group genes. “Transcription factor functions” are defined herein as the binding of specific DNA sequences to facilitate the transcription of DNA to RNA, either alone or as part of a complex. The transcription factor group includes RUNX1 and genes that co-express with RUNX1 with a Pearson correlation coefficient greater than or equal to 0.6. Exemplary co-expressed genes and/or gene cliques encompassed by the transcription factor group are provided in Tables 5 and 6.


The gene subset defined herein as the “MSI group” includes genes which are known to have a statistically significant correlation with microsatellite instability high (MSI-H) status and genes that co-express with MSI group genes. Practice guidelines indicate that MSI-H histology is one factor to consider in making cancer screening recommendations for colorectal cancer patients. (See, e.g., NCCN Practice Guidelines in Oncology, v.2.2008.) The MSI group includes AXIN2 and genes that are (1) significantly associated with MSI-H status; or (2) co-express with AXIN2 with a correlation coefficient greater than or equal to 0.4. Exemplary co-expressed genes and/or gene cliques encompassed by the MSI group are provided in Table 5.


The present disclosure also provides methods to determine a threshold expression level for a particular gene. A threshold expression level may be calculated for a prognostic or predictive gene. A threshold expression level for a gene may be based on a normalized expression level. In one example, a Ct threshold expression level may be calculated by assessing functional forms using logistic regression.


The disclosure further provides methods to determine genes that co-express with particular target genes identified by quantitative RT-PCR (qRT-PCR), e.g. validated biomarkers relevant to a particular type of cancer. The co-expressed genes are themselves useful biomarkers. The co-expressed genes may be substituted for the prognostic or predictive gene marker with which they co-express. The methods can include identifying gene cliques from microarray data, normalizing the microarray data, computing a pairwise Spearman correlation matrix for the array probes, filtering out significant co-expressed probes across different studies, building a graph, mapping the probe to genes, and generating a gene clique report. For example, the expression levels of one or more genes of a prognostic and/or predictive gene clique may be used to calculate the likelihood that a patient with colorectal cancer will experience a recurrence and/or respond to chemotherapy. A “prognostic gene clique”, as used herein, refers to a gene clique that includes a prognostic gene. A “predictive gene clique”, as used herein, refers to a gene clique that includes a predictive gene.


Various technological approaches for determination of expression levels of the disclosed genes are set forth in this specification, including, without limitation, RT-PCR, microarrays, high-throughput sequencing, serial analysis of gene expression (SAGE) and Digital Gene Expression (DGE), which will be discussed in detail below. In particular aspects, the expression level of each gene may be determined in relation to various features of the expression products of the gene including exons, introns, protein epitopes and protein activity. One or more of the prognostic and/or predictive genes, or their expression products, may be analyzed for microsatellite instability (MSI) status.


The expression levels of prognostic and/or predictive genes may be measured in tumor tissue. For example, the tumor tissue is obtained upon surgical removal or resection of the tumor, or by tumor biopsy. The expression level of prognostic and/or predictive genes may also be measured in tumor cells recovered from sites distant from the tumor, for example circulating tumor cells, body fluid (e.g., urine, blood, blood fraction, etc.).


The expression product that is assayed can be, for example, RNA or a polypeptide. The expression product may be fragmented. For example, the assay may use primers that are complementary to target sequences of an expression product and could thus measure full transcripts as well as those fragmented expression products containing the target sequence. Further information is provided in Tables A and B (inserted in specification prior to claims).


The RNA expression product may be assayed directly or by detection of a cDNA product resulting from a PCR-based amplification method, e.g., quantitative reverse transcription polymerase chain reaction (qRT-PCR). (See e.g., U.S. Pub. No. US2006-0008809A1.) Polypeptide expression product may be assayed using immunohistochemistry (IHC). Further, both RNA and polypeptide expression products may also be is assayed using microarrays.


Clinical Utility


The algorithm-based assay and associated information provided by the practice of the methods disclosed herein facilitates physicians in making more well-informed treatment decisions, and to customize the treatment of colorectal cancer to the needs of individual patients, thereby maximizing the benefit of treatment and minimizing the exposure of patients to unnecessary treatments which may provide little or no significant benefits and often carry serious risks due to toxic side-effects.


Multi-analyte gene expression tests can be used measure the expression level of one or more genes involved in each of several relevant physiologic processes or component cellular characteristics.


The algorithm used to calculate such a score in a method disclosed herein may group the expression level values of genes. The grouping of genes may be performed at least in part based on knowledge of the contribution of the genes according to physiologic functions or component cellular characteristics, such as in the groups discussed above. The formation of groups, in addition, can facilitate the mathematical weighting of the contribution of various expression levels to the recurrence and/or treatment scores. The weighting of a gene group representing a physiological process or component cellular characteristic can reflect the contribution of that process or characteristic to the pathology of the cancer and clinical outcome. Accordingly, the present disclosure provides subsets of the prognostic and predictive genes identified herein for use in the methods disclosed herein.


Based on the determination of a recurrence and/or treatment score, patients can be partitioned into subgroups (e.g., tertiles or quartiles) based on a selected value(s) of the recurrence and/or treatment score(s), where all patients with values in a given range can be classified as belonging to a particular risk group or treatment benefit group. Thus, the values chosen will define subgroups of patients with respectively greater or lesser risk and/or greater or lesser benefit.


The utility of a gene marker in predicting colorectal cancer outcome and/or response to chemotherapy may not be unique to that marker. An alternative marker having an expression pattern that is parallel to that of a selected marker gene may be substituted for, or used in addition to, a test marker. Due to the co-expression of such genes, substitution of expression level values should have little impact on the overall prognostic and/or predictive utility of the test. The closely similar expression patterns of two genes may result from involvement of both genes in the same process and/or being under common regulatory control in colon tumor cells. The present disclosure thus contemplates the use of such co-expressed genes or gene sets as substitutes for, or in addition to, prognostic and/or predictive methods of the present disclosure.


The present methods can provide for identification of colorectal cancer patients are likely to recur after surgery, and who will benefit from adjuvant chemotherapy. Such methods can be used alone or in combination with other clinical methods for patient stratification, e.g., using pathologic (tumor grade and histology) or molecular markers (e.g., levels of expression of genes such as thymidine synthase, thymidine phosphorylase (TP), dihydropyrimidine dehydrogenase (DPD), or microsatellite instability (MSI) status).


The algorithm-based molecular assay and associated information provided by the methods disclosed herein for predicting the clinical outcome in Stage II and/or Stage III cancers of the colon and/or rectum have utility in many areas, including in the development and appropriate use of drugs to treat Stage II and/or Stage III cancers of the colon and/or rectum, to stratify cancer patients for inclusion in (or exclusion from) clinical studies, to assist patients and physicians in making treatment decisions, provide economic benefits by targeting treatment based on personalized genomic profile, and the like. For example, the recurrence score may be used on samples collected from patients in a clinical trial and the results of the test used in conjunction with patient outcomes in order to determine whether subgroups of patients are more or less likely to show a response to a new drug than the whole group or other subgroups. Further, such methods can be used to identify from clinical data subsets of patients who can benefit from therapy. Additionally, a patient is more likely to be included in a clinical trial if the results of the test indicate a higher likelihood that the patient will have a poor clinical outcome if treated with surgery alone and a patient is less likely to be included in a clinical trial if the results of the test indicate a lower likelihood that the patient will have a poor clinical outcome if treated with surgery alone.


Staging of rectal tumors can be carried out based on similar criteria as for colon tumor staging, although there are some differences resulting, for example, from differences in the arrangement of the draining lymph nodes. As a result, Stage II/III rectal tumors bear a reasonable correlation to Stage II/III colon tumors as to their state of progression. As noted above, the rate of local recurrence and other aspects of prognosis differ between rectal cancer and colon cancer, and these differences may arise from difficulties in accomplishing total resection of rectal tumors. Nevertheless, there is no compelling evidence that there is a difference between colon cancer and rectal cancer as to the molecular characteristics of the respective tumors. Tests able to predict chemotherapy treatment benefit for rectal cancer patients have utility similar in nature as described for colon cancer tests and the same markers might well have utility in both cancer types.


Tests that identify patients more likely to be those that fail to respond to standard-of-care are useful in drug development, for example in identifying patients for inclusion in clinical trials testing the efficacy of alternative drugs. For example, 30-35% of Stage III colon cancer patients fail to survive five years when treated with fluorouracil-based chemotherapy after surgical resection of tumor. Preferential inclusion of these patients in a clinical trial for a new Stage III colon cancer treatment could substantially improve the efficiency and reduce the costs of such a clinical trial.


Methods of Assaying Expression Levels of a Gene Product


The methods and compositions of the present disclosure will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, and biochemistry, which are within the skill of the art. Exemplary techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, 2nd edition (Sambrook et al., 1989); “Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal Cell Culture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (Academic Press, Inc.); “Handbook of Experimental Immunology”, 4th edition (D. M. Weir & C. C. Blackwell, eds., Blackwell Science Inc., 1987); “Gene Transfer Vectors for Mammalian Cells” (J. M. Miller & M. P. Calos, eds., 1987); “Current Protocols in Molecular Biology” (F. M. Ausubel et al., eds., 1987); and “PCR: The Polymerase Chain Reaction”, (Mullis et al., eds., 1994).


Methods of gene expression profiling include methods based on hybridization analysis of polynucleotides, methods based on sequencing of polynucleotides, and proteomics-based methods. Exemplary methods known in the art for the quantification of mRNA expression in a sample include northern blotting and in situ hybridization (Parker & Barnes, Methods in Molecular Biology 106:247-283 (1999)); RNAse protection assays (Hod, Biotechniques 13:852-854 (1992)); and PCR-based methods, such as reverse transcription PCT (RT-PCR) (Weis et al., Trends in Genetics 8:263-264 (1992)). Antibodies may be employed that can recognize sequence-specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. Representative methods for sequencing-based gene expression analysis include Serial Analysis of Gene Expression (SAGE), and gene expression analysis by massively parallel signature sequencing (MPSS).


Reverse Transcriptase PCR (RT-PCR)


Typically, mRNA is isolated from a test sample. The starting material is typically total RNA isolated from a human tumor, usually from a primary tumor. Optionally, normal tissues from the same patient can be used as an internal control. mRNA can be extracted from a tissue sample, e.g., from a sample that is fresh, frozen (e.g. fresh frozen), or paraffin-embedded and fixed (e.g. formalin-fixed).


General methods for mRNA extraction are well known in the art and are disclosed in standard textbooks of molecular biology, including Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997). Methods for RNA extraction from paraffin embedded tissues are disclosed, for example, in Rupp and Locker, Lab Invest. 56:A67 (1987), and De Andrés et al., BioTechniques 18:42044 (1995). In particular, RNA isolation can be performed using a purification kit, buffer set and protease from commercial manufacturers, such as Qiagen, according to the manufacturer's instructions. For example, total RNA from cells in culture can be isolated using Qiagen RNeasy mini-columns. Other commercially available RNA isolation kits include MasterPure™ Complete DNA and RNA Purification Kit (EPICENTRE®, Madison, Wis.), and Paraffin Block RNA Isolation Kit (Ambion, Inc.). Total RNA from tissue samples can be isolated using RNA Stat-60 (Tel-Test). RNA prepared from tumor can be isolated, for example, by cesium chloride density gradient centrifugation.


The sample containing the RNA is then subjected to reverse transcription to produce cDNA from the RNA template, followed by exponential amplification in a PCR reaction. The two most commonly used reverse transcriptases are avilo myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT). The reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the circumstances and the goal of expression profiling. For example, extracted RNA can be reverse-transcribed using a GeneAmp RNA PCR kit (Perkin Elmer, Calif., USA), following the manufacturer's instructions. The derived cDNA can then be used as a template in the subsequent PCR reaction.


PCR-based methods use a thermostable DNA-dependent DNA polymerase, such as a Taq DNA polymerase. For example, TaqMan® PCR typically utilizes the 5′-nuclease activity of Taq or Tth polymerase to hydrolyze a hybridization probe bound to its target amplicon, but any enzyme with equivalent 5′ nuclease activity can be used. Two oligonucleotide primers are used to generate an amplicon typical of a PCR reaction product. A third oligonucleotide, or probe, can be designed to facilitate detection of a nucleotide sequence of the amplicon located between the hybridization sites the two PCR primers. The probe can be detectably labeled, e.g., with a reporter dye, and can further be provided with both a fluorescent dye, and a quencher fluorescent dye, as in a Taqman® probe configuration. Where a Taqman® probe is used, during the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.


TaqMan® RT-PCR can be performed using commercially available equipment, such as, for example, ABI PRISM 7700™ Sequence Detection System™ (Perkin-Elmer-Applied Biosystems, Foster City, Calif., USA), or Lightcycler (Roche Molecular Biochemicals, Mannheim, Germany). In a preferred embodiment, the 5′ nuclease procedure is run on a real-time quantitative PCR device such as the ABI PRISM 7700™ Sequence Detection System™. The system consists of a thermocycler, laser, charge-coupled device (CCD), camera and computer. The system amplifies samples in a 384-well format on a thermocycler. The RT-PCR may be performed in triplicate wells with an equivalent of 2 ng RNA input per 10 μL-reaction volume. During amplification, laser-induced fluorescent signal is collected in real-time through fiber optics cables for all wells, and detected at the CCD. The system includes software for running the instrument and for analyzing the data.


5′-Nuclease assay data are initially expressed as a threshold cycle (“Ct”). Fluorescence values are recorded during every cycle and represent the amount of product amplified to that point in the amplification reaction. The threshold cycle (Ct) is generally described as the point when the fluorescent signal is first recorded as statistically significant.


To minimize errors and the effect of sample-to-sample variation, RT-PCR is usually performed using an internal standard. The ideal internal standard gene (also referred to as a reference gene) is expressed at a constant level among cancerous and non-cancerous tissue of the same origin (i.e., a level that is not significantly different among normal and cancerous tissues), and is not significantly unaffected by the experimental treatment (i.e., does not exhibit a significant difference in expression level in the relevant tissue as a result of exposure to chemotherapy). For example, reference genes useful in the methods disclosed herein should not exhibit significantly different expression levels in cancerous colon as compared to normal colon tissue. RNAs most frequently used to normalize patterns of gene expression are mRNAs for the housekeeping genes glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and β-actin. Exemplary reference genes used for normalization comprise one or more of the following genes: ATP5E, GPX1, PGK1, UBB, and VDAC2. Gene expression measurements can be normalized relative to the mean of one or more (e.g., 2, 3, 4, 5, or more) reference genes. Reference-normalized expression measurements can range from 0 to 15, where a one unit increase generally reflects a 2-fold increase in RNA quantity.


Real time PCR is compatible both with quantitative competitive PCR, where internal competitor for each target sequence is used for normalization, and with quantitative comparative PCR using a normalization gene contained within the sample, or a housekeeping gene for RT-PCR. For further details see, e.g. Held et al., Genome Research 6:986-994 (1996).


The steps of a representative protocol for use in the methods of the present disclosure use fixed, paraffin-embedded tissues as the RNA source. mRNA isolation, purification, primer extension and amplification can be preformed according to methods available in the art. (see, e.g., Godfrey et al. J. Molec. Diagnostics 2: 84-91 (2000); Specht et al., Am. J. Pathol. 158: 419-29 (2001)). Briefly, a representative process starts with cutting about 10 μm thick sections of paraffin-embedded tumor tissue samples. The RNA is then extracted, and protein and DNA depleted from the RNA-containing sample. After analysis of the RNA concentration, RNA is reverse transcribed using gene specific primers followed by RT-PCR to provide for cDNA amplification products.


Design of Intron-Based PCR Primers and Probes


PCR primers and probes can be designed based upon exon or intron sequences present in the mRNA transcript of the gene of interest. Primer/probe design can be performed using publicly available software, such as the DNA BLAT software developed by Kent, W. J., Genome Res. 12(4):656-64 (2002), or by the BLAST software including its variations.


Where necessary or desired, repetitive sequences of the target sequence can be masked to mitigate non-specific signals. Exemplary tools to accomplish this include the Repeat Masker program available on-line through the Baylor College of Medicine, which screens DNA sequences against a library of repetitive elements and returns a query sequence in which the repetitive elements are masked. The masked intron sequences can then be used to design primer and probe sequences using any commercially or otherwise publicly available primer/probe design packages, such as Primer Express (Applied Biosystems); MGB assay-by-design (Applied Biosystems); Primer3 (Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Rrawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, N.J., pp 365-386).


Other factors that can influence PCR primer design include primer length, melting temperature (Tm), and G/C content, specificity, complementary primer sequences, and 3′-end sequence. In general, optimal PCR primers are generally 17-30 bases in length, and contain about 20-80%, such as, for example, about 50-60% G+C bases, and exhibit Tm's between 50 and 80° C., e.g. about 50 to 70° C.


For further guidelines for PCR primer and probe design see, e.g. Dieffenbach, C W. et al, “General Concepts for PCR Primer Design” in: PCR Primer, A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York, 1995, pp. 133-155; Innis and Gelfand, “Optimization of PCRs” in: PCR Protocols, A Guide to Methods and Applications, CRC Press, London, 1994, pp. 5-11; and Plasterer, T. N. Primerselect: Primer and probe design. Methods MoI. Biol. 70:520-527 (1997), the entire disclosures of which are hereby expressly incorporated by reference.


Tables A and B provide further information concerning the primer, probe, and amplicon sequences associated with the Examples disclosed herein.


MassARRAY® System


In MassARRAY-based methods, such as the exemplary method developed by Sequenom, Inc. (San Diego, Calif.) following the isolation of RNA and reverse transcription, the obtained cDNA is spiked with a synthetic DNA molecule (competitor), which matches the targeted cDNA region in all positions, except a single base, and serves as an internal standard. The cDNA/competitor mixture is PCR amplified and is subjected to a post-PCR shrimp alkaline phosphatase (SAP) enzyme treatment, which results in the dephosphorylation of the remaining nucleotides. After inactivation of the alkaline phosphatase, the PCR products from the competitor and cDNA are subjected to primer extension, which generates distinct mass signals for the competitor- and cDNA-derives PCR products. After purification, these products are dispensed on a chip array, which is pre-loaded with components needed for analysis with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The cDNA present in the reaction is then quantified by analyzing the ratios of the peak areas in the mass spectrum generated. For further details see, e.g. Ding and Cantor, Proc. Natl. Acad. Sci. USA 100:3059-3064 (2003).


Other PCR-Based Methods


Further PCR-based techniques that can find use in the methods disclosed herein include, for example, BeadArray® technology (Illumina, San Diego, Calif.; Oliphant et al., Discovery of Markers for Disease (Supplement to Biotechniques), June 2002; Ferguson et al., Analytical Chemistry 72:5618 (2000)); BeadsArray for Detection of Gene Expression® (BADGE), using the commercially available LuminexlOO LabMAP® system and multiple color-coded microspheres (Luminex Corp., Austin, Tex.) in a rapid assay for gene expression (Yang et al., Genome Res. 11:1888-1898 (2001)); and high coverage expression profiling (HiCEP) analysis (Fukumura et al., Nucl. Acids. Res. 31(16) e94 (2003).


Microarrays


Expression levels of a gene of interest can also be assessed using the microarray technique. In this method, polynucleotide sequences of interest (including cDNAs and oligonucleotides) are arrayed on a substrate. The arrayed sequences are then contacted under conditions suitable for specific hybridization with detectably labeled cDNA generated from mRNA of a test sample. As in the RT-PCR method, the source of mRNA typically is total RNA isolated from a tumor sample, and optionally from normal tissue of the same patient as an internal control or cell lines. mRNA can be extracted, for example, from frozen or archived paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples.


For example, PCR amplified inserts of cDNA clones of a gene to be assayed are applied to a substrate in a dense array. Usually at least 10,000 nucleotide sequences are applied to the substrate. For example, the microarrayed genes, immobilized on the microchip at 10,000 elements each, are suitable for hybridization under stringent conditions. Fluorescently labeled cDNA probes may be generated through incorporation of fluorescent nucleotides by reverse transcription of RNA extracted from tissues of interest. Labeled cDNA probes applied to the chip hybridize with specificity to each spot of DNA on the array. After washing under stringent conditions to remove non-specifically bound probes, the chip is scanned by confocal laser microscopy or by another detection method, such as a CCD camera. Quantitation of hybridization of each arrayed element allows for assessment of corresponding mRNA abundance.


With dual color fluorescence, separately labeled cDNA probes generated from two sources of RNA are hybridized pair wise to the array. The relative abundance of the transcripts from the two sources corresponding to each specified gene is thus determined simultaneously. The miniaturized scale of the hybridization affords a convenient and rapid evaluation of the expression pattern for large numbers of genes. Such methods have been shown to have the sensitivity required to detect rare transcripts, which are expressed at a few copies per cell, and to reproducibly detect at least approximately two-fold differences in the expression levels (Schena et at, Proc. Natl. Acad. ScL USA 93(2):106-149 (1996)). Microarray analysis can be performed by commercially available equipment, following manufacturer's protocols, such as by using the Affymetrix GenChip® technology, or Incyte's microarray technology.


Serial Analysis of Gene Expression (SAGE)


Serial analysis of gene expression (SAGE) is a method that allows the simultaneous and quantitative analysis of a large number of gene transcripts, without the need of providing an individual hybridization probe for each transcript. First, a short sequence tag (about 10-14 bp) is generated that contains sufficient information to uniquely identify a transcript, provided that the tag is obtained from a unique position within each transcript. Then, many transcripts are linked together to form long serial molecules, that can be sequenced, revealing the identity of the multiple tags simultaneously. The expression pattern of any population of transcripts can be quantitatively evaluated by determining the abundance of individual tags, and identifying the gene corresponding to each tag. For more details see, e.g. Velculescu et al., Science 270:484-487 (1995); and Velculescu et al., Cell 88:243-51 (1997).


Gene Expression Analysis by Nucleic Acid Sequencing


Nucleic acid sequencing technologies are suitable methods for analysis of gene expression. The principle underlying these methods is that the number of times a cDNA sequence is detected in a sample is directly related to the relative expression of the mRNA corresponding to that sequence. These methods are sometimes referred to by the term Digital Gene Expression (DGE) to reflect the discrete numeric property of the resulting data. Early methods applying this principle were Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS). See, e.g., S. Brenner, et al., Nature Biotechnology 18(6):630-634 (2000). More recently, the advent of “next-generation” sequencing technologies has made DGE simpler, higher throughput, and more affordable. As a result, more laboratories are able to utilize DGE to screen the expression of more genes in more individual patient samples than previously possible. See, e.g., J. Marioni, Genome Research 18(9):1509-1517 (2008); R. Morin, Genome Research 18(4):610-621 (2008); A. Mortazavi, Nature Methods 5(7):621-628 (2008); N. Cloonan, Nature Methods 5(7):613-619 (2008).


Isolating RNA from Body Fluids


Methods of isolating RNA for expression analysis from blood, plasma and serum (See for example, Tsui N B et al. (2002) 48, 1647-53 and references cited therein) and from urine (See for example, Boom R et al. (1990) J Clin Microbiol. 28, 495-503 and reference cited therein) have been described.


Immunohistochemistry


Immunohistochemistry methods are also suitable for detecting the expression levels of genes and applied to the method disclosed herein. Antibodies (e.g., monoclonal antibodies) that specifically bind a gene product of a gene of interest can be used in such methods. The antibodies can be detected by direct labeling of the antibodies themselves, for example, with radioactive labels, fluorescent labels, hapten’ labels such as, biotin, or an enzyme such as horse radish peroxidase or alkaline phosphatase. Alternatively, unlabeled primary antibody can be used in conjunction with a labeled secondary antibody specific for the primary antibody Immunohistochemistry protocols and kits are well known in the art and are commercially available.


Proteomics


The term “proteome” is defined as the totality of the proteins present in a sample (e.g. tissue, organism, or cell culture) at a certain point of time. Proteomics includes, among other things, study of the global changes of protein expression in a sample (also referred to as “expression proteomics”). Proteomics typically includes the following steps: (1) separation of individual proteins in a sample by 2-D gel electrophoresis (2-D PAGE); (2) identification of the individual proteins recovered from the gel, e.g. my mass spectrometry or N-terminal sequencing, and (3) analysis of the data using bioinformatics.


General Description of the mRNA Isolation, Purification and Amplification


The steps of a representative protocol for profiling gene expression using fixed, paraffin-embedded tissues as the RNA source, including mRNA isolation, purification, primer extension and amplification are provided in various published journal articles. (See, e.g., T. E. Godfrey et al., J. Molec. Diagnostics 2: 84-91 (2000); K. Specht et al., Am. J. Pathol. 158: 419-29 (2001), M. Cronin, et al., Am J Pathol 164:35-42 (2004)). Briefly, a representative process starts with cutting a tissue sample section (e.g. about 10 μm thick sections of a paraffin-embedded tumor tissue sample). The RNA is then extracted, and protein and DNA are removed. After analysis of the RNA concentration, RNA repair is performed if desired. The sample can then be subjected to analysis, e.g., by reverse transcribed using gene specific promoters followed by RT-PCR.


Statistical Analysis of Gene Expression Levels in Identification of Marker Genes for Use in Prognostic and/or Predictive Methods


One skilled in the art will recognize that there are many statistical methods that may be used to determine whether there is a significant relationship between an outcome of interest (e.g., likelihood of survival, likelihood of response to chemotherapy) and expression levels of a marker gene as described here. This relationship can be presented as a continuous recurrence score (RS), or patients may stratified into risk groups (e.g., low, intermediate, high). For example, a Cox proportional hazards regression model may fit to a particular clinical endpoint (e.g., RFI, DFS, OS). One assumption of the Cox proportional hazards regression model is the proportional hazards assumption, i.e. the assumption that effect parameters multiply the underlying hazard. Assessments of model adequacy may be performed including, but not limited to, examination of the cumulative sum of martingale residuals. One skilled in the art would recognize that there are numerous statistical methods that may be used (e.g., Royston and Parmer (2002), smoothing spline, etc.) to fit a flexible parametric model using the hazard scale and the Weibull distribution with natural spline smoothing of the log cumulative hazards function, with effects for treatment (chemotherapy or observation) and RS allowed to be time-dependent. (See, P. Royston, M. Parmer, Statistics in Medicine 21(15:2175-2197 (2002).) The relationship between recurrence risk and (1) recurrence risk groups; and (2) clinical/pathologic covariates (e.g., number of nodes examined, pathological T stage, tumor grade, MSI status, lymphatic or vascular invasion, etc.) may also be tested for significance.


Many statistical methods may be used to determine if there is a significant interaction between expression levels of predictive genes and beneficial response to treatment (“treatment benefit”). For example, this relationship can be presented as a continuous treatment score (TS), or patients may stratified into benefit groups (e.g., low, intermediate, high). The interaction studied may vary, e.g. standard of care vs. new treatment, or surgery alone vs. surgery followed by chemotherapy. For example, a Cox proportional hazards regression could be used to model the follow-up data, i.e. censoring time to recurrence at a certain time (e.g., 3 years) after randomization for patients who have not experienced a recurrence before that time, to determine if the TS is associated with the magnitude of chemotherapy benefit. One might use the likelihood ratio test to compare the reduced model with RS, TS and the treatment main effect, with the full model that includes RS, TS, the treatment main effect, and the interaction of treatment and TS. A pre-determined p-value cut-off (e.g., p<0.05) may be used to determine significance.


Alternatively, the method of Royston and Parmer (2002) can be used to fit a flexible parametric model using the hazard scale and the Weibull distribution with natural spline smoothing of the log cumulative hazards function, with effects for treatment (chemotherapy or observation), RS, TS and the interaction of TS with treatment, allowing the effects of RS, TS and TS interaction with treatment to be time dependent. To assess relative chemotherapy benefit across the benefit groups, pre-specified cut-points for the RS and TS may be used to define low, intermediate, and high chemotherapy benefit groups. The relationship between treatment and (1) benefit groups; and (2) clinical/pathologic covariates may also be tested for significance. For example, one skilled in the art could identify significant trends in absolute chemotherapy benefit for recurrence at 3 years across the low, intermediate, and high chemotherapy benefit groups for surgery alone or surgery followed by chemotherapy groups. An absolute benefit of at least 3-6% in the high chemotherapy benefit group would be considered clinically significant.


In an exemplary embodiment, power calculations were carried for the Cox proportional hazards model with a single non-binary covariate using the method proposed by F. Hsieh and P. Lavori, Control Clin Trials 21:552-560 (2000) as implemented in PASS 2008.


Coexpression Analysis


The present disclosure provides genes that co-express with particular prognostic and/or predictive gene that has been identified as having a significant correlation to recurrence and/or treatment benefit. To perform particular biological processes, genes often work together in a concerted way, i.e. they are co-expressed. Co-expressed gene groups identified for a disease process like cancer can serve as biomarkers for disease progression and response to treatment. Such co-expressed genes can be assayed in lieu of, or in addition to, assaying of the prognostic and/or predictive gene with which they are co-expressed.


One skilled in the art will recognize that many co-expression analysis methods now known or later developed will fall within the scope and spirit of the present invention. These methods may incorporate, for example, correlation coefficients, co-expression network analysis, clique analysis, etc., and may be based on expression data from RT-PCR, microarrays, sequencing, and other similar technologies. For example, gene expression clusters can be identified using pair-wise analysis of correlation based on Pearson or Spearman correlation coefficients. (See, e.g., Pearson K. and Lee A., Biometrika 2, 357 (1902); C. Spearman, Amer. J. Psychol 15:72-101 (1904); J. Myers, A. Well, Research Design and Statistical Analysis, p. 508 (2nd Ed., 2003).) In general, a correlation coefficient of equal to or greater than 0.3 is considered to be statistically significant in a sample size of at least 20. (See, e.g., G. Norman, D. Streiner, Biostatistics: The Bare Essentials, 137-138 (3rd Ed. 2007).)


General Description of Exemplary Embodiments


This disclosure provides a method to determine a patient's likelihood of experiencing a cancer recurrence by assaying expression levels of certain prognostic genes from a tumor sample obtained from the patient. Such methods involve use of gene subsets that are created based on similar functions of gene products. For example, prognostic methods disclosed herein involve assaying expression levels of gene subsets that include at least one gene each from each of a stromal group and a cell cycle group, and calculating a recurrence score (RS) for the patient by weighting the expression levels of each of the gene subsets by their respective contributions to cancer recurrence. The weighting may be different for each gene subset, and may be either positive or negative. For example, the stromal group score could be weighted by multiplying by a factor of 0.15, the cell cycle group score by a factor of −0.3, the cell signaling group score by a factor of 0.15, and so on. Gene subsets in such prognostic methods can further include at least one gene from a cell signaling group, apoptosis group, or transcription factor group.


For example, the weights assigned to each gene subset in the exemplary embodiments is set forth below:

RS1=Ws×Stromal Group Score+Wz×Angiogenesis Group Score−Wcc×Cell Cycle Group Score+Wcs×Cell Signaling Group Score−Wa×Apoptosis Group Score


Where:

    • Stromal Group Score=(SG1+ . . . SGn)/n (SG=Stromal gene normalized expression level (NEL))
    • Cell Cycle Group Score=(CCG1+ . . . CCGn)/n (CCG=Cell cycle gene NEL)
    • Cell Signaling Group Score=(CSG1+ . . . CSGn) (CSG=Cell signaling gene NEL)
    • Apoptosis Group Score=(AG1+ . . . AGn)/n (AG=Apoptosis gene)
    • Angiogenesis Group Score=(AgG1+ . . . AgGn)/n (AgG=Angiogenesis gene)
    • Wx=weighting factor for each gene subset


Alternatively, the genes within each gene subset may be weighted individually. Assuming standardized expression, the weights assigned to each gene subset in the exemplary embodiment is set forth below:

Stromal Group Score2=+BGN score+FAP score+INHBA score
Cell Cycle Group Score2=−2[Ki-67 score+MAD2L1 score+0.75(cMYC score)+0.25(MYBL2 score)]
Apoptosis Group Score2=−2(BIK score)
Cell Signaling Group Score2=+0.33(GADD45B score)
Angiogenesis Group Score2=+EFNB2 score


To translate the RS2 model into non-standardized expression, the weights may be divided by gene standard deviation. For example, assuming non-standardized expression, the weights assigned to each gene subset in the exemplary embodiment is set forth below:

Stromal Group Scorens=+1.06(BGN score)+1.38(FAP score)+1.14(INHBA score)
Angiogenesis Group Scorens=+1.34(EFNB2)
Cell Signaling Group Scorens=+0.44GADD45B
Cell Cycle Group Scorens=−2[1.85(Ki-67 score)+1.32(MAD2L1+0.83(cMYC score)+0.45(MYBL2 score)]
Apoptosis Group Scorens=−2(BIK score)


In exemplary embodiments, RS is calculated using expression levels of one or more of BGN, FAP, INHBA, EFNB2, MYBL2, Ki-67, cMYC, MAD2L1, HSPE1, GADD45B, BIK, and RUNX1. The disclosure provides substitute prognostic genes, the expression levels of which may similarly be used to calculate RS. These substitute predictive genes include genes that co-express with BGN, FAP, INHBA, EFNB2, MYBL2, Ki-67, cMYC, MAD2L1, HSPE1, GADD45B, BIK, or RUNX1


The RSu (recurrence score unscaled) may be rescaled, for example to be between 0 and 100. More particularly, the RSu may be rescaled as follows:






RS
=

{



0




if





44
×

(


RS
U

+
0.82

)


<
0






44
×

(


RS
U

+
0.82

)






if





0



44
×

(


RS
U

+
0.82

)



100





100




if





44
×

(


RS
U

+
0.82

)


>
100









The RS may be used to determine a recurrence risk group for each patient. For example, recurrence scores may be divided into three risk classification groups using predefined cut-points. The cut-points between the low, intermediate, and high recurrence risk groups may be defined, for example, as in Table 1.









TABLE 1







Recurrence Risk Stratification










Recurrence Risk Group
Recurrence Score






Low risk of recurrence
Less than 30



Intermediate risk of
Greater than or equal to 30



recurrence
and less than 41



High risk of recurrence
Greater than or equal to 41









The RS may be rounded to the nearest integer before the cut-points defining recurrence risk groups are applied.


The disclosure also provides methods to determine the likelihood that a patient with colorectal cancer will have a beneficial response to chemotherapy including assaying expression levels of predictive genes, where the expression levels are used in an algorithm based on gene subsets that include at least one gene each from a growth factor receptor group, an apoptosis group, and a MSI group, and calculating a treatment score (TS) for the patient by weighting the expression levels of each of the gene subsets by their respective contributions to response to chemotherapy. The weighting may be different for each gene subset, and may be either positive or negative. For example, the stromal group could be weighted by multiplying by a factor of −0.3, the transcription factor by a factor of −0.04, the apoptosis group by a factor of 0.3, the cell cycle group by a factor of 0.1, and the MSI group by a factor of 0.1. The gene subsets may additionally comprise at least one gene from a transcription factor group and/or a cell cycle group.


In the exemplary embodiments, the weights assigned to each gene subset is set forth below:

TS=−Ws×Stromal Group Score−Wtf×Transcription Factor Group Score+Wa×Apoptosis Group Score+Wcc×Cell Cycle Group Score+Wmsi×MSI Group Score

    • Where:
      • Stromal Group Score=(SG1+ . . . SGn) (SG=stromal gene normalized expression level (NEL))
      • Transcription Factor Group Score=(TFG1+ . . . TFGn) (TFG=transcription factor gene NEL)
      • Apoptosis Group Score=(AG1+ . . . AGn) (AG=apoptosis gene NEL)
      • Cell Cycle Group Score=(CCG1+ . . . CCGn) (CCG=cell cycle gene NEL)
      • MSI Group Score=(MG1+ . . . MGn) (MG=MSI gene NEL)
      • Wx=weighting factor for each gene subset


In exemplary embodiments, TS is calculated using expression levels for AXIN2, BIK, EFNB2, HSPE1, MAD2L1, and RUNX1.


The disclosure provides other predictive genes, the expression levels of which may similarly be used to calculate a TS. These substitute predictive genes include RANBP2, BUB1, TOP2A, C20_ORF1, CENPF, STK15, AURKB, HIF1A, UBE2C, and MSH2, and gene that co-express with said substitute predictive genes with a Pearson correlation co-efficient of at least 0.60.


The TSu (Treatment Score unsealed) may be rescaled, for example it may be rescaled to be between 0 and 100. More particularly, TSu may be rescaled as follows:






TS
=

{



0




if





37
×

(


TS
U

-
1

)


<
0






37
×

(


TS
U

-
1

)






if





0



37
×

(


TS
U

-
1

)



100





100




if





37
×

(


TS
U

-
1

)


>
100









In addition, the TS may be used to determine a “benefit score” for each patient. For example, the patient may be classified as one who is expected to have a low, medium, or high benefit from chemotherapy. In a particular example, the RS, TS, and predefined cut-points can be used to determine a benefit score for each patient. The low, intermediate, and high benefit scores or groups may be defined as in Table 2.









TABLE 2







Beneficial Response to Chemotherapy Stratification











X = 0.859exp[1.839×RSu +3.526−1.781×TSu]



Benefit Group
0.859exp[1.839×RSu]







Low Benefit
X less than 2%



Intermediate Benefit
X greater than or equal to 2% and




less than 6%



High Benefit
X greater than or equal to 6%










Data Aggregation


The expression data may be aggregated. The purpose of data aggregation is to combine information across replicate qRT-PCR wells for individual genes. For example, during qRT-PCR, triplicate wells may be run for each gene and sample. Valid triplicate wells for each gene may be aggregated into a single weighted average Ct value. The resulting weighted average Ct effectively down weights the influence of outlier observations. The data aggregation module may include the following steps for each gene and sample:

    • (1) Retrieve calculated Ct values and status data.
    • (2) Aggregate plate level statistics and record module version, date and time of processing.
    • (3) Aggregate Ct values for each gene and store statistics using all wells (valid and invalid).
    • (4) Compute gene validity based on the number of valid wells.
    • (5) Compute the weighted average of the valid wells for each gene.


Normalization of Expression Levels


The expression data used in the methods disclosed herein can be normalized. Normalization refers to a process to correct for (normalize away), for example, differences in the amount of RNA assayed and variability in the quality of the RNA used, to remove unwanted sources of systematic variation in Ct measurements, and the like. With respect to RT-PCR experiments involving archived fixed paraffin embedded tissue samples, sources of systematic variation are known to include the degree of RNA degradation relative to the age of the patient sample and the type of fixative used to store the sample. Other sources of systematic variation are attributable to laboratory processing conditions.


Assays can provide for normalization by incorporating the expression of certain normalizing genes, which genes do not significantly differ in expression levels under the relevant conditions. Exemplary normalization genes include housekeeping genes such as PGK1 and UBB. (See, e.g., E. Eisenberg, et al., Trends in Genetics 19(7):362-365 (2003).) Normalization can be based on the mean or median signal (CT) of all of the assayed genes or a large subset thereof (global normalization approach). In general, the normalizing genes, also referred to as reference genes should be genes that are known not to exhibit significantly different expression in colorectal cancer as compared to non-cancerous colorectal tissue, and are not significantly affected by various sample and process conditions, thus provide for normalizing away extraneous effects.


Unless noted otherwise, normalized expression levels for each mRNA/tested tumor/patient will be expressed as a percentage of the expression level measured in the reference set. A reference set of a sufficiently high number (e.g. 40) of tumors yields a distribution of normalized levels of each mRNA species. The level measured in a particular tumor sample to be analyzed falls at some percentile within this range, which can be determined by methods well known in the art.


In exemplary embodiments, one or more of the following genes are used as references by which the expression data is normalized: ATP5E, GPX1, PGK1, UBB, and VDAC2. The calibrated weighted average Ct measurements for each of the prognostic and predictive genes may be normalized relative to the mean of five or more reference genes.


Those skilled in the art will recognize that normalization may be achieved in numerous ways, and the techniques described above are intended only to be exemplary, not exhaustive.


Bridging Expression Measurements and Calibration


An oligonucleotide set represents a forward primer, reverse primer, and probe that are used to build a primer and probe (P3) pool and gene specific primer (GSP) pool. Systematic differences in RT-PCR cycle threshold (Ct) measurements can result between different oligonucleotide sets due to inherent variations oligonucleotide syntheses. For example, differences in oligonucleotide sets may exist between development, production (used for validation), and future production nucleotide sets. Thus, use of statistical calibration procedures to adjust for systematic differences in oligonucleotide sets resulting in translation in the gene coefficients used in calculating RS and TS may be desirable. For example, for each of the genes assayed for use in an algorithm, one may use a scatterplot of Ct measurements for production oligonucleotide sets versus Ct measurements from a corresponding sample used in different oligonucleotide set to create linear regression model that treats the effect of lot-to-lot differences as a random effect. Examination of such a plot will reveal that the variance of Ct measurements increases exponentially as a function of the mean Ct. The random effects linear regression model can be evaluated with log-linear variance, to obtain a linear calibration equation. A calculated mean squared error (MSE) for the scores can be compared to the MSE if no calibration scheme is used at all.


As another example, a latent variable measurement of Ct (e.g. first principle component) may be derived from various oligonucleotide sets. The latent variable is a reasonable measure of the “true” underlying Ct measurement. Similar to the method described above, a linear regression model may be fit to the sample pairs treating the effects of differences as a random effect, and the weighted average Ct value adjusted to a calibrated Ct.


Centering and Data Compression/Scaling


Systematic differences in the distribution of patient RS and TS due to analytical or sample differences may exist between early development, clinical validation and commercial samples. A constant centering tuning parameter may be used in the algorithm to account for such difference.


Data compression is a procedure used to reduce the variability in observed normalized Ct values beyond the limit of quantitation (LOQ) of the assay. Specifically, for each of the colon cancer assay genes, variance in Ct measurements increase exponentially as the normalized Ct for a gene extends beyond the LOQ of the assay. To reduce such variation, normalized Ct values for each gene may be compressed towards the LOQ of the assay. Additionally, normalized Ct values may be resealed. For example, normalized Ct values of the prognostic, predictive, and reference genes may be resealed to a range of 0 to 15, where a one-unit increase generally reflects a 2-fold increase in RNA quantity.


Threshold Values


The present invention describes a method to determine a threshold value for expression of a cancer-related gene, comprising measuring an expression level of a gene, or its expression product, in a tumor section obtained from a cancer patient, normalizing the expression level to obtain a normalized expression level, calculating a threshold value for the normalized expression level, and determining a score based on the likelihood of recurrence or clinically beneficial response to treatment, wherein if the normalized expression level is less than the threshold value, the threshold value is used to determine the score, and wherein if the normalized expression level is greater or equal to the threshold value, the normalized expression level is used to determine the score.


For example, a threshold value for each cancer-related gene may be determined through examination of the functional form of relationship between gene expression and outcome. Examples of such analyses are presented for Cox PH regression on recurrence free interval where gene expression is modeled using natural splines and for logistic regression on recurrence status where gene expression is modeled using lowess smoother.—(See, e.g., FIGS. 6-10.)


Thresholded Ct values for each prognostic, predictive, and reference genes can be used to calculate RS and TS. Exemplary thresholded Ct values for the 18-gene assay described herein are set forth in Table 3.









TABLE 3







Gene expression panel and threshold values













Accession


Accession
Thres-


Gene
Number
Threshold
Gene
Number
hold















ATP5E
NM_006886
None
MYBL2
NM_002466
6


GPX1
NM_000581
None
Ki-67
NM_002417
6


PGK1
NM_000291
None
GADD45B
NM_015675
4.5


UBB
NM_018955
None
EFNB2
NM_004093
4


VDAC2
NM_003375
None
RUNX1
NM_001754
4.5


BGN
NM_001711
None
BIK
NM_001197
4.5


FAP
NM_004460
6
MAD2L1
NM_002358
3


INHBA
NM_002192
None
HSPE1
NM_002157
None


cMYC
NM_002467
None
AXIN2
NM_004655
None









Thresholded Ct values for each gene are calculated according to the formula:








{





if





Normalized






C
T


<
Threshold





Threshold






C
T


=
Threshold







if





Normalized






C
T



Threshold





Threshold






C
T


=

Normalized






C
T











It will be appreciated by one of ordinary skill in the art that a purpose of thresholding is to address non-linear functional forms for gene expression measurements. However, it will be readily appreciated that other nonlinear transforms other than thresholding can be used to accomplish the same effect.


Building Gene Cliques from Validated Biomarkers


This disclosure contemplates using co-expressed genes and/or gene cliques, identified with respect to prognostic and/or predictive genes, as substitutes for, or for analysis with, the prognostic and/or predictive genes disclosed herein. One method disclosed to analyze gene cliques that co-express with a target gene (i.e., a gene of interest) involves normalizing microarray gene expression data for cancer tumor samples based on array probes, calculating a correlation coefficient (e.g., using Spearman or Pearson correlation coefficients) based on gene expression levels for every unique pair of array probes, determining significant probe pairs, wherein significant probe pairs are a target gene probe and an array probe with a correlation co-efficient greater than a significant threshold value (e.g., a Spearman correlation co-efficient ≥0.5), mapping the target gene to its corresponding target gene probe, selecting a candidate probe set, wherein each candidate probe is part of a significant probe pair, and identifying an official gene symbol for each candidate probe (e.g., Entrez Gene Symbol). For example, Table 6 lists the gene cliques associated with FAP, INHBA, Ki-67, HSPE1, MAD2L1, and RUNX1.


Kits of the Invention


The materials for use in the methods of the present invention are suited for preparation of kits produced in accordance with well known procedures. The present disclosure thus provides kits comprising agents, which may include gene-specific or gene-selective probes and/or primers, for quantitating the expression of the disclosed genes for predicting prognostic outcome or response to treatment. Such kits may optionally contain reagents for the extraction of RNA from tumor samples, in particular fixed paraffin-embedded tissue samples and/or reagents for RNA amplification. In addition, the kits may optionally comprise the reagent(s) with an identifying description or label or instructions relating to their use in the methods of the present invention. The kits may comprise containers (including microliter plates suitable for use in an automated implementation of the method), each with one or more of the various reagents (typically in concentrated form) utilized in the methods, including, for example, pre-fabricated microarrays, buffers, the appropriate nucleotide triphosphates (e.g., dATP, dCTP, dGTP and dTTP; or rATP, rCTP, rGTP and UTP), reverse transcriptase, DNA polymerase, RNA polymerase, and one or more probes and primers of the present invention (e.g., appropriate length poly(T) or random primers linked to a promoter reactive with the RNA polymerase). Mathematical algorithms used to estimate or quantify prognostic or predictive information are also properly potential components of kits.


Reports


The methods of this invention, when practiced for commercial diagnostic purposes, generally produce a report or summary of information obtained from the herein-described methods. For example, a report may include information concerning expression levels of prognostic and/or predictive genes, a prediction of the predicted clinical outcome or response to chemotherapy for a particular patient, or gene cliques or thresholds. The methods and reports of this invention can further include storing the report in a database. The method can create a record in a database for the subject and populate the record with data. The report may be a paper report, an auditory report, or an electronic record. The report may be displayed and/or stored on a computing device (e.g., handheld device, desktop computer, smart device, website, etc.). It is contemplated that the report is provided to a physician and/or the patient. The receiving of the report can further include establishing a network connection to a server computer that includes the data and report and requesting the data and report from the server computer.


Computer Program


The values from the assays described above, such as expression data, recurrence score, treatment score and/or benefit score, can be calculated and stored manually. Alternatively, the above-described steps can be completely or partially performed by a computer program product. The present invention thus provides a computer program product including a computer readable storage medium having a computer program stored on it. The program can, when read by a computer, execute relevant calculations based on values obtained from analysis of one or more biological sample from an individual (e.g., gene expression levels, normalization, thresholding, and conversion of values from assays to a score and/or graphical depiction of likelihood of recurrence/response to chemotherapy, gene co-expression or clique analysis, and the like). The computer program product has stored therein a computer program for performing the calculation.


The present disclosure provides systems for executing the program described above, which system generally includes: a) a central computing environment; b) an input device, operatively connected to the computing environment, to receive patient data, wherein the patient data can include, for example, expression level or other value obtained from an assay using a biological sample from the patient, or microarray data, as described in detail above; c) an output device, connected to the computing environment, to provide information to a user (e.g., medical personnel); and d) an algorithm executed by the central computing environment (e.g., a processor), where the algorithm is executed based on the data received by the input device, and wherein the algorithm calculates a RS, TS, risk or benefit group classification, gene co-expression analysis, thresholding, or other functions described herein. The methods provided by the present invention may also be automated in whole or in part.


All aspects of the present invention may also be practiced such that a limited number of additional genes that are co-expressed with the disclosed genes, for example as evidenced by statistically meaningful Pearson and/or Spearman correlation coefficients, are included in a prognostic or predictive test in addition to and/or in place of disclosed genes.


Having described the invention, the same will be more readily understood through reference to the following Examples, which are provided by way of illustration, and are not intended to limit the invention in any way.


EXAMPLE 1
Gene Expression Analysis for Colon Cancer Recurrence

Methods and Materials:


Patients and Samples


Tumor tissue samples were from two cohorts of patients with stage II or stage III colon cancer treated with surgery alone form the basis for this report. Further details concerning the NSABP protocols C-01, C-02, C-03, and C-04 are available in C. Allegra, J Clin Oncology 21(2):241-250 (2003) and related U.S. application Ser. Nos. 11/653,102 and 12/075,813, the contents of which are incorporated herein by reference.


The first cohort pooled available patient samples from NSABP protocols C-01 or C-02 in which patients were randomly assigned to receive either colon resection alone or resection+bacillus Calmette-Guerin (“BCG”) immunotherapy. The second cohort (CCF) included stage II and stage III colon cancer patients treated with surgery alone at CCF between the years 1981 and 2000. None of the patients in either group received adjuvant chemotherapy. In both cohorts, gene expression measurements were obtained from archived, formalin-fixed, paraffin-embedded (FPE) colon tumor tissue.


Differential Expression Data:


The final number of evaluable FPE blocks was 270 in the NSABP cohort and 765 in the CCF cohort (n=1035). The primary reasons for exclusion were failure to meet minimum RNA yield (10% of samples in NSABP and 8% in CCF) and failure to meet quality control criteria for RT-qPCR (7% in NSABP and 2% in CCF).


The primary analysis in both studies investigated the relationship between the expression of 761 genes and RFI. This analysis identified sixty-five genes were found to be nominally significant in both studies. (See FIG. 1.) The high level of agreement was observed between the univariate hazard ratios for 63 (97%) of 65 genes significantly related to RFI in both studies. Of the genes found to be significantly related to RFI in either study, the majority were also related to both DFS and OS within the same study.


In both cohorts, the relationship between the expression of each gene and RFI was investigated, controlling for study and baseline characteristics. Any of the baseline clinical characteristics or study design attributes that had at least a modest association (p<0.2) with RFI were included in the multivariate analysis. Sixty-one (43%) of the 143 genes significant in univariate analyses in the NSABP cohort were statistically significant after controlling for nodal status, tumor location, tumor grade, mucinous tumor type, study protocol (C-01 vs. C-02), treatment assignment (BCG vs. none), and year of surgery. Eighty-eight (74%) of the 119 genes significant in univariate analysis in the CCF cohort retained significance after adjustment for age, nodal status, number of lymph nodes examined, tumor grade, mucinous tumor type, fixative, surgery year and T stage. There was agreement between the multivariate hazard ratios for the 65 genes significantly related to RFI in both studies. The hazard ratios were concordant for 63 of 65 genes. The consistency of hazard ratio estimates from the uni- and multivariate Cox regression analyses indicates that expression levels of these genes provide prognostic information which is relatively independent of traditional clinical predictors.


These 65 genes represent pathways that would be expected to be important in colon cancer recurrence. To identify genes that were co-expressed and therefore possibly members of the same functional gene family, hierarchical cluster analysis and forest plots were created using the genes that were significantly related to RFI in that study (not shown) as well as for the genes significantly related to RFI in both studies. Cluster analysis identified that the majority (48) of the prognostic genes fell into two relatively distinct gene groups: a stromal gene group (containing several subgroups) and a cell cycle gene group. The stromal group contained genes which, when highly expressed, were associated with a worse outcome and increased likelihood of recurrence, such as BGN, FAP, INHBA, and EFNB2. The cell cycle group contained genes which, when highly expressed, were associated with a better outcome and decreased likelihood of recurrence, such as cMYC, MYBL2, Ki-67, MAD2L1, and HSPE1.


EXAMPLE 2
Gene Expression Analysis for Prognostic and Predictive Genes

A study was conducted to assay gene expression levels in tumor samples obtained from patients with stage II or III colon cancer treated with surgery and 5FU/LV and perform analysis across four independent studies to identify genes that quantitate both the individual risk of recurrence in patients treated with surgery alone (prognosis) and the individual treatment benefit of 5-FU/LV adjuvant chemotherapy (prediction). Further information about these studies can be found in related U.S. application Ser. Nos. 11/653,102 and 12/075,813, the contents of which are incorporated herein by reference.


Methods and Materials


Patients and Samples


Tissue samples were obtained from two cohorts of patients with stage II or stage III colon cancer treated with surgery and 5FU/LV. The first cohort included available patient samples from the 5FU/LV arm of NSABP Study C-04 in which patients were randomly assigned to receive either 5FU/LV, 5FU+levamisole or 5FU/LV+levamisole. (See, N. Wolmark, et al., J Clin Oncol 17:3553-3559 (1999). The second cohort included available patient samples from the 5FU/LV arm of NSABP Study C-06 in which patients were randomly assigned to receive 5FU/LV or oral uracil/tegafur plus leucovorin. (See, B. Lembersky, et al., J Clin Oncol 24:2059-2064 (2006). The 5FU/LV regimen was the same in both studies. In both cohorts, gene expression measurements were obtained from archived, formalin-fixed, paraffin-embedded (FPE) colon tumor tissue.


Based on treatment assignment and eligibility in the original NSABP studies, 691 C-04 patients and 792 C-06 patients qualified for this study. Available formalin-fixed paraffin-embedded (FPE) blocks for patients enrolled in C-04 (n=360) and C-06 (n=573) were assayed. After applying pre-specified exclusion criteria, the final number of evaluable patients was 308 in the C-04 cohort and 508 in the C-06 cohort. The primary reasons for exclusion were failure to satisfy pathology requirements (8.6% in C-04 and 1.7% in C-06) and failure to meet clinical eligibility criteria (1.7% in C-04 and 7.5% in C-06).


Analysis Methods


The primary analysis in both studies investigated the relationship between the expression of each gene and RFI. This analysis identified 143 (19%) of the 761 genes as being significantly related to RFI in the C-04 cohort compared to 169 (45%) of the 375 genes in the C-06 cohort. Seventy-five genes were found to be nominally significant in both studies. The hazard ratios were concordant (i.e. in similar direction) for 73 (97%) of these 75 genes. Of the genes found to be significantly related to RFI in either study, the majority were also related to both DFS and OS within the same study. Seventy-one (50%) of 143 genes significantly associated with RFI in univariate analyses in the C-04 study were statistically significant after controlling for nodal status and age. One hundred thirty-seven (81%) of the 169 genes significant in univariate analyses in the C-06 study were statistically significant after controlling for nodal involvement and mucinous tumor type. A high level of agreement between the univariate and multivariate hazard ratios for genes significantly related to RFI in both studies was observed.


To identify prognostic genes across the four colon development studies, the focus was on the genes which significantly and consistently associated with RFI in both surgery only (C-01/C-02 and CCF studies described in Example 1) and surgery+5FU/LV-treated (C-04 and C-06) patients since prognostic genes are expected to have a similar relationship (i.e. similar direction and magnitude of the HR's) with outcome when measured in patients treated with the standard of care or in patients treated with a new intervention. A total of 48 (13%) of 375 genes studied in all four development studies were significantly (p<0.05) associated with RFI in both surgery only studies and at least one surgery+5FU/LV study. Due to type II error considerations, genes were not required to be significant in all four studies. The univariate hazard ratios and associated confidence intervals for the 48 genes in each of the four colon development studies are presented in FIG. 2. Cluster analysis identified two relatively distinct gene groups among the 48 prognostic genes: a stromal activation gene group (containing several subgroups) and a cell cycle gene group. The stromal group contained genes which, when highly expressed, were associated with a worse outcome and increased likelihood of recurrence, such as BGN, FAP, INHBA, and EFNB2. The cell cycle group contained genes which, when highly expressed, were associated with a better outcome and decreased likelihood of recurrence, such as cMYC, MYBL2, Ki-67, MAD2L1, and HSPE1.


In contrast to prognostic genes, the predictive genes are expected to exhibit a different relationship with outcome (i.e. different HR's) in patients treated with surgery only as compared to patients treated with surgery+5FU/LV. To identify predictive genes, multivariate Cox proportional hazards models were examined, including main effects of gene and treatment and an interaction of gene and treatment for each of the 375 genes pooling the data across the four colon development studies. A total of 66 (18%) of 375 genes studied in all four development studies had an interaction of gene expression and treatment significant at 0.10 level. Only 4 of these 66 genes had significant association with RFI in the two independent surgery alone studies and at least one of the surgery+5 FU/LV study (i.e. were included in the set of 48 prognostic genes), indicating that a small minority of predictive genes are both prognostic and predictive. Fifty-nine of the 66 genes were not associated with RFI in both surgery only studies, indicating that the majority of predictive genes are not also prognostic genes.


These 66 genes represent pathways that would be expected to be important in response to chemotherapy. Cluster analysis identified two relatively distinct gene groups among 66 potentially predictive genes. One group contains a large number of cell cycle related genes such as centromere and spindle associated proteins (CENPA, KIFC1, KIF22, STK15, MAD2L1, AURKB), checkpoint regulation (CDC2, BUB1), and a DNA topoisomerase (TOP2A). The second group contains genes which represent several different biological pathways, including a tight group of stromal activation genes (BGN, SPARC, COL1A1, CDH11, MMP2, and TIMP1), and genes associated with apoptosis (BIK), 5FU metabolism (UPP), and B-catenin/wnt signaling (AXIN2, LEF). It is of note that the two mismatch repair genes (MSH2 and MSH3) and several hypoxia/stress response genes (NR4A1, RhoB, HIF1A, CREBBP, PKR2, EPAS1) were also associated with response to 5-FU/LV chemotherapy.


Preliminary prognostic models were built using subsets of the 48 prognostic genes. The results from a representative model containing 10 prognostic genes are shown in FIGS. 3a and 3b for stage II and stage III patients, respectively, treated with surgery only (C-01/C-02 and CCF cohorts). Patients were divided into three equally sized groups based on the calculated Recurrence Score. This model separated the 628 Stage II patients into groups with low, intermediate and high risk of recurrence: the lowest tertile had a 5% (95% CI 3%, 9%) risk of recurrence at 3 years vs. 14% (10%, 20%) and 22% (16%, 28%), respectively, for the middle and highest tertiles. (See, FIG. 4a.) For 395 Stage III patients, the two lowest tertiles had 26% (19%, 35%) and 26% (19%, 34%) risk of recurrence at 3 years vs. a 47% (39%, 56%) risk for the highest tertile. (See FIG. 4b.) For comparison, the overall 3-year risks of recurrence of Stage II and Stage III patients were 13% and 33%, respectively. When bootstrap was applied, the average Kaplan-Meier estimates (and associated 95% confidence intervals) of recurrence rates at 3 years for stage II patients were 5% (2%, 9%), 12% (8%, 17%) and 22% (18%, 27%) for the 1st, 2nd and 3rd tertile, respectively. For stage III patients, the corresponding estimates were 23% (16%, 30%), 28% (19%, 37%) and 48% (40%, 56%), respectively.


EXAMPLE 3
Validation of Algorithm-Based Molecular Diagnostic Assay

After the 65 prognostic and 66 predictive gene candidates were identified, the genes were examined further for consistency in association between gene expression and RFI (prognosis) and differential relationship between with RFI in treated vs. untreated patients (prediction) across the four colon development studies using univariate and multivariate Cox proportional hazards models. Representation of the relevant biologic pathways, distribution of gene expression, functional form of the relationship between gene expression, and RFI and analytical performance of individual genes were also taken into account.


Forest plots for the predictive genes (after thresholding) were reviewed and genes were identified that (1) displayed predictive effects either in both Stage II and Stage III colorectal cancer, or in Stage III only; (2) had significant (e.g., p<0.10) gene by treatment interaction in a model of gene (n=9) or median Ct<4 (n=2); and (3) had significant (p<0.10) gene by treatment interaction after RSu and TRT were forced into the model. Genes with consistent univariate hazard ratios (HRs) were preferred. In addition, forest plots for the predictive genes were examined qualitatively and genes displaying predictive effects either in both Stage II and Stage III colorectal cancer, or in Stage III only were identified. Through this analysis the following additional 10 predictive gene candidates were identified (in addition to the 6 predictive genes in the final algorithm): RANBP2, BUB1, TOP2A, C20_ORF1, CENPF, STK15, AURKB, HIF1A, UBE2C, and MSH2. Based on these results, multi-gene models were designed and analyzed across all four studies. Those analyses, together with a methodical evaluation of analytical performance of each candidate gene, led to the design of a multi-gene RT-PCR-based clinical assay to predict recurrence risk and treatment benefit from 5FU/LV. The genes represent biological categories that are important in colon cancer: stromal group (BGN, FAP, INHBA, EFNB2), cell cycle group (Ki-67, MYBL2, cMYC, MAD2L1, HSPE1), cell signaling (GADD45B), apoptosis group (BIK), transcription factor group (RUNX1), and MSI group (AXIN2), as well as 5 reference genes (ATP5E, GPX1, PGK1, UBB, VDAC2) for normalization of gene expression.


Methods and Materials


Patients and Samples


The developed algorithm may be validated using samples obtained from the QUASAR study. The QUASAR Collaborative Group trial is the largest reported single randomized study of observation versus adjuvant chemotherapy in patients with resected stage II colon cancer. (See, Lancet 370:2020-2029 (2007).) In that study, patients with resected stage II and III colon and rectal cancer were assigned by treating physicians to one of two arms of the study based on either a “clear” or “uncertain” indication for adjuvant therapy. In the “clear” arm, all patients (n=4320) received adjuvant 5-FU/leucovorin (LV) chemotherapy with or without levamisole. In the “uncertain” arm, patients (n=3239) were randomized to either observation (n=1617) or adjuvant 5-FU/LV chemotherapy (n=1622). As expected, the “clear” arm enrolled primarily stage III patients (70%), and the “uncertain” arm enrolled a high proportion of stage II patients (91% stage II, 71% colon cancer).


These results from QUASAR demonstrate that adjuvant 5-FU/LV treatment benefits a small but significant subset of stage II colon cancer patients. (See, e.g., FIG. 5.) Nevertheless, the physician managing stage II colon cancer still faces considerable challenges, including the fact that the majority of such patients are cured with surgery alone and that adjuvant 5-FU/LV chemotherapy carries potential toxicities of leucopenia, stomatitis, and diarrhea. Clearly, the decision to administer adjuvant 5-FU/LV chemotherapy would be greatly aided by the ability to identify reliably: 1) patients who are likely to be cured with surgery alone and 2) patients who are at substantial risk of recurrence following surgery and have a significant likelihood of clinical benefit with adjuvant treatment. With regard to the latter, it is worth emphasizing that the clinically relevant information for patients and oncologists includes not only the magnitude of the baseline risk of recurrence but also the magnitude of potential benefit (i.e. the absolute clinical benefit) associated with adjuvant 5-FU/LV treatment.


The validation study entailed the use of a pre-specified RT-PCR-based 18-gene clinical assay (see genes listed in Table 3) applied to archival paraffin-embedded tumor tissue specimens from colon cancer patients studied in QUASAR. The study considered the relationship between (1) a continuous RS and recurrence risk in patients randomized to surgery alone, and compared to that of patients randomized to surgery followed by adjuvant 5-FU/LV chemotherapy (controlling for simultaneous prognostic effects of clinical and pathological covariates); and (2) a continuous TS and chemotherapy benefit in patients randomized to surgery alone or surgery followed by adjuvant 5-FU/LV chemotherapy. The study compared the risk of recurrence between the high and low recurrence risk groups based on pre-specified cut-points for RS. A two-fold higher recurrence risk at 3 years in the high recurrence risk group compared to the low recurrence risk group was considered clinically significant. Alternative clinical endpoints, including RFI, DFS and OS, were considered. The study also looked for a significant (1) trend in absolute chemotherapy benefit for recurrence at 3 years across the low, intermediate, and high chemotherapy benefit groups; (2) interaction between the continuous TS and treatment relative to alternative clinical endpoints, including RFI, OS and DFS; (3) interaction between MMR status and treatment after controlling for the prognostic effects of the continuous RS and prognostic covariates.


Fixed paraffin-embedded colon tumor tissue from approximately 1,500 patients from QUASAR with stage II colon cancer. The RNA was extracted from the tumor tissue and RT-PCR analysis was conducted to determine expression levels of 13 cancer-related and 5 reference genes (Table 3). A prospectively-defined algorithm was used to calculate a RS and TS for each patient. Patients were classified into low, intermediate, and high recurrence risk groups using the RS and pre-specified cut-points (Table 1). Similarly, patients were classified into low, intermediate, and high chemotherapy benefit groups based on the combination of the RS and TS and on pre-specified cut-points (Table 2). These cut-points define the boundaries between low and intermediate benefit groups and between intermediate and high benefit groups.


The specimens were also assessed by pathology to determine: tumor type, tumor grade, presence of lymphatic and/or vascular invasion, number of nodes examined, depth of invasion (pathologic T stage), MMR status, and other QC metrics. This information was used to determine whether there was a significant relationship between risk of recurrence and individual and pathologic covariates.


Expression levels of 13 cancer-related genes used in the calculation of the RS and TS were reported as values from the RT-PCR assay. Gene expression measurements were normalized relative to the mean of five reference genes (ATP5E, GPX1, PGK1, UBB, VDAC2). For each cancer-related gene, a cycle threshold (CT) measurement was obtained by RT-PCR, and then normalized relative to a set of five reference genes. Reference-normalized expression measurements typically range from 0 to 15, where a one unit increase generally reflects a 2-fold increase in RNA quantity.


Analysis Methods:


Unless otherwise stated, all significance tests were conducted at the 0.05 significance level, and two-sided p-values and confidence intervals will be reported. To preserve the overall family-wise error rate for testing the primary objectives at the 0.05 significance level, the analysis applied conditional fixed sequential testing. A Cox proportional hazards regression model was fit to the clinical endpoint RFI for the patients who were randomized to surgery alone and a likelihood ratio test used to determine if the RS is significantly associated with the risk of recurrence (i.e. if the hazard ratio associated with the RS is significantly different from 1).


A Cox proportional hazards regression was used to model the first 3 years of follow-up data, that is, censoring time to recurrence at 3 years after randomization for patients who have not experienced a recurrence before that time, to determine if the TS is associated with the magnitude of chemotherapy benefit. The likelihood ratio test was used to compare the reduced model with RS, TS and the treatment main effect, with the full model that includes RS, TS, the treatment main effect, and the interaction of treatment and TS. In addition, we will use the method of Royston and Parmar (2002) to fit a flexible parametric model to RFI using all available follow-up data. The method will model the hazard of recurrence using the Weibull distribution with natural spline smoothing of the log cumulative hazards function, with effects for treatment (chemotherapy or observation), RS, TS and the interaction of TS with treatment, allowing the effects of treatment, RS, TS and TS interaction with treatment to be time dependent. The predicted effect of chemotherapy as a function of TS will be estimated at follow-up times of 2, 3, and 5 years.


Power calculations were carried for the Cox proportional hazards model with a single non-binary covariate using the method proposed by Hsieh and Lavori (2000) as implemented in PASS 2008. One skilled in the art would recognize that power at alpha 0.01-0.05 alpha would be sufficient to control for type I error.


For example, a test comparing a reduced Cox proportional hazards regression model of gene expression and treatment to a full model containing gene expression, treatment and interaction of gene expression and treatment indicated an association of chemotherapy benefit and expression of RUNX1 (p=0.030, Interaction HR=0.59, HR 95% CI (0.37, 0.95) and FAP (p=0.065, Interaction HR=0.66, HR 95% CI (0.42, 1.03).


The association of gene expression and recurrence risk in surgery alone patients was examined for the 13 cancer-related genes. Multivariate Cox proportional hazards regression model allows estimation of recurrence risk adjusted for a specific distribution of clinical covariates. Recurrence risk estimates were produced from this multivariate model, adjusting for distribution of clinical covariates, differences in distribution in various study populations (if any), and baseline survival.


Table 8 presents the results of the univariate Cox proportional hazards regression models of gene expression on RFI. FIG. 12 demonstrates the group risk (by Kaplan Meier curve) for Stage II colon cancer patients following surgery based on risk of recurrence at three years and recurrence score (including stromal and cell cycle group genes). FIG. 13 demonstrates the risk profile plot (by Kaplan Meier curve) for risk of recurrence at five years (QUASAR—surgery only) and recurrence score (including stromal, cell cycle, and (for RS2) apoptosis genes).


In addition, the analyses combining the results from the four colon development studies and the QUASAR validation study were carried out to assess the performance of the 13 cancer-related genes across more than 3000 patients. Two different analysis methods were applied to combine the results across studies: (1) meta-analysis treating inter-study variation as random using the method of Paule and Mandel (1982) as implemented by DerSimonian and Kacker (2007); and (2) Cox proportional hazards regression model stratified by study, stage and treatment. Table 9 presents the results of these analyses. As can be observed, all but AXIN were shown to be associated with risk of recurrence in colon cancer (i.e. 95% CI did not include 1). (See, e.g., R. Paule, J. Mandel, Journal of Research of the National Bureau of Standards 87:377-385 (1982); R. der Simonian and R. Kacker, Cotemp. Clin Trials 28:105-144 (2007), both incorporated herein by reference.)


EXAMPLE 4
Alternative Algorithm-Based Assay

Further analysis of data from the studies outlined in the Examples above suggested that incorporating additional genes into the Recurrence Score gene panel may yield improved performance. For example, BIK and EFNB2 were significantly associated with recurrence risk in both surgery alone and 5FU-treated patients. Statistical modeling was conducted to explore the strength of association between several multi-gene modules and recurrence of colon cancer. Table 10 and FIGS. 17-19 demonstrate comparative prognostic performance of selected multi-gene models.


Table 10: Multi-gene models based on standardized gene expression.












TABLE 10









SCORE












STD
LR
Genes















N
Variable
N
HR
Chisq
Est
StdHR
LRChisq
LRPVal


















1
BGN
3137
1.57
140.2
0.09
1.09
1.13
0.29



FAP



−0.09
0.91
1.93
0.16



INHBA



0.10
1.11
2.29
0.13



EFNB2



0.19
1.22
26.02
3.4E−07



GADD45B



0.02
1.02
0.16
0.69



Ki-67



−0.13
0.88
6.37
0.01



MAD2L1



−0.13
0.88
6.35
0.01



BIK



−0.15
0.86
12.91
3.3E−04



cMYC



−0.13
0.88
9.10
0.003



MYBL2



−0.02
0.98
0.25
6.2E−01


2
BGN + INHBA + FAP +
3137
1.52
120.7
0.07
1.23
19.85
8.4E−06



EFNB2



GADD45B



−0.02
0.98
0.13
0.72



Ki-67 + MAD2L1 +



−0.13
0.77
39.19
3.8E−10



BIK



cMYC



−0.10
0.91
5.50
0.02



MYBL21



−0.01
0.99
0.10
0.75


3
BGN + INHBA + FAP +
3137
1.51
118.9
0.06
1.22
25.61
4.2E−07



EFNB2 +



⅓ GADD45B



Ki-67 + MAD2L1 +



−0.12
0.74
54.97
1.2E−13



BIK + ¾cMYC +



½ MYBL2


4
BGN + INHBA + FAP +
3137
1.51
119.6
0.06
1.21
24.60
7.1E−07



EFNB2 + ⅓



GADD45B



Ki-67 + MAD2L1 +



−0.13
0.74
55.61
8.8E−14



BIK + ½cMYC +



½ MYBL2









Based on the statistical modeling, it was determined that a multi-gene model using BGN and Ki-67, or BGN, Ki-67 and BIK, can provide minimal prognostic information to colon cancer patients. See FIG. 18-19. However, a model consisting of ten prognostic genes (BGN, FAP, INHBA, EFNB2, GADD45B, Ki-67, MAD2L1, BIK, cMYC, MYBL2), plus reference genes (“RS2”), provided a highly accurate assessment of risk of recurrence in colon cancer. See FIG. 20.


EXAMPLE 5
Identifying Co-Expressed Genes and Gene Cliques

Gene cliques that co-express with the validated prognostic and predictive genes are set forth in Tables 4-6. These gene cliques were identified using the method described herein.


Materials and Methods:


Microarray data for colon tumor samples may be obtained internally, or derived from a public database, such as Gene Expression Omnibus (GEO). Microarray data was normalized and a pairwise Spearman correlation matrix computed for all array probes. Significant co-expressed probes across different studies was filtered out, and a graph built to compute probe cliques, map the probes to genes, and generate the gene cliques.


Download Colon Cancer Microarray Datasets


Five datasets from the Gene Expression Omnibus (GEO) database were used to compute the colon cliques. These datasets were identified as colon tumor expression experiments using the Affymetrix® HG-U133A microarray chip (Affimetrix Inc., Santa Clara, Calif.). Detailed information regarding the GEO database can be found at the National Center for Biotechnology Information (NCBI) website. Table 7 provides the accession number for the Geo datasets and the number of tumor samples in each dataset.


Array Data Normalization


The array data from GEO may be normalized using appropriate software, e.g. Affymetrix MAS5.0, or an open source RMA software like the bioconductor package.


If the sample array data are of MAS5.0 type, they are normalized with the following steps:

    • 1. Expression level is changed to “10” if the value is <10.
    • 2. Expression level is then log transformed.
    • 3. Median is computed on the log transformed values for the whole array probes.
    • 4. Each probe value subtracts the median and the resulting value will be defined as normalized value


If the sample array data are of RMA type, they are normalized with the following steps:

    • 1. Median is computed on the RMA generated values for the whole array probes.
    • 2. Each probe value subtracts the median and the resulting value will be defined as normalized value


Array Probe Co-Expression Pair Generation


The Spearman's rank correlation coefficient (rs) was calculated for every unique pair of probes in the dataset (22283 probes resulting 248,254,903 unique pairs for each dataset). These pairs were then filtered by a significant threshold value T; any probe pair which has an rs>=T was considered significant. Significant correlation pairs (had Spearman correlation values above threshold) were generated for each GEO dataset. For a given seeding gene probe, if the significant pairs involving the seeding probe or its directly connected probes existed across all five GEO datasets, they were placed in a graph and used to calculate maximal cliques.


Array Probe Clique Generation


The Brön-Kerbosch algorithm was used to generate the maximal cliques from a graph of significant probe pairs generated from the above step. First, three “sets” of nodes were created. The first set, compsub, was the set to be extended or shrunk on traveling along a branch of the backtracking tree. The second set, candidates, was the set of all points that will be added to compsub. The third set, not, was the set of nodes already added to compsub. The recursive mechanism for generating cliques is as follows:

    • 1. Selection of a candidate node.
    • 2. Adding the selected candidate node to compsub.
    • 3. Creating new sets candidates and not from the old sets by removing all nodes not connected to the selected candidate, keeping the old sets in tact.
    • 4. Calling the extension operator to operate on the sets just formed.
    • 5. Upon return, removal of the selected candidate from compsub and its addition to the old set not.


If after the extension operator, the candidates and not sets were empty, then the nodes on compsub were a clique and the mechanism starts over with a new candidate node. (See FIG. 11.)


Gene Clique Reporting


After the probe cliques had been computed, each probe in the cliques was mapped to genes as identified by Entrez Gene Symbol (Official Gene Symbol). Table 6 lists the report for the cliques associated with FAP, INHBA, Ki-67, HSPE1, MAD2L1, and RUNX1.


Certain probes have multiple mapping to Genes. They are listed as the same AffyProbeID within a SeedingGene but have multiple ambiguous map to Official Genes (listed as CliquedGene column). Certain CliquedGenes are listed as “---” in Table 6. That means the AffyProbes do not map to any current Official Genes. The weight column list out the weight as we merged cliques. It is essentially is the number of clique evidence for coexpression with the seeding gene.


EXAMPLE 6
Use of Thresholding

Thresholding can be used to improve the reproducibility in recurrence score (RS) and treatment score (TS) reporting by accounting for significant losses in precision as gene expression measurements approach the limit of quantitation (LOQ) of the assay. The LOQ of an assay represents the lowest concentration of RNA at which results can reliably be reported and have been estimated for each of the 18 colon cancer genes.


As an example, FIG. 26 shows the effects of diluting RNA concentration on (non-normalized) gene expression (Ct) measurements of Ki-67. The variance in Ct measurement clearly increases as RNA concentration decreases. In fact, it may be shown that the log variance in Ct measurement is roughly proportional to the mean Ct measurement for a gene. As a consequence, the variability in RS and TS may be further reduced by truncating gene expression measurements at or near the LOQ, thereby reducing the potential for noise being introduced into RS and TS estimation.


EXAMPLE 7
Calculating Gene Expression: Tumor Region Ratios

The clinical development studies in stage II/III colon cancer described above illustrated that genes which are frequently associated with stroma are correlated with increased risk of recurrence, whereas cell cycle genes are correlated with decreased risk of recurrence. This fact may account for the variability of RS/TS scores, and could be taken into account if the algorithm described herein considered the amount of stroma and luminal area, as well as localized gene expression in these regions. For example, an algorithm taking into account the ratios of stromal gene expression values per stroma area unit, and cell cycle gene expression values per epithelial area unit, would increase the precision and reproducibility of a recurrence risk prediction by decreasing heterogeneity within tumor blocks for a given patient.


A study was conducted to clarify the impact of variable tumor region areas and stromal/cell cycle gene expression on recurrence risk. RNA was extracted from different regions of colon tumors—the luminal part of the tumor and the tumor-associated stroma. FIG. 14 shows that there are higher expression levels of the stromal genes in the tumor-associated stroma and higher expression levels of the cell cycle genes in the luminal part of the tumor. It is therefore likely that the stroma is contributing significantly to the stromal group score (SG or SGS) and the epithelia is significantly contributing to the cell cycle gene score (CCG or CCGS). Given these assumptions, the area of stroma within the sample contributes to the variability of the SG (within and between blocks) and therefore the score(s). Similarly, the area of epithelia within the sample analyzed could contribute to the variability of the CCG (within and between blocks) and therefore the score(s).


Gene expression within tumor epithelia cells and stroma varies from patient to patient. For example, FIG. 15 demonstrates that some patients may have higher levels of gene expression in their tumor-associated stroma for stromal genes than do other patients. Thus, some patients can have large amounts of stroma but low activity, whereas other patients can have smaller amounts of stroma but high activity. In addition, gene expression levels for the same patient can vary depending on the location of the tumor (e.g., within and between tumor blocks). This variability can impact reproducibility of recurrence and treatment scores for a patient. For example, FIG. 16 demonstrates the variability, by tissue section of the same tumor block, of stromal group score (SG), cell cycle group score CCG), cell signaling group (CSG or GADD45B), and recurrence score (RS). This analysis was done on multiple sections from the same tumor block, and included data from 11 patients.


Therefore, taking into account the area of the tumor-associated stroma and the area of the tumor-luminal regions in calculating the RS algorithm and in calculating the TS algorithm can enhance the reproducibility of the RS and TS, respectively, thus leading to greater accuracy of recurrence risk prediction.


For example, the expression level of stromal group genes can be provided as a ratio of the expression level of one or more stromal group genes to the tumor-associated stroma unit area (“sua”) assayed. In another example, the expression level of cell cycle group genes can be provided as a ratio of the expression level of one or more cell cycle group genes to the tumor epithelial unit area (“cua”) are assayed. The RS algorithm could be modified in the following form: RS=[(SG×sua coefficient)±(CCG×sua coefficient)]+[(SG×cua coefficient)±(CCG×cua coefficient)]±(repeat analysis for other gene groups, e.g., CSG, AG, and/or TFG). Similarly, the TS algorithm could be modified in the following form: TS=[(SG×sua coefficient)±(CCG×sua coefficient)]+[(SG×cua coefficient)±(CCG×cua coefficient)]±(repeat analysis for other gene groups, e.g., AG, TFG, and/or MG.)


In addition, the following exemplary algorithm provides a method to analyze and remove variability associated with gene expression in different portions of the block. For example, for cell cycle and stromal gene expression in different portions of a tumor block one could calculate: SGSij=SGi+SBij (Stromal gene group value for subject i block j is sum of a Gene effect and a Block effect) and CCGSij=CCGi+CCBij (Cell cycle gene group value for subject i block j is sum of a Gene effect and a Block effect).


SGS and CCGS are not correlated across subjects: SGS and CCGS variability is mostly from SG and CCG, the gene expression factor, and these are not correlated.


SGS and CCGS are correlated within subjects: There is a common effect underlying CCB and SB. Calculate: SGSrij=SGSij−SGSi=SBij−SBi.

CCGSrij=CCGSij−CCGSi.=CCBij−CCBi.


Correlation between SGSrij and CCGSrij can be thought of as a within subjects correlation pooled across subjects, i.e. an average within patient correlation. An informal approach to estimating ρ in (Yij, Xij)˜N((μyi, μxi), [σy, ρyx//ρyx, σx]). Alternatively could assume Yij=αi+βXij+εij


If % Stroma correlates with the SGS within subject, it could provide a means of removing this source of variability in the RS and/or TS values.


EXAMPLE 8
Stromal Risk Analysis

Methods and Materials


A study involving 444 patients from a subset of the Cleveland Clinic Foundation (CCF) cohort described in Example 1 was conducted to clarify how the amount of tumor-associated stroma (“stroma area”) in a colon cancer tumor sample impacts the recurrence risk for stage II/III colon cancer patients (“Stromal Risk”). Specifically, a subset of the CCF cohort (cohort-sampling study design) involving all 148 recurrences from the CCF cohort and a random sample of approximately twice as many (i.e., 296) non-recurrences was used, resulting in 444 patients treated by resection of the colon.


Inclusion criteria included:

    • Either stage II or stage III colon cancer patient.
    • Patient treated with colon resection (surgery) at CCF between the years of 1981 and 2000.


Exclusion criteria included:

    • No tumor block available from initial diagnosis in the CCF archive.
    • No tumor or very little tumor (<5% of the area occupied by invasive cancer cells compared to the area occupied by other epithelial elements, such as normal epithelium, or lymphatic) in block as assessed by examination of the H&E slide by the CCF and Genomic Health Pathologist.
    • Patients diagnosed with stage II or stage III signet ring colon cancer (WHO classification)
    • Insufficient RNA (<586 ng) for RT-PCR analysis.
    • Average non-normalized CT for the 5 reference genes≥35.


The full CCF cohort included a total of 886 FPE tumor tissue blocks. Of these, 108 were excluded due to failure to satisfy pathology and/or laboratory requirements described below. An additional 13 patients were excluded after the laboratory, pathology and clinical data were merged because of failure to satisfy all study inclusion and exclusion criteria, leaving 765 evaluable patients. The initial histological assessment by a Genomic Health pathologist was to evaluate the slide for the quantity of tumor and, where necessary, mark for manual micro dissection to enrich the tumor region. In this initial pathology review 8 cases were found to have insufficient tumor tissue (<5% tumor tissue) and thus failed the initial pathology review. The samples then underwent full histology review. Grade was captured by CCF and Genomic Health pathologists and each pathology read was analyzed separately (i.e. no attempt was made to create a ‘combined’ pathology score). An additional 11 cases failed this full pathology review due to the presence of a signet ring morphology comprising greater than 50% of the invasive component, lack of sufficient invasive tumor tissue (<5% cancer cells) or tissue type other than colon. Patient and sample disposition from the CCF study are summarized in Table 11.









TABLE 11







Patient Disposition from CCF Study











Category
N Patients
% Patients














Patients with available blocks
886
100% 



Excluded due to:
121
13.7% 



Failed pathology review
18
2.0%



Insufficient RNA
73
8.2%



QC of RT-PCR (incomplete or poor
17
1.9%



data quality)





Failure to satisfy all clinical
13
1.5%



eligibility criteria*





Evaluable patients
765
86.3% 









All 444 evaluable samples underwent both standard and digital pathology assessments. Using the 120-slide capacity ScanScope XT system, automated scanning of all study H&E slides were conducted at 20× scanning magnification with autopopulation of patient identification fields with barcode data using the Spectrum information management system. The 20× scanning magnification was selected because this magnification gives superior optimization of image quality and scanning speed.


Digital H&E scans were obtained from the Aperio® Digital Pathology System. Two different software systems—the Aperio® Genie Digital Pathology Image Analysis software and the Definiens® Digital Pathology Image Analysis software—were used to generate digital H&E measurements. The Definiens image analysis software, based on the Definiens Cognition Network Technology®, examines pixels in context and builds up a picture iteratively, recognizing groups of pixels as objects.


The pathologist and assistant trained the image analysis applications to detect regions of interest (e.g., mucin, tumor glands and tumor stroma) using previously captured digital images of the entire enriched tumor portion. These training slides were representative of the slides to be assessed by the Aperio system. Several variations of the two image analysis algorithms were developed for low and high grade carcinomas and mucinous carcinomas. These were developed by identification of regions of interest, and then having the programs “learn” from the training slides. The resulting algorithms were applied to the entire patient cohort, analyzing the enriched tumor portions of the patient samples. The patient samples were batched into three digital study sets (i.e., low grade, high grade and mucinous carcinomas) as determined by the GHI pathologist and all images were processed using batch processing.


Findings and Statistical Analysis


The surface area of tumor-associated stroma varies from patient to patient. For example, FIG. 21 provides a variability plot for natural logarithm of stroma area, as measured by the Aperio digital pathology system, for the 444 patients under study, stratified by recurrence-free interval status.


Statistical analyses were performed to determine if there was a significant relationship between stroma area and recurrence-free interval (RFI) Specifically, we compared the (reduced) Weighted Cox Proportional Hazards model for RFI based on the main effect for tumor stage (Stage II and Stage III), versus the (full) Weighted Cox Proportional Hazards model for RFI based on the main effects of tumor stage and stroma area as measured by the Aperio digital image analysis system. Weighted Pseudo Partial Likelihood approach was used to accommodate the use of a case-cohort sampling study design. A Wald test for the hypothesis that the hazard ratio for stroma area is 1 versus the 2-sided alternative hypothesis that the hazard ratio is not 1 was performed. The resulting Wald χ2=15.64 with 1 degree of freedom resulting in a 2-sided p-value <0.001, indicating that stroma area is prognostic of disease recurrence (beyond tumor stage alone) in colon cancer patients treated with colon resection. The resulting standardized hazard ratio for stroma area is 1.45, indicating that there is a 45% increase in the relative risk for disease recurrence for each standard deviation increase in stroma area.









TABLE 12







Proportional Hazard Regression for Recurrence-Free


Interval: Stage and Stroma Area Alone


PH Regression on RFI for Stage, Stroma Area Alone
















Robust

HR

Wald



Variable
Coef
SE
HR
95% CI
DF
ChiSq
P value





Stage (III vs II)
0.66
0.19
1.94
(1.34, 2.82)
1
12.27
<.001


Standard Area -
0.37
0.09
1.45
(1.20, 1.74)
1
15.64
<.001


Stroma Area, Aperio









In addition to testing if stroma area is prognostic of disease recurrence, statistical analyses were performed to determine if stroma area provides additional prognostic information beyond both stage and Recurrence Score. Specifically, we compared the (reduced) Weighted Cox Proportional Hazards model for RFI based on the main effect for stage (Stage II and Stage III) and Recurrence Score, versus the (full) Weighted Cox Proportional Hazards model for RFI based on the main effects of tumor stage, Recurrence Score and stroma area as measured by the Aperio digital image analysis system. A Wald test for the hypothesis that the hazard ratio for stroma area is 1 versus the 2-sided alternative hypothesis that the hazard ratio is not 1 was performed. The resulting Wald ratio χ2=13.17 with 1 degree of freedom resulting in a 2-sided p-value <0.001, indicating that stroma area is prognostic of disease recurrence beyond tumor stage and Recurrence Score. The resulting standardized hazard ratio for stroma area is 1.41, indicating that there is a 41% increase in the relative risk for disease recurrence for each standard deviation increase in stroma area.









TABLE 13







Proportional Hazard Regression for Recurrence-Free Interval:


Stage, Stroma Area and Recurrence Score


PH Regression on RFI for Stage, Stroma Area Alone, and R2
















Robust

HR

Wald



Variable
Coef
SE
HR
95% CI
DF
ChiSq
P value

















Stage (III vs II)
0.65
0.19
1.88
(1.32, 2.81)
1
11.49
<.001


Standard Area -
0.34
0.10
1.44
(1.17, 1.70)
1
13.17
<.001


Stroma Area, Aperio


RS2/25
0.57
0.19
1.46
(1.122, 2.55)
1
9.19
0.002









Similar analyses were performed to test if stroma area provides additional prognostic information beyond both stage and RS2. Specifically, we compared the (reduced) Weighted Cox Proportional Hazards model for RFI based on the main effect for stage (Stage II and Stage III) and RS2, versus the (full) Weighted Cox Proportional Hazards model for RFI based on the main effects of tumor stage, RS2 and stroma area as measured by the Aperio digital image analysis system. A Wald test for the hypothesis that the hazard ratio for stroma area is 1 versus the 2-sided alternative hypothesis that the hazard ratio is not 1 was performed. The resulting Wald ratio χ2=14.86 with 1 degree of freedom resulting in a 2-sided p-value <0.001, indicating that stroma area is prognostic of disease recurrence beyond tumor stage and RS2. The resulting standardized hazard ratio for stroma area is 1.44, indicating that there is a 44% increase in the relative risk for disease recurrence for each standard deviation increase in stroma area.









TABLE 14







Proportional Hazard Regression for Recurrence-Free Interval:


Stage, Stroma Area and RS2


PH Regression on RFI for Stage, Stroma Area Alone, and RS2
















Robust

HR

Wald



Variable
Coef
SE
HR
95% CI
DF
ChiSq
P value

















Stage (III vs II)
0.63
0.19
1.88
(1.29, 2.74)
1
10.87
<.001


Standard Area -
0.36
0.09
1.44
(1.19, 1.73)
1
14.86
<.001


Stroma Area, Aperio


RS2/25
0.38
0.12
1.46
(1.15, 1.85)
1
9.79
0.002









For analysis purposes, stroma area can be stratified into low and high Stroma Risk Groups. Specifically, we define low risk (stroma score ≤0) and high risk (stroma score >0) where stroma score=(stroma area−mean)/standard deviation. Kaplan-Meier Plots for Stage II and Stage III patients stratified by Stroma Risk Group, provided in FIGS. 22 and 23 respectively, clearly show separation between risk groups (Logrank p-value <0.01). Similarly, Kaplan-Meier Plots for Stage II and Stage III patients stratified by both Stroma Risk Group and Recurrence Score Risk Group, provided in FIGS. 24 and 25 respectively, show even greater separation between risk groups (Logrank p-value <0.01).


CONCLUSION

These analyses show that stroma area is independently prognostic of disease recurrence in stage II and stage III patients and that RS, stromal area, and nodal status all provide important prognostic information in stage II and III colon cancer. The discovery that it is surface area of tumor-associated stroma that is most strongly associated with risk of recurrence, rather that proportional measurements of tumor regions, was an unexpected result of this study.













TABLE A





Gene
Accession
Reagt
Sequence
SEQ ID NO




















A-Catenin
NM_001903.1
FPr
CGTTCCGATCCTCTATACTGCAT
SEQ ID NO: 1





Probe
ATGCCTACAGCACCCTGATGTCGCA
SEQ ID NO: 2




RPr
AGGTCCCTGTTGGCCTTATAGG
SEQ ID NO: 3





ABCB1
NM_000927.2
FPr
AAACACCACTGGAGCATTGA
SEQ ID NO: 4




Probe
CTCGCCAATGATGCTGCTCAAGTT
SEQ ID NO: 5




RPr
CAAGCCTGGAACCTATAGCC
SEQ ID NO: 6





ABCC5
NM_005688.1
FPr
TGCAGACTGTACCATGCTGA
SEQ ID NO: 7




Probe
CTGCACACGGTTCTAGGCTCCG
SEQ ID NO: 8




RPr
GGCCAGCACCATAATCCTAT
SEQ ID NO: 9





ABCC6
NM_001171.2
FPr
GGATGAACCTCGACCTGC
SEQ ID NO: 10




Probe
CCAGATAGCCTCGTCCGAGTGCTC
SEQ ID NO: 11




RPr
GAGCTGCACCGTCTCCAG
SEQ ID NO: 12





ACP1
NM_004300.2
FPr
GCTACCAAGTCCGTGCTGT
SEQ ID NO: 13




Probe
TGATCGACAAATGTTACCCAGACACACA
SEQ ID NO: 14




RPr
GAAAACTGCTTCTGCAATGG
SEQ ID NO: 15





ADAM10
NM_001110.1
FPr
CCCATCAACTTGTGCCAGTA
SEQ ID NO: 16




Probe
TGCCTACTCCACTGCACAGACCCT
SEQ ID NO: 17




RPr
GGTGATGGTTCGACCACTG
SEQ ID NO: 18





ADAM17
NM_003183.3
FPr
GAAGTGCCAGGAGGCGATTA
SEQ ID NO: 19




Probe
TGCTACTTGCAAAGGCGTGTCCTACTGC
SEQ ID NO: 20




RPr
CGGGCACTCACTGCTATTACC
SEQ ID NO: 21





ADAMTS12
NM_030955.2
FPr
GGAGAAGGGTGGAGTGCAG
SEQ ID NO: 22




Probe
CGCACAGTCAGAATCCATCTGGGT
SEQ ID NO: 23




RPr
CAGGGTCAGGTCTCTGGATG
SEQ ID NO: 24





ADPRT
NM_001618.2
FPr
TTGACAACCTGCTGGACATC
SEQ ID NO: 25




Probe
CCCTGAGCAGACTGTAGGCCACCT
SEQ ID NO: 26




RPr
ATGGGATCCTTGCTGCTATC
SEQ ID NO: 27





AGXT
NM_000030.1
FPr
CTTTTCCCTCCAGTGGCA
SEQ ID NO: 28




Probe
CTCCTGGAAACAGTCCACTTGGGC
SEQ ID NO: 29




RPr
ATTTGGAAGGCACTGGGTTT
SEQ ID NO: 30





AKAP12
NM_005100.2
FPr
TAGAGAGCCCCTGACAATCC
SEQ ID NO: 31




Probe
TGGCTCTAGCTCCTGATGAAGCCTC
SEQ ID NO: 32




RPr
GGTTGGTCTTGGAAAGAGGA
SEQ ID NO: 33





AKT1
NM_005163.1
FPr
CGCTTCTATGGCGCTGAGAT
SEQ ID NO: 34




Probe
CAGCCCTGGACTACCTGCACTCGG
SEQ ID NO: 35




RPr
TCCCGGTACACCACGTTCTT
SEQ ID NO: 36





AKT2
NM_001626.2
FPr
TCCTGCCACCCTTCAAACC
SEQ ID NO: 37




Probe
CAGGTCACGTCCGAGGTCGACACA
SEQ ID NO: 38




RPr
GGCGGTAAATTCATCATCGAA
SEQ ID NO: 39





AKT3
NM_005465.1
FPr
TTGTCTCTGCCTTGGACTATCTACA
SEQ ID NO: 40




Probe
TCACGGTACACAATCTTTCCGGA
SEQ ID NO: 41




RPr
CCAGCATTAGATTCTCCAACTTGA
SEQ ID NO: 42





AL137428
AL137428.1
FPr
CAAGAAGAGGCTCTACCCTGG
SEQ ID NO: 43




Probe
ACTGGGAATTTCCAAGGCCACCTT
SEQ ID NO: 44




RPr
AAATGAGCTCTGCGATCCTC
SEQ ID NO: 45





ALCAM
NM_001627.1
FPr
GAGGAATATGGAATCCAAGGG
SEQ ID NO: 46




Probe
CCAGTTCCTGCCGTCTGCTCTTCT
SEQ ID NO: 47




RPr
GTGGCGGAGATCAAGAGG
SEQ ID NO: 48





ALDH1A1
NM_000689.1
FPr
GAAGGAGATAAGGAGGATGTTGACA
SEQ ID NO: 49




Probe
AGTGAAGGCCGCAAGACAGGCTTTTC
SEQ ID NO: 50




RPr
CGCCACGGAGATCCAATC
SEQ ID NO: 51





ALDOA
NM_000034.2
FPr
GCCTGTACGTGCCAGCTC
SEQ ID NO: 52




Probe
TGCCAGAGCCTCAACTGTCTCTGC
SEQ ID NO: 53




RPr
TCATCGGAGCTTGATCTCG
SEQ ID NO: 54





AMFR
NM_001144.2
FPr
GATGGTTCAGCTCTGCAAGGA
SEQ ID NO: 55




Probe
CGATTTGAATATCTTTCCTTCTCGCCCACC
SEQ ID NO: 56




RPr
TCGACCGTGGCTGCTCAT
SEQ ID NO: 57





ANGPT2
NM_001147.1
FPr
CCGTGAAAGCTGCTCTGTAA
SEQ ID NO: 58




Probe
AAGCTGACACAGCCCTCCCAAGTG
SEQ ID NO: 59




RPr
TTGCAGTGGGAAGAACAGTC
SEQ ID NO: 60





ANTXR1
NM_032208.1
FPr
CTCCAGGTGTACCTCCAACC
SEQ ID NO: 61




Probe
AGCCTTCTCCCACAGCTGCCTACA
SEQ ID NO: 62




RPr
GAGAAGGCTGGGAGACTCTG
SEQ ID NO: 63





ANXA1
NM_000700.1
FPr
GCCCCTATCCTACCTTCAATCC
SEQ ID NO: 64




Probe
TCCTCGGATGTCGCTGCCT
SEQ ID NO: 65




RPr
CCTTTAACCATTATGGCCTTATGC
SEQ ID NO: 66





ANXA2
NM_004039.1
FPr
CAAGACACTAAGGGCGACTACCA
SEQ ID NO: 67




Probe
CCACCACACAGGTACAGCAGCGCT
SEQ ID NO: 68




RPr
CGTGTCGGGCTTCAGTCAT
SEQ ID NO: 69





ANXA5
NM_001154.2
FPr
GCTCAAGCCTGGAAGATGAC
SEQ ID NO: 70




Probe
AGTACCCTGAAGTGTCCCCCACCA
SEQ ID NO: 71




RPr
AGAACCACCAACATCCGCT
SEQ ID NO: 72





AP-1 (JUN
NM_002228.2
FPr
GACTGCAAAGATGGAAACGA
SEQ ID NO: 73


official)




Probe
CTATGACGATGCCCTCAACGCCTC
SEQ ID NO: 74




RPr
TAGCCATAAGGTCCGCTCTC
SEQ ID NO: 75





APC
NM_000038.1
FPr
GGACAGCAGGAATGTGTTTC
SEQ ID NO: 76




Probe
CATTGGCTCCCCGTGACCTGTA
SEQ ID NO: 77




RPr
ACCCACTCGATTTGTTTCTG
SEQ ID NO: 78





APEX-1
NM_001641.2
FPr
GATGAAGCCTTTCGCAAGTT
SEQ ID NO: 79




Probe
CTTTCGGGAAGCCAGGCCCTT
SEQ ID NO: 80




RPr
AGGTCTCCACACAGCACAAG
SEQ ID NO: 81





APG-1
NM_014278.2
FPr
ACCCCGGCCTGTATATCAT
SEQ ID NO: 82




Probe
CCAATGGCTCGAGTTCTTGATCCC
SEQ ID NO: 83




RPr
CTATCTGGCTCTTTGCTGCAT
SEQ ID NO: 84





APN
NM_001150.1
FPr
CCACCTTGGACCAAAGTAAAGC
SEQ ID NO: 85


(ANPEP


official)




Probe
CTCCCCAACACGCTGAAACCCG
SEQ ID NO: 86




RPr
TCTCAGCGTCACCTGGTAGGA
SEQ ID NO: 87





APOC1
NM_001645.3
FPr
GGAAACACACTGGAGGACAAG
SEQ ID NO: 88




Probe
TCATCAGCCGCATCAAACAGAGTG
SEQ ID NO: 89




RPr
CGCATCTTGGCAGAAAGTT
SEQ ID NO: 90





AREG
NM_001657.1
FPr
TGTGAGTGAAATGCCTTCTAGTAGTGA
SEQ ID NO: 91




Probe
CCGTCCTCGGGAGCCGACTATGA
SEQ ID NO: 92




RPr
TTGTGGTTCGTTATCATACTCTTCTGA
SEQ ID NO: 93





ARG
NM_005158.2
FPr
CGCAGTGCAGCTGAGTATCTG
SEQ ID NO: 94




Probe
TCGCACCAGGAAGCTGCCATTGA
SEQ ID NO: 95




RPr
TGCCCAGGGCTACTCTCACTT
SEQ ID NO: 96





ARHF
NM_019034.2
FPr
ACTGGCCCACTTAGTCCTCA
SEQ ID NO: 97




Probe
CTCCCAACCTGCTGTCCCTCAAG
SEQ ID NO: 98




RPr
CTGAACTCCACAGGCTGGTA
SEQ ID NO: 99





ATOH1
NM_005172.1
FPr
GCAGCCACCTGCAACTTT
SEQ ID NO: 100




Probe
CAGGCGAGAGAGCATCCCGTCTAC
SEQ ID NO: 101




RPr
TCCAGGAGGGACAGCTCA
SEQ ID NO: 102





ATP5A1
NM_004046.3
FPr
GATGCTGCCACTCAACAACT
SEQ ID NO: 103




Probe
AGTTAGACGCACGCCACGACTCAA
SEQ ID NO: 104




RPr
TGTCCTTGCTTCAGCAACTC
SEQ ID NO: 105





ATP5E
NM_006886.2
FPr
CCGCTTTCGCTACAGCAT
SEQ ID NO: 106




Probe
TCCAGCCTGTCTCCAGTAGGCCAC
SEQ ID NO: 107




RPr
TGGGAGTATCGGATGTAGCTG
SEQ ID NO: 108





AURKB
NM_004217.1
FPr
AGCTGCAGAAGAGCTGCACAT
SEQ ID NO: 109




Probe
TGACGAGCAGCGAACAGCCACG
SEQ ID NO: 110




RPr
GCATCTGCCAACTCCTCCAT
SEQ ID NO: 111





Axin 2
NM_004655.2
FPr
GGCTATGTCTTTGCACCAGC
SEQ ID NO: 112




Probe
ACCAGCGCCAACGACAGTGAGATA
SEQ ID NO: 113




RPr
ATCCGTCAGCGCATCACT
SEQ ID NO: 114





axin1
NM_003502.2
FPr
CCGTGTGACAGCATCGTT
SEQ ID NO: 115




Probe
CGTACTACTTCTGCGGGGAACCCA
SEQ ID NO: 116




RPr
CTCACCAGGGTGCGGTAG
SEQ ID NO: 117





B-Catenin
NM_001904.1
FPr
GGCTCTTGTGCGTACTGTCCTT
SEQ ID NO: 118




Probe
AGGCTCAGTGATGTCTTCCCTGTCACCAG
SEQ ID NO: 119




RPr
TCAGATGACGAAGAGCACAGATG
SEQ ID NO: 120





BAD
NM_032989.1
FPr
GGGTCAGGTGCCTCGAGAT
SEQ ID NO: 121




Probe
TGGGCCCAGAGCATGTTCCAGATC
SEQ ID NO: 122




RPr
CTGCTCACTCGGCTCAAACTC
SEQ ID NO: 123





BAG1
NM_004323.2
FPr
CGTTGTCAGCACTTGGAATACAA
SEQ ID NO: 124




Probe
CCCAATTAACATGACCCGGCAACCAT
SEQ ID NO: 125




RPr
GTTCAACCTCTTCCTGTGGACTGT
SEQ ID NO: 126





BAG2
NM_004282.2
FPr
CTAGGGGCAAAAAGCATGA
SEQ ID NO: 127




Probe
TTCCATGCCAGACAGGAAAAAGCA
SEQ ID NO: 128




RPr
CTAAATGCCCAAGGTGACTG
SEQ ID NO: 129





BAG3
NM_004281.2
FPr
GAAAGTAAGCCAGGCCCAGTT
SEQ ID NO: 130




Probe
CAGAACTCCCTCCTGGACACATCCCAA
SEQ ID NO: 131




RPr
ACCTCTTTGCGGATCACTTGA
SEQ ID NO: 132





Bak
NM_001188.1
FPr
CCATTCCCACCATTCTACCT
SEQ ID NO: 133




Probe
ACACCCCAGACGTCCTGGCCT
SEQ ID NO: 134




RPr
GGGAACATAGACCCACCAAT
SEQ ID NO: 135





Bax
NM_004324.1
FPr
CCGCCGTGGACACAGACT
SEQ ID NO: 136




Probe
TGCCACTCGGAAAAAGACCTCTCGG
SEQ ID NO: 137




RPr
TTGCCGTCAGAAAACATGTCA
SEQ ID NO: 138





BBC3
NM_014417.1
FPr
CCTGGAGGGTCCTGTACAAT
SEQ ID NO: 139




Probe
CATCATGGGACTCCTGCCCTTACC
SEQ ID NO: 140




RPr
CTAATTGGGCTCCATCTCG
SEQ ID NO: 141





BCAS1
NM_003657.1
FPr
CCCCGAGACAACGGAGATAA
SEQ ID NO: 142




Probe
CTTTCCGTTGGCATCCGCAACAG
SEQ ID NO: 143




RPr
CTCGGGTTTGGCCTCTTTC
SEQ ID NO: 144





Bcl2
NM_000633.1
FPr
CAGATGGACCTAGTACCCACTGAGA
SEQ ID NO: 145




Probe
TTCCACGCCGAAGGACAGCGAT
SEQ ID NO: 146




RPr
CCTATGATTTAAGGGCATTTTTCC
SEQ ID NO: 147





BCL2L10
NM_020396.2
FPr
GCTGGGATGGCTTTTGTCA
SEQ ID NO: 148




Probe
TCTTCAGGACCCCCTTTCCACTGGC
SEQ ID NO: 149




RPr
GCCTGGACCAGCTGTTTTCTC
SEQ ID NO: 150





BCL2L11
NM_138621.1
FPr
AATTACCAAGCAGCCGAAGA
SEQ ID NO: 151




Probe
CCACCCACGAATGGTTATCTTACGACTG
SEQ ID NO: 152




RPr
CAGGCGGACAATGTAACGTA
SEQ ID NO: 153





BCL2L12
NM_138639.1
FPr
AACCCACCCCTGTCTTGG
SEQ ID NO: 154




Probe
TCCGGGTAGCTCTCAAACTCGAGG
SEQ ID NO: 155




RPr
CTCAGCTGACGGGAAAGG
SEQ ID NO: 156





Bclx
NM_001191.1
FPr
CTTTTGTGGAACTCTATGGGAACA
SEQ ID NO: 157




Probe
TTCGGCTCTCGGCTGCTGCA
SEQ ID NO: 158




RPr
CAGCGGTTGAAGCGTTCCT
SEQ ID NO: 159





BCRP
NM_004827.1
FPr
TGTACTGGCGAAGAATATTTGGTAAA
SEQ ID NO: 160




Probe
CAGGGCATCGATCTCTCACCCTGG
SEQ ID NO: 161




RPr
GCCACGTGATTCTTCCACAA
SEQ ID NO: 162





BFGF
NM_007083.1
FPr
CCAGGAAGAATGCTTAAGATGTGA
SEQ ID NO: 163




Probe
TTCGCCAGGTCATTGAGATCCATCCA
SEQ ID NO: 164




RPr
TGGTGATGGGAGTTGTATTTTCAG
SEQ ID NO: 165





BGN
NM_001711.3
FPr
GAGCTCCGCAAGGATGAC
SEQ ID NO: 166




Probe
CAAGGGTCTCCAGCACCTCTACGC
SEQ ID NO: 167




RPr
CTTGTTGTTCACCAGGACGA
SEQ ID NO: 168





BID
NM_001196.2
FPr
GGACTGTGAGGTCAACAACG
SEQ ID NO: 169




Probe
TGTGATGCACTCATCCCTGAGGCT
SEQ ID NO: 170




RPr
GGAAGCCAAACACCAGTAGG
SEQ ID NO: 171





BIK
NM_001197.3
FPr
ATTCCTATGGCTCTGCAATTGTC
SEQ ID NO: 172




Probe
CCGGTTAACTGTGGCCTGTGCCC
SEQ ID NO: 173




RPr
GGCAGGAGTGAATGGCTCTTC
SEQ ID NO: 174





BIN1
NM_004305.1
FPr
CCTGCAAAAGGGAACAAGAG
SEQ ID NO: 175




Probe
CTTCGCCTCCAGATGGCTCCC
SEQ ID NO: 176




RPr
CGTGGTTGACTCTGATCTCG
SEQ ID NO: 177





BLMH
NM_000386.2
FPr
GGTTGCTGCCTCCATCAAAG
SEQ ID NO: 178




Probe
ACATCACAGCCAAACCACACAGCCTCT
SEQ ID NO: 179




RPr
CCAGCTTGCTATTGAAGTGTTTTC
SEQ ID NO: 180





BMP2
NM_001200.1
FPr
ATGTGGACGCTCTTTCAATG
SEQ ID NO: 181




Probe
ACCGCAGTCCGTCTAAGAAGCACG
SEQ ID NO: 182




RPr
ACCATGGTCGACCTTTAGGA
SEQ ID NO: 183





BMP4
NM_001202.2
FPr
GGGCTAGCCATTGAGGTG
SEQ ID NO: 184




Probe
CTCACCTCCATCAGACTCGGACCC
SEQ ID NO: 185




RPr
GCTAATCCTGACATGCTGGC
SEQ ID NO: 186





BMP7
NM_001719.1
FPr
TCGTGGAACATGACAAGGAATT
SEQ ID NO: 187




Probe
TTCCACCCACGCTACCACCATCG
SEQ ID NO: 188




RPr
TGGAAAGATCAAACCGGAACTC
SEQ ID NO: 189





BMPR1A
NM_004329.2
FPr
TTGGTTCAGCGAACTATTGC
SEQ ID NO: 190




Probe
CAAACAGATTCAGATGGTCCGGCA
SEQ ID NO: 191




RPr
TCTCCATATCGGCCTTTACC
SEQ ID NO: 192





BRAF
NM_004333.1
FPr
CCTTCCGACCAGCAGATGAA
SEQ ID NO: 193




Probe
CAATTTGGGCAACGAGACCGATCCT
SEQ ID NO: 194




RPr
TTTATATGCACATTGGGAGCTGAT
SEQ ID NO: 195





BRCA1
NM_007295.1
FPr
TCAGGGGGCTAGAAATCTGT
SEQ ID NO: 196




Probe
CTATGGGCCCTTCACCAACATGC
SEQ ID NO: 197




RPr
CCATTCCAGTTGATCTGTGG
SEQ ID NO: 198





BRCA2
NM_000059.1
FPr
AGTTCGTGCTTTGCAAGATG
SEQ ID NO: 199




Probe
CATTCTTCACTGCTTCATAAAGCTCTGCA
SEQ ID NO: 200




RPr
AAGGTAAGCTGGGTCTGCTG
SEQ ID NO: 201





BRK
NM_005975.1
FPr
GTGCAGGAAAGGTTCACAAA
SEQ ID NO: 202




Probe
AGTGTCTGCGTCCAATACACGCGT
SEQ ID NO: 203




RPr
GCACACACGATGGAGTAAGG
SEQ ID NO: 204





BTF3
NM_001207.2
FPr
CAGTGATCCACTTTAACAACCCTAAAG
SEQ ID NO: 205




Probe
TCAGGCATCTCTGGCAGCGAACAC
SEQ ID NO: 206




RPr
AGCATGGCCTGTAATGGTGAA
SEQ ID NO: 207





BTRC
NM_033637.2
FPr
GTTGGGACACAGTTGGTCTG
SEQ ID NO: 208




Probe
CAGTCGGCCCAGGACGGTCTACT
SEQ ID NO: 209




RPr
TGAAGCAGTCAGTTGTGCTG
SEQ ID NO: 210





BUB1
NM_004336.1
FPr
CCGAGGTTAATCCAGCACGTA
SEQ ID NO: 211




Probe
TGCTGGGAGCCTACACTTGGCCC
SEQ ID NO: 212




RPr
AAGACATGGCGCTCTCAGTTC
SEQ ID NO: 213





BUB1B
NM_001211.3
FPr
TCAACAGAAGGCTGAACCACTAGA
SEQ ID NO: 214




Probe
TACAGTCCCAGCACCGACAATTCC
SEQ ID NO: 215




RPr
CAACAGAGTTTGCCGAGACACT
SEQ ID NO: 216





BUB3
NM_004725.1
FPr
CTGAAGCAGATGGTTCATCATT
SEQ ID NO: 217




Probe
CCTCGCTTTGTTTAACAGCCCAGG
SEQ ID NO: 218




RPr
GCTGATTCCCAAGAGTCTAACC
SEQ ID NO: 219





c-abl
NM_005157.2
FPr
CCATCTCGCTGAGATACGAA
SEQ ID NO: 220




Probe
GGGAGGGTGTACCATTACAGGATCAACA
SEQ ID NO: 221




RPr
AGACGTAGAGCTTGCCATCA
SEQ ID NO: 222





c-kit
NM_000222.1
FPr
GAGGCAACTGCTTATGGCTTAATTA
SEQ ID NO: 223




Probe
TTACAGCGACAGTCATGGCCGCAT
SEQ ID NO: 224




RPr
GGCACTCGGCTTGAGCAT
SEQ ID NO: 225





c-myb
NM_005375.1
FPr
AACTCAGACTTGGAAATGCCTTCT
SEQ ID NO: 226


(MYB


official)




Probe
AACTTCCACCCCCCTCATTGGTCACA
SEQ ID NO: 227




RPr
CTGGTCTCTATGAAATGGTGTTGTAAC
SEQ ID NO: 228





c-Src
NM_005417.3
FPr
TGAGGAGTGGTATTTTGGCAAGA
SEQ ID NO: 229




Probe
AACCGCTCTGACTCCCGTCTGGTG
SEQ ID NO: 230




RPr
CTCTCGGGTTCTCTGCATTGA
SEQ ID NO: 231





C20 orf1
NM_012112.2
FPr
TCAGCTGTGAGCTGCGGATA
SEQ ID NO: 232




Probe
CAGGTCCCATTGCCGGGCG
SEQ ID NO: 233




RPr
ACGGTCCTAGGTTTGAGGTTAAGA
SEQ ID NO: 234





C20ORF126
NM_030815.2
FPr
CCAGCACTGCTCGTTACTGT
SEQ ID NO: 235




Probe
TGGGACCTCAGACCACTGAAGGC
SEQ ID NO: 236




RPr
TTGACTTCACGGCAGTTCATA
SEQ ID NO: 237





C8orf4
NM_020130.2
FPr
CTACGAGTCAGCCCATCCAT
SEQ ID NO: 238




Probe
CATGGCTACCACTTCGACACAGCC
SEQ ID NO: 239




RPr
TGCCCACGGCTTTCTTAC
SEQ ID NO: 240





CA9
NM_001216.1
FPr
ATCCTAGCCCTGGTTTTTGG
SEQ ID NO: 241




Probe
TTTGCTGTCACCAGCGTCGC
SEQ ID NO: 242




RPr
CTGCCTTCTCATCTGCACAA
SEQ ID NO: 243





Cad17
NM_004063.2
FPr
GAAGGCCAAGAACCGAGTCA
SEQ ID NO: 244




Probe
TTATATTCCAGTTTAAGGCCAATCCTC
SEQ ID NO: 245




RPr
TCCCCAGTTAGTTCAAAAGTCACA
SEQ ID NO: 246





CALD1
NM_004342.4
FPr
CACTAAGGTTTGAGACAGTTCCAGAA
SEQ ID NO: 247




Probe
AACCCAAGCTCAAGACGCAGGACGAG
SEQ ID NO: 248




RPr
GCGAATTAGCCCTCTACAACTGA
SEQ ID NO: 249





CAPG
NM_001747.1
FPr
GATTGTCACTGATGGGGAGG
SEQ ID NO: 250




Probe
AGGACCTGGATCATCTCAGCAGGC
SEQ ID NO: 251




RPr
CCTTCAGAGCAGGCTTGG
SEQ ID NO: 252





CAPN1
NM_005186.2
FPr
CAAGAAGCTGTACGAGCTCATCA
SEQ ID NO: 253




Probe
CCGCTACTCGGAGCCCGACCTG
SEQ ID NO: 254




RPr
GCAGCAAACGAAATTGTCAAAG
SEQ ID NO: 255





CASP8
NM_033357.1
FPr
CCTCGGGGATACTGTCTGAT
SEQ ID NO: 256




Probe
CAACAATCACAATTTTGCAAAAGCACG
SEQ ID NO: 257




RPr
GAAGTTTGGGCACTTTCTCC
SEQ ID NO: 258





CASP9
NM_001229.2
FPr
TGAATGCCGTGGATTGCA
SEQ ID NO: 259




Probe
CACTAGCCCTGGACCAGCCACTGCT
SEQ ID NO: 260




RPr
ACAGGGATCATGGGACACAAG
SEQ ID NO: 261





CAT
NM_001752.1
FPr
ATCCATTCGATCTCACCAAGGT
SEQ ID NO: 262




Probe
TGGCCTCACAAGGACTACCCTCTCATCC
SEQ ID NO: 263




RPr
TCCGGTTTAAGACCAGTTTACCA
SEQ ID NO: 264





CAV1
NM_001753.3
FPr
GTGGCTCAACATTGTGTTCC
SEQ ID NO: 265




Probe
ATTTCAGCTGATCAGTGGGCCTCC
SEQ ID NO: 266




RPr
CAATGGCCTCCATTTTACAG
SEQ ID NO: 267





CBL
NM_005188.1
FPr
TCATTCACAAACCTGGCAGT
SEQ ID NO: 268




Probe
TTCCGGCTGAGCTGTACTCGTCTG
SEQ ID NO: 269




RPr
CATACCCAATAGCCCACTGA
SEQ ID NO: 270





CCL20
NM_004591.1
FPr
CCATGTGCTGTACCAAGAGTTTG
SEQ ID NO: 271




Probe
CAGCACTGACATCAAAGCAGCCAGGA
SEQ ID NO: 272




RPr
CGCCGCAGAGGTGGAGTA
SEQ ID NO: 273





CCL3
NM_002983.1
FPr
AGCAGACAGTGGTCAGTCCTT
SEQ ID NO: 274




Probe
CTCTGCTGACACTCGAGCCCACAT
SEQ ID NO: 275




RPr
CTGCATGATTCTGAGCAGGT
SEQ ID NO: 276





CCNA2
NM_001237.2
FPr
CCATACCTCAAGTATTTGCCATCAG
SEQ ID NO: 277




Probe
ATTGCTGGAGCTGCCTTTCATTTAGCACT
SEQ ID NO: 278




RPr
AGCTTTGTCCCGTGACTGTGTA
SEQ ID NO: 279





CCNB1
NM_031966.1
FPr
TTCAGGTTGTTGCAGGAGAC
SEQ ID NO: 280




Probe
TGTCTCCATTATTGATCGGTTCATGCA
SEQ ID NO: 281




RPr
CATCTTCTTGGGCACACAAT
SEQ ID NO: 282





CCNB2
NM_004701.2
FPr
AGGCTTCTGCAGGAGACTCTGT
SEQ ID NO: 283




Probe
TCGATCCATAATGCCAACGCACATG
SEQ ID NO: 284




RPr
GGGAAACTGGCTGAACCTGTAA
SEQ ID NO: 285





CCND1
NM_001758.1
FPr
GCATGTTCGTGGCCTCTAAGA
SEQ ID NO: 286




Probe
AAGGAGACCATCCCCCTGACGGC
SEQ ID NO: 287




RPr
CGGTGTAGATGCACAGCTTCTC
SEQ ID NO: 288





CCND3
NM_001760.2
FPr
CCTCTGTGCTACAGATTATACCTTTGC
SEQ ID NO: 289




Probe
TACCCGCCATCCATGATCGCCA
SEQ ID NO: 290




RPr
CACTGCAGCCCCAATGCT
SEQ ID NO: 291





CCNE1
NM_001238.1
FPr
AAAGAAGATGATGACCGGGTTTAC
SEQ ID NO: 292




Probe
CAAACTCAACGTGCAAGCCTCGGA
SEQ ID NO: 293




RPr
GAGCCTCTGGATGGTGCAAT
SEQ ID NO: 294





CCNE2
NM_057749.1
FPr
GGTCACCAAGAAACATCAGTATGAA
SEQ ID NO: 295




Probe
CCCAGATAATACAGGTGGCCAACAATTC
SEQ ID NO: 296





CT




RPr
TTCAATGATAATGCAAGGACTGATC
SEQ ID NO: 297





CCNE2
NM_057749var1
FPr
ATGCTGTGGCTCCTTCCTAACT
SEQ ID NO: 298


variant 1




Probe
TACCAAGCAACCTACATGTCAAGAAAGC
SEQ ID NO: 299





CC




RPr
ACCCAAATTGTGATATACAAAAAGGTT
SEQ ID NO: 300





CCR7
NM_001838.2
FPr
GGATGACATGCACTCAGCTC
SEQ ID NO: 301




Probe
CTCCCATCCCAGTGGAGCCAA
SEQ ID NO: 302




RPr
CCTGACATTTCCCTTGTCCT
SEQ ID NO: 303





CD105
NM_000118.1
FPr
GCAGGTGTCAGCAAGTATGATCAG
SEQ ID NO: 304




Probe
CGACAGGATATTGACCACCGCCTCATT
SEQ ID NO: 305




RPr
TTTTTCCGCTGTGGTGATGA
SEQ ID NO: 306





CD134
NM_003327.1
FPr
GCCCAGTGCGGAGAACAG
SEQ ID NO: 307


(TNFRSF4


official)




Probe
CCAGCTTGATTCTCGTCTCTGCACTTAAGC
SEQ ID NO: 308




RPr
AATCACACGCACCTGGAGAAC
SEQ ID NO: 309





CD18
NM_000211.1
FPr
CGTCAGGACCCACCATGTCT
SEQ ID NO: 310




Probe
CGCGGCCGAGACATGGCTTG
SEQ ID NO: 311




RPr
GGTTAATTGGTGACATCCTCAAGA
SEQ ID NO: 312





CD24
NM_013230.1
FPr
TCCAACTAATGCCACCACCAA
SEQ ID NO: 313




Probe
CTGTTGACTGCAGGGCACCACCA
SEQ ID NO: 314




RPr
GAGAGAGTGAGACCACGAAGAGACT
SEQ ID NO: 315





CD28
NM_006139.1
FPr
TGTGAAAGGGAAACACCTTTG
SEQ ID NO: 316




Probe
CCAAGTCCCCTATTTCCCGGACCT
SEQ ID NO: 317




RPr
AGCACCCAAAAGGGCTTAG
SEQ ID NO: 318





CD31
NM_000442.1
FPr
TGTATTTCAAGACCTCTGTGCACTT
SEQ ID NO: 319




Probe
TTTATGAACCTGCCCTGCTCCCACA
SEQ ID NO: 320




RPr
TTAGCCTGAGGAATTGCTGTGTT
SEQ ID NO: 321





CD34
NM_001773.1
FPr
CCACTGCACACACCTCAGA
SEQ ID NO: 322




Probe
CTGTTCTTGGGGCCCTACACCTTG
SEQ ID NO: 323




RPr
CAGGAGTTTACCTGCCCCT
SEQ ID NO: 324





CD3z
NM_000734.1
FPr
AGATGAAGTGGAAGGCGCTT
SEQ ID NO: 325




Probe
CACCGCGGCCATCCTGCA
SEQ ID NO: 326




RPr
TGCCTCTGTAATCGGCAACTG
SEQ ID NO: 327





CD44E
X55150
FPr
ATCACCGACAGCACAGACA
SEQ ID NO: 328




Probe
CCCTGCTACCAATATGGACTCCAGTCA
SEQ ID NO: 329




RPr
ACCTGTGTTTGGATTTGCAG
SEQ ID NO: 330





CD44s
M59040.1
FPr
GACGAAGACAGTCCCTGGAT
SEQ ID NO: 331




Probe
CACCGACAGCACAGACAGAATCCC
SEQ ID NO: 332




RPr
ACTGGGGTGGAATGTGTCTT
SEQ ID NO: 333





CD44v3
AJ251595v3
FPr
CACACAAAACAGAACCAGGACT
SEQ ID NO: 334




Probe
ACCCAGTGGAACCCAAGCCATTC
SEQ ID NO: 335




RPr
CTGAAGTAGCACTTCCGGATT
SEQ ID NO: 336





CD44v6
AJ251595v6
FPr
CTCATACCAGCCATCCAATG
SEQ ID NO: 337




Probe
CACCAAGCCCAGAGGACAGTTCCT
SEQ ID NO: 338




RPr
TTGGGTTGAAGAAATCAGTCC
SEQ ID NO: 339





CD68
NM_001251.1
FPr
TGGTTCCCAGCCCTGTGT
SEQ ID NO: 340




Probe
CTCCAAGCCCAGATTCAGATTCGAGTCA
SEQ ID NO: 341




RPr
CTCCTCCACCCTGGGTTGT
SEQ ID NO: 342





CD80
NM_005191.2
FPr
TTCAGTTGCTTTGCAGGAAG
SEQ ID NO: 343




Probe
TTCTGTGCCCACCATATTCCTCTAGACA
SEQ ID NO: 344




RPr
TTGATCAAGGTCACCAGAGC
SEQ ID NO: 345





CD82
NM_002231.2
FPr
GTGCAGGCTCAGGTGAAGTG
SEQ ID NO: 346




Probe
TCAGCTTCTACAACTGGACAGACAACGC
SEQ ID NO: 347





TG




RPr
GACCTCAGGGCGATTCATGA
SEQ ID NO: 348





CD8A
NM_171827.1
FPr
AGGGTGAGGTGCTTGAGTCT
SEQ ID NO: 349




Probe
CCAACGGCAAGGGAACAAGTACTTCT
SEQ ID NO: 350




RPr
GGGCACAGTATCCCAGGTA
SEQ ID NO: 351





CD9
NM_001769.1
FPr
GGGCGTGGAACAGTTTATCT
SEQ ID NO: 352




Probe
AGACATCTGCCCCAAGAAGGACGT
SEQ ID NO: 353




RPr
CACGGTGAAGGTTTCGAGT
SEQ ID NO: 354





CDC2
NM_001786.2
FPr
GAGAGCGACGCGGTTGTT
SEQ ID NO: 355




Probe
TAGCTGCCGCTGCGGCCG
SEQ ID NO: 356




RPr
GTATGGTAGATCCCGGCTTATTATTC
SEQ ID NO: 357





CDC20
NM_001255.1
FPr
TGGATTGGAGTTCTGGGAATG
SEQ ID NO: 358




Probe
ACTGGCCGTGGCACTGGACAACA
SEQ ID NO: 359




RPr
GCTTGCACTCCACAGGTACACA
SEQ ID NO: 360





cdc25A
NM_001789.1
FPr
TCTTGCTGGCTACGCCTCTT
SEQ ID NO: 361




Probe
TGTCCCTGTTAGACGTCCTCCGTCCATA
SEQ ID NO: 362




RPr
CTGCATTGTGGCACAGTTCTG
SEQ ID NO: 363





CDC25B
NM_021874.1
FPr
AAACGAGCAGTTTGCCATCAG
SEQ ID NO: 364




Probe
CCTCACCGGCATAGACTGGAAGCG
SEQ ID NO: 365




RPr
GTTGGTGATGTTCCGAAGCA
SEQ ID NO: 366





CDC25C
NM_001790.2
FPr
GGTGAGCAGAAGTGGCCTAT
SEQ ID NO: 367




Probe
CTCCCCGTCGATGCCAGAGAACT
SEQ ID NO: 368




RPr
CTTCAGTCTTGGCCTGTTCA
SEQ ID NO: 369





CDC4
NM_018315.2
FPr
GCAGTCCGCTGTGTTCAA
SEQ ID NO: 370




Probe
TGCTCCACTAACAACCCTCCTGCC
SEQ ID NO: 371




RPr
GGATCCCACACCTTTACCATAA
SEQ ID NO: 372





CDC42
NM_001791.2
FPr
TCCAGAGACTGCTGAAAA
SEQ ID NO: 373




Probe
CCCGTGACCTGAAGGCTGTCAAG
SEQ ID NO: 374




RPr
TGTGTAAGTGCAGAACAC
SEQ ID NO: 375





CDC42BPA
NM_003607.2
FPr
GAGCTGAAAGACGCACACTG
SEQ ID NO: 376




Probe
AATTCCTGCATGGCCAGTTTCCTC
SEQ ID NO: 377




RPr
GCCGCTCATTGATCTCCA
SEQ ID NO: 378





CDC6
NM_001254.2
FPr
GCAACACTCCCCATTTACCTC
SEQ ID NO: 379




Probe
TTGTTCTCCACCAAAGCAAGGCAA
SEQ ID NO: 380




RPr
TGAGGGGGACCATTCTCTTT
SEQ ID NO: 381





CDCA7 v2
NM_145810.1
FPr
AAGACCGTGGATGGCTACAT
SEQ ID NO: 382




Probe
ATGAAGATGACCTGCCCAGAAGCC
SEQ ID NO: 383




RPr
AGGGTCACGGATGATCTGG
SEQ ID NO: 384





CDH1
NM_004360.2
FPr
TGAGTGTCCCCCGGTATCTTC
SEQ ID NO: 385




Probe
TGCCAATCCCGATGAAATTGGAAATTT
SEQ ID NO: 386




RPr
CAGCCGCTTTCAGATTTTCAT
SEQ ID NO: 387





CDH11
NM_001797.2
FPr
GTCGGCAGAAGCAGGACT
SEQ ID NO: 388




Probe
CCTTCTGCCCATAGTGATCAGCGA
SEQ ID NO: 389




RPr
CTACTCATGGGCGGGATG
SEQ ID NO: 390





CDH3
NM_001793.3
FPr
ACCCATGTACCGTCCTCG
SEQ ID NO: 391




Probe
CCAACCCAGATGAAATCGGCAACT
SEQ ID NO: 392




RPr
CCGCCTTCAGGTTCTCAAT
SEQ ID NO: 393





CDK2
NM_001798.2
FPr
AATGCTGCACTACGACCCTA
SEQ ID NO: 394




Probe
CCTTGGCCGAAATCCGCTTGT
SEQ ID NO: 395




RPr
TTGGTCACATCCTGGAAGAA
SEQ ID NO: 396





CDX1
NM_001804.1
FPr
AGCAACACCAGCCTCCTG
SEQ ID NO: 397




Probe
CACCTCCTCTCCAATGCCTGTGAA
SEQ ID NO: 398




RPr
GGGCTATGGCAGAAACTCCT
SEQ ID NO: 399





Cdx2
NM_001265.2
FPr
GGGCAGGCAAGGTTTACA
SEQ ID NO: 400




Probe
ATCTTAGCTGCCTTTGGCTTCCGC
SEQ ID NO: 401




RPr
GTCTTTGGTCAGTCCAGCTTTC
SEQ ID NO: 402





CEACAM1
NM_001712.2
FPr
ACTTGCCTGTTCAGAGCACTCA
SEQ ID NO: 403




Probe
TCCTTCCCACCCCCAGTCCTGTC
SEQ ID NO: 404




RPr
TGGCAAATCCGAATTAGAGTGA
SEQ ID NO: 405





CEACAM6
NM_002483.2
FPr
CACAGCCTCACTTCTAACCTTCTG
SEQ ID NO: 406




Probe
ACCCACCCACCACTGCCAAGCTC
SEQ ID NO: 407




RPr
TTGAATGGCGTGGATTCAATAG
SEQ ID NO: 408





CEBPB
NM_005194.2
FPr
GCAACCCACGTGTAACTGTC
SEQ ID NO: 409




Probe
CCGGGCCCTGAGTAATCGCTTAA
SEQ ID NO: 410




RPr
ACAAGCCCGTAGGAACATCT
SEQ ID NO: 411





CEGP1
NM_020974.1
FPr
TGACAATCAGCACACCTGCAT
SEQ ID NO: 412




Probe
CAGGCCCTCTTCCGAGCGGT
SEQ ID NO: 413




RPr
TGTGACTACAGCCGTGATCCTTA
SEQ ID NO: 414





CENPA
NM_001809.2
FPr
TAAATTCACTCGTGGTGTGGA
SEQ ID NO: 415




Probe
CTTCAATTGGCAAGCCCAGGC
SEQ ID NO: 416




RPr
GCCTCTTGTAGGGCCAATAG
SEQ ID NO: 417





CENPE
NM_001813.1
FPr
GGATGCTGGTGACCTCTTCT
SEQ ID NO: 418




Probe
TCCCTCACGTTGCAACAGGAATTAA
SEQ ID NO: 419




RPr
GCCAAGGCACCAAGTAACTC
SEQ ID NO: 420





CENPF
NM_016343.2
FPr
CTCCCGTCAACAGCGTTC
SEQ ID NO: 421




Probe
ACACTGGACCAGGAGTGCATCCAG
SEQ ID NO: 422




RPr
GGGTGAGTCTGGCCTTCA
SEQ ID NO: 423





CES2
NM_003869.4
FPr
ACTTTGCGAGAAATGGGAAC
SEQ ID NO: 424




Probe
AGTGTGGCAGACCCTCGCCATT
SEQ ID NO: 425




RPr
CAGGTATTGCTCCTCCTGGT
SEQ ID NO: 426





CGA
NM_001275.2
FPr
CTGAAGGAGCTCCAAGACCT
SEQ ID NO: 427


(CHGA


official)




Probe
TGCTGATGTGCCCTCTCCTTGG
SEQ ID NO: 428




RPr
CAAAACCGCTGTGTTTCTTC
SEQ ID NO: 429





CGB
NM_000737.2
FPr
CCACCATAGGCAGAGGCA
SEQ ID NO: 430




Probe
ACACCCTACTCCCTGTGCCTCCAG
SEQ ID NO: 431




RPr
AGTCGTCGAGTGCTAGGGAC
SEQ ID NO: 432





CHAF1B
NM_005441.1
FPr
GAGGCCAGTGGTGGAAACAG
SEQ ID NO: 433




Probe
AGCTGATGAGTCTGCCCTACCGCCTG
SEQ ID NO: 434




RPr
TCCGAGGCCACAGCAAAC
SEQ ID NO: 435





CHD2
NM_001271.1
FPr
CTCTGTGCGAGGCTGTCA
SEQ ID NO: 436




Probe
ACCCATCTCGGGATCCCTGATACC
SEQ ID NO: 437




RPr
GGTAAGGACTGTGGGCTGG
SEQ ID NO: 438





CHFR
NM_018223.1
FPr
AAGGAAGTGGTCCCTCTGTG
SEQ ID NO: 439




Probe
TGAAGTCTCCAGCTTTGCCTCAGC
SEQ ID NO: 440




RPr
GACGCAGTCTTTCTGTCTGG
SEQ ID NO: 441





Chk1
NM_001274.1
FPr
GATAAATTGGTACAAGGGATCAGCTT
SEQ ID NO: 442




Probe
CCAGCCCACATGTCCTGATCATATGC
SEQ ID NO: 443




RPr
GGGTGCCAAGTAACTGACTATTCA
SEQ ID NO: 444





Chk2
NM_007194.1
FPr
ATGTGGAACCCCCACCTACTT
SEQ ID NO: 445




Probe
AGTCCCAACAGAAACAAGAACTTCAGGCG
SEQ ID NO: 446




RPr
CAGTCCACAGCACGGTTATACC
SEQ ID NO: 447





CIAP1
NM_001166.2
FPr
TGCCTGTGGTGGGAAGCT
SEQ ID NO: 448




Probe
TGACATAGCATCATCCTTTGGTTCCCAGTT
SEQ ID NO: 449




RPr
GGAAAATGCCTCCGGTGTT
SEQ ID NO: 450





cIAP2
NM_001165.2
FPr
GGATATTTCCGTGGCTCTTATTCA
SEQ ID NO: 451




Probe
TCTCCATCAAATCCTGTAAACTCCAGAG
SEQ ID NO: 452





CA




RPr
CTTCTCATCAAGGCAGAAAAATCTT
SEQ ID NO: 453





CKS1B
NM_001826.1
FPr
GGTCCCTAAAACCCATCTGA
SEQ ID NO: 454




Probe
TGAACGCCAAGATTCCTCCATTCA
SEQ ID NO: 455




RPr
TAATGGACCCATCCCTGACT
SEQ ID NO: 456





CKS2
NM_001827.1
FPr
GGCTGGACGTGGTTTTGTCT
SEQ ID NO: 457




Probe
CTGCGCCCGCTCTTCGCG
SEQ ID NO: 458




RPr
CGCTGCAGAAAATGAAACGA
SEQ ID NO: 459





Claudin 4
NM_001305.2
FPr
GGCTGCTTTGCTGCAACTG
SEQ ID NO: 460




Probe
CGCACAGACAAGCCTTACTCCGCC
SEQ ID NO: 461




RPr
CAGAGCGGGCAGCAGAATA
SEQ ID NO: 462





CLDN1
NM_021101.3
FPr
TCTGGGAGGTGCCCTACTT
SEQ ID NO: 463




Probe
TGTTCCTGTCCCCGAAAAACAACC
SEQ ID NO: 464




RPr
TGGATAGGGCCTTGGTGTT
SEQ ID NO: 465





CLDN7
NM_001307.3
FPr
GGTCTGCCCTAGTCATCCTG
SEQ ID NO: 466




Probe
TGCACTGCTCTCCTGTTCCTGTCC
SEQ ID NO: 467




RPr
GTACCCAGCCTTGCTCTCAT
SEQ ID NO: 468





CLIC1
NM_001288.3
FPr
CGGTACTTGAGCAATGCCTA
SEQ ID NO: 469




Probe
CGGGAAGAATTCGCTTCCACCTG
SEQ ID NO: 470




RPr
TCGATCTCCTCATCATCTGG
SEQ ID NO: 471





CLTC
NM_004859.1
FPr
ACCGTATGGACAGCCACAG
SEQ ID NO: 472




Probe
TCTCACATGCTGTACCCAAAGCCA
SEQ ID NO: 473




RPr
TGACTACAGGATCAGCGCTTC
SEQ ID NO: 474





CLU
NM_001831.1
FPr
CCCCAGGATACCTACCACTACCT
SEQ ID NO: 475




Probe
CCCTTCAGCCTGCCCCACCG
SEQ ID NO: 476




RPr
TGCGGGACTTGGGAAAGA
SEQ ID NO: 477





cMet
NM_000245.1
FPr
GACATTTCCAGTCCTGCAGTCA
SEQ ID NO: 478




Probe
TGCCTCTCTGCCCCACCCTTTGT
SEQ ID NO: 479




RPr
CTCCGATCGCACACATTTGT
SEQ ID NO: 480





cMYC
NM_002467.1
FPr
TCCCTCCACTCGGAAGGACTA
SEQ ID NO: 481




Probe
TCTGACACTGTCCAACTTGACCCTCTT
SEQ ID NO: 482




RPr
CGGTTGTTGCTGATCTGTCTCA
SEQ ID NO: 483





CNN
NM_001299.2
FPr
TCCACCCTCCTGGCTTTG
SEQ ID NO: 484




Probe
TCCTTTCGTCTTCGCCATGCTGG
SEQ ID NO: 485




RPr
TCACTCCCACGTTCACCTTGT
SEQ ID NO: 486





COL1A1
NM_000088.2
FPr
GTGGCCATCCAGCTGACC
SEQ ID NO: 487




Probe
TCCTGCGCCTGATGTCCACCG
SEQ ID NO: 488




RPr
CAGTGGTAGGTGATGTTCTGGGA
SEQ ID NO: 489





COL1A2
NM_000089.2
FPr
CAGCCAAGAACTGGTATAGGAGCT
SEQ ID NO: 490




Probe
TCTCCTAGCCAGACGTGTTTCTTGTCCTTG
SEQ ID NO: 491




RPr
AAACTGGCTGCCAGCATTG
SEQ ID NO: 492





COPS3
NM_003653.2
FPr
ATGCCCAGTGTTCCTGACTT
SEQ ID NO: 493




Probe
CGAAACGCTATTCTCACAGGTTCAGC
SEQ ID NO: 494




RPr
CTCCCCATTACAAGTGCTGA
SEQ ID NO: 495





COX2
NM_000963.1
FPr
TCTGCAGAGTTGGAAGCACTCTA
SEQ ID NO: 496




Probe
CAGGATACAGCTCCACAGCATCGATGTC
SEQ ID NO: 497




RPr
GCCGAGGCTTTTCTACCAGAA
SEQ ID NO: 498





COX3
MITO_COX3
FPr
TCGAGTCTCCCTTCACCATT
SEQ ID NO: 499




Probe
CGACGGCATCTACGGCTCAACAT
SEQ ID NO: 500




RPr
GACGTGAAGTCCGTGGAAG
SEQ ID NO: 501





CP
NM_000096.1
FPr
CGTGAGTACACAGATGCCTCC
SEQ ID NO: 502




Probe
TCTTCAGGGCCTCTCTCCTTTCGA
SEQ ID NO: 503




RPr
CCAGGATGCCAAGATGCT
SEQ ID NO: 504





CRBP
NM_002899.2
FPr
TGGTCTGCAAGCAAGTATTCAAG
SEQ ID NO: 505




Probe
TCTGCTTGGGCCTCACTGCACCT
SEQ ID NO: 506




RPr
GCTGATTGGTTGGGACAAGGT
SEQ ID NO: 507





CREBBP
NM_004380.1
FPr
TGGGAAGCAGCTGTGTACCAT
SEQ ID NO: 508




Probe
CCTCGCGATGCTGCCTACTACAGCTATC
SEQ ID NO: 509




RPr
GAAACACTTCTCACAGAAATGATACCTA
SEQ ID NO: 510





TT





CRIP2
NM_001312.1
FPr
GTGCTACGCCACCCTGTT
SEQ ID NO: 511




Probe
CCGATGTTCACGCCTTTGGGTC
SEQ ID NO: 512




RPr
CAGGGGCTTCTCGTAGATGT
SEQ ID NO: 513





cripto
NM_003212.1
FPr
GGGTCTGTGCCCCATGAC
SEQ ID NO: 514


(TDGF1


official)




Probe
CCTGGCTGCCCAAGAAGTGTTCCCT
SEQ ID NO: 515




RPr
TGACCGTGCCAGCATTTACA
SEQ ID NO: 516





CRK(a)
NM_016823.2
FPr
CTCCCTAACCTCCAGAATGG
SEQ ID NO: 517




Probe
ACTCGCTTCTGGATAACCCTGGCA
SEQ ID NO: 518




RPr
TGTCTTGTCGTAGGCATTGG
SEQ ID NO: 519





CRMP1
NM_001313.1
FPr
AAGGTTTTTGGATTGCAAGG
SEQ ID NO: 520




Probe
ACCGTCATACATGCCCCTGGAAAC
SEQ ID NO: 521




RPr
GGGTGTAGCTGGTACCTCGT
SEQ ID NO: 522





CRYAB
NM_001885.1
FPr
GATGTGATTGAGGTGCATGG
SEQ ID NO: 523




Probe
TGTTCATCCTGGCGCTCTTCATGT
SEQ ID NO: 524




RPr
GAACTCCCTGGAGATGAAACC
SEQ ID NO: 525





CSEL1
NM_001316.2
FPr
TTACGCAGCTCATGCTCTTG
SEQ ID NO: 526




Probe
ACGGCTCTTTACTATGCGAGGGCC
SEQ ID NO: 527




RPr
GCAGCTGTAAAGAGAGTGGCAT
SEQ ID NO: 528





CSF1
NM_000757.3
FPr
TGCAGCGGCTGATTGACA
SEQ ID NO: 529




Probe
TCAGATGGAGACCTCGTGCCAAATTACA
SEQ ID NO: 530




RPr
CAACTGTTCCTGGTCTACAAACTCA
SEQ ID NO: 531





CSK (SRC)
NM_004383.1
FPr
CCTGAACATGAAGGAGCTGA
SEQ ID NO: 532




Probe
TCCCGATGGTCTGCAGCAGCT
SEQ ID NO: 533




RPr
CATCACGTCTCCGAACTCC
SEQ ID NO: 534





CTAG1B
NM_001327.1
FPr
GCTCTCCATCAGCTCCTGTC
SEQ ID NO: 535




Probe
CCACATCAACAGGGAAAGCTGCTG
SEQ ID NO: 536




RPr
AACACGGGCAGAAAGCACT
SEQ ID NO: 537





CTGF
NM_001901.1
FPr
GAGTTCAAGTGCCCTGACG
SEQ ID NO: 538




Probe
AACATCATGTTCTTCTTCATGACCTCGC
SEQ ID NO: 539




RPr
AGTTGTAATGGCAGGCACAG
SEQ ID NO: 540





CTHRC1
NM_138455.2
FPr
GCTCACTTCGGCTAAAATGC
SEQ ID NO: 541




Probe
ACCAACGCTGACAGCATGCATTTC
SEQ ID NO: 542




RPr
TCAGCTCCATTGAATGTGAAA
SEQ ID NO: 543





CTLA4
NM_005214.2
FPr
CACTGAGGTCCGGGTGACA
SEQ ID NO: 544




Probe
CACCTGGCTGTCAGCCTGCCG
SEQ ID NO: 545




RPr
GTAGGTTGCCGCACAGACTTC
SEQ ID NO: 546





CTNNBIP1
NM_020248.2
FPr
GTTTTCCAGGTCGGAGACG
SEQ ID NO: 547




Probe
CTTTGCAGCTACTGCCTCCGGTCT
SEQ ID NO: 548




RPr
AGCATCCAGGGTGTTCCA
SEQ ID NO: 549





CTSB
NM_001908.1
FPr
GGCCGAGATCTACAAAAACG
SEQ ID NO: 550




Probe
CCCCGTGGAGGGAGCTTTCTC
SEQ ID NO: 551




RPr
GCAGGAAGTCCGAATACACA
SEQ ID NO: 552





CTSD
NM_001909.1
FPr
GTACATGATCCCCTGTGAGAAGGT
SEQ ID NO: 553




Probe
ACCCTGCCCGCGATCACACTGA
SEQ ID NO: 554




RPr
GGGACAGCTTGTAGCCTTTGC
SEQ ID NO: 555





CTSH
NM_004390.1
FPr
GCAAGTTCCAACCTGGAAAG
SEQ ID NO: 556




Probe
TGGCTACATCCTTGACAAAGCCGA
SEQ ID NO: 557




RPr
CATCGCTTCCTCGTCATAGA
SEQ ID NO: 558





CTSL
NM_001912.1
FPr
GGGAGGCTTATCTCACTGAGTGA
SEQ ID NO: 559




Probe
TTGAGGCCCAGAGCAGTCTACCAGATTCT
SEQ ID NO: 560




RPr
CCATTGCAGCCTTCATTGC
SEQ ID NO: 561





CTSL2
NM_001333.2
FPr
TGTCTCACTGAGCGAGCAGAA
SEQ ID NO: 562




Probe
CTTGAGGACGCGAACAGTCCACCA
SEQ ID NO: 563




RPr
ACCATTGCAGCCCTGATTG
SEQ ID NO: 564





CUL1
NM_003592.2
FPr
ATGCCCTGGTAATGTCTGCAT
SEQ ID NO: 565




Probe
CAGCCACAAAGCCAGCGTCATTGT
SEQ ID NO: 566




RPr
GCGACCACAAGCCTTATCAAG
SEQ ID NO: 567





CUL4A
NM_003589.1
FPr
AAGCATCTTCCTGTTCTTGGA
SEQ ID NO: 568




Probe
TATGTGCTGCAGAACTCCACGCTG
SEQ ID NO: 569




RPr
AATCCCATATCCCAGATGGA
SEQ ID NO: 570





CXCL12
NM_000609.3
FPr
GAGCTACAGATGCCCATGC
SEQ ID NO: 571




Probe
TTCTTCGAAAGCCATGTTGCCAGA
SEQ ID NO: 572




RPr
TTTGAGATGCTTGACGTTGG
SEQ ID NO: 573





CXCR4
NM_003467.1
FPr
TGACCGCTTCTACCCCAATG
SEQ ID NO: 574




Probe
CTGAAACTGGAACACAACCACCCACAAG
SEQ ID NO: 575




RPr
AGGATAAGGCCAACCATGATGT
SEQ ID NO: 576





CYBA
NM_000101.1
FPr
GGTGCCTACTCCATTGTGG
SEQ ID NO: 577




Probe
TACTCCAGCAGGCACACAAACACG
SEQ ID NO: 578




RPr
GTGGAGCCCTTCTTCCTCTT
SEQ ID NO: 579





CYP1B1
NM_000104.2
FPr
CCAGCTTTGTGCCTGTCACTAT
SEQ ID NO: 580




Probe
CTCATGCCACCACTGCCAACACCTC
SEQ ID NO: 581




RPr
GGGAATGTGGTAGCCCAAGA
SEQ ID NO: 582





CYP2C8
NM_000770.2
FPr
CCGTGTTCAAGAGGAAGCTC
SEQ ID NO: 583




Probe
TTTTCTCAACTCCTCCACAAGGCA
SEQ ID NO: 584




RPr
AGTGGGATCACAGGGTGAAG
SEQ ID NO: 585





CYP3A4
NM_017460.3
FPr
AGAACAAGGACAACATAGATCCTTACAT
SEQ ID NO: 586





AT




Probe
CACACCCTTTGGAAGTGGACCCAGAA
SEQ ID NO: 587




RPr
GCAAACCTCATGCCAATGC
SEQ ID NO: 588





CYR61
NM_001554.3
FPr
TGCTCATTCTTGAGGAGCAT
SEQ ID NO: 589




Probe
CAGCACCCTTGGCAGTTTCGAAAT
SEQ ID NO: 590




RPr
GTGGCTGCATTAGTGTCCAT
SEQ ID NO: 591





DAPK1
NM_004938.1
FPr
CGCTGACATCATGAATGTTCCT
SEQ ID NO: 592




Probe
TCATATCCAAACTCGCCTCCAGCCG
SEQ ID NO: 593




RPr
TCTCTTTCAGCAACGATGTGTCTT
SEQ ID NO: 594





DCC
NM_005215.1
FPr
AAATGTCCTCCTCGACTGCT
SEQ ID NO: 595




Probe
ATCACTGGAACTCCTCGGTCGGAC
SEQ ID NO: 596




RPr
TGAATGCCATCTTTCTTCCA
SEQ ID NO: 597





DCC_exons
X76132_18-23
FPr
GGTCACCGTTGGTGTCATCA
SEQ ID NO: 598


18-23




Probe
CAGCCACGATGACCACTACCAGCACT
SEQ ID NO: 599




RPr
GAGCGTCGGGTGCAAATC
SEQ ID NO: 600





DCC_exons
X76132_6-7
FPr
ATGGAGATGTGGTCATTCCTAGTG
SEQ ID NO: 601


6-7




Probe
TGCTTCCTCCCACTATCTGAAAATAA
SEQ ID NO: 602




RPr
CACCACCCCAAGTATCCGTAAG
SEQ ID NO: 603





DCK
NM_000788.1
FPr
GCCGCCACAAGACTAAGGAAT
SEQ ID NO: 604




Probe
AGCTGCCCGTCTTTCTCAGCCAGC
SEQ ID NO: 605




RPr
CGATGTTCCCTTCGATGGAG
SEQ ID NO: 606





DDB1
NM_001923.2
FPr
TGCGGATCATCCGGAATG
SEQ ID NO: 607




Probe
AATTGGAATCCACGAGCATGCCAGC
SEQ ID NO: 608




RPr
TCCTTTGATGCCTGGTAAGTCA
SEQ ID NO: 609





DET1
NM_017996.2
FPr
CTTGTGGAGATCACCCAATCAG
SEQ ID NO: 610




Probe
CTATGCCCGGGACTCGGGCCT
SEQ ID NO: 611




RPr
CCCGCCTGGATCTCAAACT
SEQ ID NO: 612





DHFR
NM_000791.2
FPr
TTGCTATAACTAAGTGCTTCTCCAAGA
SEQ ID NO: 613




Probe
CCCAACTGAGTCCCCAGCACCT
SEQ ID NO: 614




RPr
GTGGAATGGCAGCTCACTGTAG
SEQ ID NO: 615





DHPS
NM_013407.1
FPr
GGGAGAACGGGATCAATAGGAT
SEQ ID NO: 616




Probe
CTCATTGGGCACCAGCAGGTTTCC
SEQ ID NO: 617




RPr
GCATCAGCCAGTCCTCAAACT
SEQ ID NO: 618





DIABLO
NM_019887.1
FPr
CACAATGGCGGCTCTGAAG
SEQ ID NO: 619




Probe
AAGTTACGCTGCGCGACAGCCAA
SEQ ID NO: 620




RPr
ACACAAACACTGTCTGTACCTGAAGA
SEQ ID NO: 621





DIAPH1
NM_005219.2
FPr
CAAGCAGTCAAGGAGAACCA
SEQ ID NO: 622




Probe
TTCTTCTGTCTCCCGCCGCTTC
SEQ ID NO: 623




RPr
AGTTTTGCTCGCCTCATCTT
SEQ ID NO: 624





DICER1
NM_177438.1
FPr
TCCAATTCCAGCATCACTGT
SEQ ID NO: 625




Probe
AGAAAAGCTGTTTGTCTCCCCAGCA
SEQ ID NO: 626




RPr
GGCAGTGAAGGCGATAAAGT
SEQ ID NO: 627





DKK1
NM_012242.1
FPr
TGACAACTACCAGCCGTACC
SEQ ID NO: 628




Probe
AGTGCCGCACTCCTCGTCCTCT
SEQ ID NO: 629




RPr
GGGACTAGCGCAGTACTCATC
SEQ ID NO: 630





DLC1
NM_006094.3
FPr
GATTCAGACGAGGATGAGCC
SEQ ID NO: 631




Probe
AAAGTCCATTTGCCACTGATGGCA
SEQ ID NO: 632




RPr
CACCTCTTGCTGTCCCTTTG
SEQ ID NO: 633





DPYD
NM_000110.2
FPr
AGGACGCAAGGAGGGTTTG
SEQ ID NO: 634




Probe
CAGTGCCTACAGTCTCGAGTCTGCCAGTG
SEQ ID NO: 635




RPr
GATGTCCGCCGAGTCCTTACT
SEQ ID NO: 636





DR4
NM_003844.1
FPr
TGCACAGAGGGTGTGGGTTAC
SEQ ID NO: 637




Probe
CAATGCTTCCAACAATTTGTTTGCTTGCC
SEQ ID NO: 638




RPr
TCTTCATCTGATTTACAAGCTGTACATG
SEQ ID NO: 639





DR5
NM_003842.2
FPr
CTCTGAGACAGTGCTTCGATGACT
SEQ ID NO: 640




Probe
CAGACTTGGTGCCCTTTGACTCC
SEQ ID NO: 641




RPr
CCATGAGGCCCAACTTCCT
SEQ ID NO: 642





DRG1
NM_004147.3
FPr
CCTGGATCTCCCAGGTATCA
SEQ ID NO: 643




Probe
ACCTTTCCCATCCTTGGCACCTTC
SEQ ID NO: 644




RPr
TGCAATGACTTGACGACCTC
SEQ ID NO: 645





DSP
NM_004415.1
FPr
TGGCACTACTGCATGATTGACA
SEQ ID NO: 646




Probe
CAGGGCCATGACAATCGCCAA
SEQ ID NO: 647




RPr
CCTGCCGCATTGTTTTCAG
SEQ ID NO: 648





DTYMK
NM_012145.1
FPr
AAATCGCTGGGAACAAGTG
SEQ ID NO: 649




Probe
CGCCCTGGCTCAACTTTTCCTTAA
SEQ ID NO: 650




RPr
AATGCGTATCTGTCCACGAC
SEQ ID NO: 651





DUSP1
NM_004417.2
FPr
AGACATCAGCTCCTGGTTCA
SEQ ID NO: 652




Probe
CGAGGCCATTGACTTCATAGACTCCA
SEQ ID NO: 653




RPr
GACAAACACCCTTCCTCCAG
SEQ ID NO: 654





DUSP2
NM_004418.2
FPr
TATCCCTGTGGAGGACAACC
SEQ ID NO: 655




Probe
CCTCCTGGAACCAGGCACTGATCT
SEQ ID NO: 656




RPr
CACCCAGTCAATGAAGCCTA
SEQ ID NO: 657





DUT
NM_001948.2
FPr
ACACATGGAGTGCTTCTGGA
SEQ ID NO: 658




Probe
ATCAGCCCACTTGACCACCCAGTT
SEQ ID NO: 659




RPr
CTCTTGCCTGTGCTTCCAC
SEQ ID NO: 660





DYRK1B
NM_004714.1
FPr
AGCATGACACGGAGATGAAG
SEQ ID NO: 661




Probe
CACCTGAAGCGGCACTTCATGTTC
SEQ ID NO: 662




RPr
AATACCAGGCACAGGTGGTT
SEQ ID NO: 663





E2F1
NM_005225.1
FPr
ACTCCCTCTACCCTTGAGCA
SEQ ID NO: 664




Probe
CAGAAGAACAGCTCAGGGACCCCT
SEQ ID NO: 665




RPr
CAGGCCTCAGTTCCTTCAGT
SEQ ID NO: 666





EDN1
NM_001955.1
FPr
TGCCACCTGGACATCATTTG
SEQ ID NO: 667


endothelin




Probe
CACTCCCGAGCACGTTGTTCCGT
SEQ ID NO: 668




RPr
TGGACCTAGGGCTTCCAAGTC
SEQ ID NO: 669





EFNA1
NM_004428.2
FPr
TACATCTCCAAACCCATCCA
SEQ ID NO: 670




Probe
CAACCTCAAGCAGCGGTCTTCATG
SEQ ID NO: 671




RPr
TTGCCACTGACAGTCACCTT
SEQ ID NO: 672





EFNA3
NM_004952.3
FPr
ACTACATCTCCACGCCCACT
SEQ ID NO: 673




Probe
CCTCAGACACTTCCAGTGCAGGTTG
SEQ ID NO: 674




RPr
CAGCAGACGAACACCTTCAT
SEQ ID NO: 675





EFNB1
NM_004429.3
FPr
GGAGCCCGTATCCTGGAG
SEQ ID NO: 676




Probe
CCCTCAACCCCAAGTTCCTGAGTG
SEQ ID NO: 677




RPr
GGATAGATCACCAAGCCCTTC
SEQ ID NO: 678





EFNB2
NM_004093.2
FPr
TGACATTATCATCCCGCTAAGGA
SEQ ID NO: 679




Probe
CGGACAGCGTCTTCTGCCCTCACT
SEQ ID NO: 680




RPr
GTAGTCCCCGCTGACCTTCTC
SEQ ID NO: 681





EFP
NM_005082.2
FPr
TTGAACAGAGCCTGACCAAG
SEQ ID NO: 682




Probe
TGATGCTTTCTCCAGAAACTCGAACTCA
SEQ ID NO: 683




RPr
TGTTGAGATTCCTCGCAGTT
SEQ ID NO: 684





EGFR
NM_005228.1
FPr
TGTCGATGGACTTCCAGAAC
SEQ ID NO: 685




Probe
CACCTGGGCAGCTGCCAA
SEQ ID NO: 686




RPr
ATTGGGACAGCTTGGATCA
SEQ ID NO: 687





EGLN1
NM_022051.1
FPr
TCAATGGCCGGACGAAAG
SEQ ID NO: 688




Probe
CATTGCCCGGATAACAAGCAACCATG
SEQ ID NO: 689




RPr
TTTGGATTATCAACATGACGTACATAAC
SEQ ID NO: 690





EGLN3
NM_022073.2
FPr
GCTGGTCCTCTACTGCGG
SEQ ID NO: 691




Probe
CCGGCTGGGCAAATACTACGTCAA
SEQ ID NO: 692




RPr
CCACCATTGCCTTAGACCTC
SEQ ID NO: 693





EGR1
NM_001964.2
FPr
GTCCCCGCTGCAGATCTCT
SEQ ID NO: 694




Probe
CGGATCCTTTCCTCACTCGCCCA
SEQ ID NO: 695




RPr
CTCCAGCTTAGGGTAGTTGTCCAT
SEQ ID NO: 696





EGR3
NM_004430.2
FPr
CCATGTGGATGAATGAGGTG
SEQ ID NO: 697




Probe
ACCCAGTCTCACCTTCTCCCCACC
SEQ ID NO: 698




RPr
TGCCTGAGAAGAGGTGAGGT
SEQ ID NO: 699





EI24
NM_004879.2
FPr
AAAGTGGTGAATGCCATTTG
SEQ ID NO: 700




Probe
CCTCAAATGCCAGGTCAGCTATATCCTG
SEQ ID NO: 701




RPr
GTGAGGCTTCCTCCCTGATA
SEQ ID NO: 702





EIF4E
NM_001968.1
FPr
GATCTAAGATGGCGACTGTCGAA
SEQ ID NO: 703




Probe
ACCACCCCTACTCCTAATCCCCCGACT
SEQ ID NO: 704




RPr
TTAGATTCCGTTTTCTCCTCTTCTG
SEQ ID NO: 705





EIF4EL3
NM_004846.1
FPr
AAGCCGCGGTTGAATGTG
SEQ ID NO: 706




Probe
TGACCCTCTCCCTCTCTGGATGGCA
SEQ ID NO: 707




RPr
TGACGCCAGCTTCAATGATG
SEQ ID NO: 708





ELAVL1
NM_001419.2
FPr
GACAGGAGGCCTCTATCCTG
SEQ ID NO: 709




Probe
CACCCCACCCTCCACCTCAATC
SEQ ID NO: 710




RPr
GTGAGGTAGGTCTGGGGAAG
SEQ ID NO: 711





EMP1
NM_001423.1
FPr
GCTAGTACTTTGATGCTCCCTTGAT
SEQ ID NO: 712




Probe
CCAGAGAGCCTCCCTGCAGCCA
SEQ ID NO: 713




RPr
GAACAGCTGGAGGCCAAGTC
SEQ ID NO: 714





EMR3
NM_032571.2
FPr
TGGCCTACCTCTTCACCATC
SEQ ID NO: 715




Probe
TCAACAGCCTCCAAGGCTTCTTCA
SEQ ID NO: 716




RPr
TGAGGAGGCAGTAGACCAAGA
SEQ ID NO: 717





EMS1
NM_005231.2
FPr
GGCAGTGTCACTGAGTCCTTGA
SEQ ID NO: 718




Probe
ATCCTCCCCTGCCCCGCG
SEQ ID NO: 719




RPr
TGCACTGTGCGTCCCAAT
SEQ ID NO: 720





ENO1
NM_001428.2
FPr
CAAGGCCGTGAACGAGAAGT
SEQ ID NO: 721




Probe
CTGCAACTGCCTCCTGCTCAAAGTCA
SEQ ID NO: 722




RPr
CGGTCACGGAGCCAATCT
SEQ ID NO: 723





EP300
NM_001429.1
FPr
AGCCCCAGCAACTACAGTCT
SEQ ID NO: 724




Probe
CACTGACATCATGGCTGGCCTTG
SEQ ID NO: 725




RPr
TGTTCAAAGGTTGACCATGC
SEQ ID NO: 726





EPAS1
NM_001430.3
FPr
AAGCCTTGGAGGGTTTCATTG
SEQ ID NO: 727




Probe
TGTCGCCATCTTGGGTCACCACG
SEQ ID NO: 728




RPr
TGCTGATGTTTTCTGACAGAAAGAT
SEQ ID NO: 729





EpCAM
NM_002354.1
FPr
GGGCCCTCCAGAACAATGAT
SEQ ID NO: 730




Probe
CCGCTCTCATCGCAGTCAGGATCAT
SEQ ID NO: 731




RPr
TGCACTGCTTGGCCTTAAAGA
SEQ ID NO: 732





EPHA2
NM_004431.2
FPr
CGCCTGTTCACCAAGATTGAC
SEQ ID NO: 733




Probe
TGCGCCCGATGAGATCACCG
SEQ ID NO: 734




RPr
GTGGCGTGCCTCGAAGTC
SEQ ID NO: 735





EPHB2
NM_004442.4
FPr
CAACCAGGCAGCTCCATC
SEQ ID NO: 736




Probe
CACCTGATGCATGATGGACACTGC
SEQ ID NO: 737




RPr
GTAATGCTGTCCACGGTGC
SEQ ID NO: 738





EPHB4
NM_004444.3
FPr
TGAACGGGGTATCCTCCTTA
SEQ ID NO: 739




Probe
CGTCCCATTTGAGCCTGTCAATGT
SEQ ID NO: 740




RPr
AGGTACCTCTCGGTCAGTGG
SEQ ID NO: 741





EphB6
NM_004445.1
FPr
ACTGGTCCTCCATCGGCT
SEQ ID NO: 742




Probe
CCTTGCACCTCAAACCAAAGCTCC
SEQ ID NO: 743




RPr
CCAGTGTAGCATGAGTGCTGA
SEQ ID NO: 744





EPM2A
NM_005670.2
FPr
ACTGTGGCACTTAGGGGAGA
SEQ ID NO: 745




Probe
CTGCCTCTGCCCAAAGCAAATGTC
SEQ ID NO: 746




RPr
AGTGGAAATGTGTCCTGGCT
SEQ ID NO: 747





ErbB3
NM_001982.1
FPr
CGGTTATGTCATGCCAGATACAC
SEQ ID NO: 748




Probe
CCTCAAAGGTACTCCCTCCTCCCGG
SEQ ID NO: 749




RPr
GAACTGAGACCCACTGAAGAAAGG
SEQ ID NO: 750





ERCC1
NM_001983.1
FPr
GTCCAGGTGGATGTGAAAGA
SEQ ID NO: 751




Probe
CAGCAGGCCCTCAAGGAGCTG
SEQ ID NO: 752




RPr
CGGCCAGGATACACATCTTA
SEQ ID NO: 753





ERCC2
NM_000400.2
FPr
TGGCCTTCTTCACCAGCTA
SEQ ID NO: 754




Probe
AGGCCACGGTGCTCTCCATGTACT
SEQ ID NO: 755




RPr
CAAGGATCCCCTGCTCATAC
SEQ ID NO: 756





EREG
NM_001432.1
FPr
ATAACAAAGTGTAGCTCTGACATGAATG
SEQ ID NO: 757




Probe
TTGTTTGCATGGACAGTGCATCTATCTGGT
SEQ ID NO: 758




RPr
CACACCTGCAGTAGTTTTGACTCA
SEQ ID NO: 759





ERK1
Z11696.1
FPr
ACGGATCACAGTGGAGGAAG
SEQ ID NO: 760




Probe
CGCTGGCTCACCCCTACCTG
SEQ ID NO: 761




RPr
CTCATCCGTCGGGTCATAGT
SEQ ID NO: 762





ERK2
NM_002745.1
FPr
AGTTCTTGACCCCTGGTCCT
SEQ ID NO: 763




Probe
TCTCCAGCCCGTCTTGGCTT
SEQ ID NO: 764




RPr
AAACGGCTCAAAGGAGTCAA
SEQ ID NO: 765





ESPL1
NM_012291.1
FPr
ACCCCCAGACCGGATCAG
SEQ ID NO: 766




Probe
CTGGCCCTCATGTCCCCTTCACG
SEQ ID NO: 767




RPr
TGTAGGGCAGACTTCCTCAAACA
SEQ ID NO: 768





EstR1
NM_000125.1
FPr
CGTGGTGCCCCTCTATGAC
SEQ ID NO: 769




Probe
CTGGAGATGCTGGACGCCC
SEQ ID NO: 770




RPr
GGCTAGTGGGCGCATGTAG
SEQ ID NO: 771





ETV4
NM_001986.1
FPr
TCCAGTGCCTATGACCCC
SEQ ID NO: 772




Probe
CAGACAAATCGCCATCAAGTCCCC
SEQ ID NO: 773




RPr
ACTGTCCAAGGGCACCAG
SEQ ID NO: 774





F3
NM_001993.2
FPr
GTGAAGGATGTGAAGCAGACGTA
SEQ ID NO: 775




Probe
TGGCACGGGTCTTCTCCTACC
SEQ ID NO: 776




RPr
AACCGGTGCTCTCCACATTC
SEQ ID NO: 777





FABP4
NM_001442.1
FPr
GCTTTGCCACCAGGAAAGT
SEQ ID NO: 778




Probe
CTGGCATGGCCAAACCTAACATGA
SEQ ID NO: 779




RPr
CATCCCCATTCACACTGATG
SEQ ID NO: 780





FAP
NM_004460.2
FPr
CTGACCAGAACCACGGCT
SEQ ID NO: 781




Probe
CGGCCTGTCCACGAACCACTTATA
SEQ ID NO: 782




RPr
GGAAGTGGGTCATGTGGG
SEQ ID NO: 783





fas
NM_000043.1
FPr
GGATTGCTCAACAACCATGCT
SEQ ID NO: 784




Probe
TCTGGACCCTCCTACCTCTGGTTCTTACGCT
SEQ ID NO: 785




RPr
GGCATTAACACTTTTGGACGATAA
SEQ ID NO: 786





fasl
NM_000639.1
FPr
GCACTTTGGGATTCTTTCCATTAT
SEQ ID NO: 787




Probe
ACAACATTCTCGGTGCCTGTAACAAAGAA
SEQ ID NO: 788




RPr
GCATGTAAGAAGACCCTCACTGAA
SEQ ID NO: 789





FASN
NM_004104.4
FPr
GCCTCTTCCTGTTCGACG
SEQ ID NO: 790




Probe
TCGCCCACCTACGTACTGGCCTAC
SEQ ID NO: 791




RPr
GCTTTGCCCGGTAGCTCT
SEQ ID NO: 792





FBXO5
NM_012177.2
FPr
GGCTATTCCTCATTTTCTCTACAAAGTG
SEQ ID NO: 793




Probe
CCTCCAGGAGGCTACCTTCTTCATGTTCAC
SEQ ID NO: 794




RPr
GGATTGTAGACTGTCACCGAAATTC
SEQ ID NO: 795





FBXW7
NM_033632.1
FPr
CCCCAGTTTCAACGAGACTT
SEQ ID NO: 796




Probe
TCATTGCTCCCTAAAGAGTTGGCACTC
SEQ ID NO: 797




RPr
GTTCCAGGAATGAAAGCACA
SEQ ID NO: 798





FDXR
NM_004110.2
FPr
GAGATGATTCAGTTACCGGGAG
SEQ ID NO: 799




Probe
AATCCACAGGATCCAAAATGGGCC
SEQ ID NO: 800




RPr
ATCTTGTCCTGGAGACCCAA
SEQ ID NO: 801





FES
NM_002005.2
FPr
CTCTGCAGGCCTAGGTGC
SEQ ID NO: 802




Probe
CTCCTCAGCGGCTCCAGCTCATAT
SEQ ID NO: 803




RPr
CCAGGACTGTGAAGAGCTGTC
SEQ ID NO: 804





FGF18
NM_003862.1
FPr
CGGTAGTCAAGTCCGGATCAA
SEQ ID NO: 805




Probe
CAAGGAGACGGAATTCTACCTGTGC
SEQ ID NO: 806




RPr
GCTTGCCTTTGCGGTTCA
SEQ ID NO: 807





FGF2
NM_002006.2
FPr
AGATGCAGGAGAGAGGAAGC
SEQ ID NO: 808




Probe
CCTGCAGACTGCTTTTTGCCCAAT
SEQ ID NO: 809




RPr
GTTTTGCAGCCTTACCCAAT
SEQ ID NO: 810





FGFR1
NM_023109.1
FPr
CACGGGACATTCACCACATC
SEQ ID NO: 811




Probe
ATAAAAAGACAACCAACGGCCGACTGC
SEQ ID NO: 812




RPr
GGGTGCCATCCACTTCACA
SEQ ID NO: 813





FGFR2
NM_000141.2
FPr
GAGGGACTGTTGGCATGCA
SEQ ID NO: 814


isoform 1




Probe
TCCCAGAGACCAACGTTCAAGCAGTTG
SEQ ID NO: 815




RPr
GAGTGAGAATTCGATCCAAGTCTTC
SEQ ID NO: 816





FHIT
NM_002012.1
FPr
CCAGTGGAGCGCTTCCAT
SEQ ID NO: 817




Probe
TCGGCCACTTCATCAGGACGCAG
SEQ ID NO: 818




RPr
CTCTCTGGGTCGTCTGAAACAA
SEQ ID NO: 819





FIGF
NM_004469.2
FPr
GGTTCCAGCTTTCTGTAGCTGT
SEQ ID NO: 820




Probe
ATTGGTGGCCACACCACCTCCTTA
SEQ ID NO: 821




RPr
GCCGCAGGTTCTAGTTGCT
SEQ ID NO: 822





FLJ12455
NM_022078.1
FPr
CCACCAGCATGAAGTTTCG
SEQ ID NO: 823




Probe
ACCCCTCACAAAGGCCATGTCTGT
SEQ ID NO: 824




RPr
GGCTGTCTGAAGCACAACTG
SEQ ID NO: 825





FLJ20712
AK000719.1
FPr
GCCACACAAACATGCTCCT
SEQ ID NO: 826




Probe
ATGTCTTTCCCAGCAGCTCTGCCT
SEQ ID NO: 827




RPr
GCCACAGGAAACTTCCGA
SEQ ID NO: 828





FLT1
NM_002019.1
FPr
GGCTCCCGAATCTATCTTTG
SEQ ID NO: 829




Probe
CTACAGCACCAAGAGCGACGTGTG
SEQ ID NO: 830




RPr
TCCCACAGCAATACTCCGTA
SEQ ID NO: 831





FLT4
NM_002020.1
FPr
ACCAAGAAGCTGAGGACCTG
SEQ ID NO: 832




Probe
AGCCCGCTGACCATGGAAGATCT
SEQ ID NO: 833




RPr
CCTGGAAGCTGTAGCAGACA
SEQ ID NO: 834





FOS
NM_005252.2
FPr
CGAGCCCTTTGATGACTTCCT
SEQ ID NO: 835




Probe
TCCCAGCATCATCCAGGCCCAG
SEQ ID NO: 836




RPr
GGAGCGGGCTGTCTCAGA
SEQ ID NO: 837





FOXO3A
NM_001455.1
FPr
TGAAGTCCAGGACGATGATG
SEQ ID NO: 838




Probe
CTCTACAGCAGCTCAGCCAGCCTG
SEQ ID NO: 839




RPr
ACGGCTTGCTTACTGAAGGT
SEQ ID NO: 840





FPGS
NM_004957.3
FPr
CAGCCCTGCCAGTTTGAC
SEQ ID NO: 841




Probe
ATGCCGTCTTCTGCCCTAACCTGA
SEQ ID NO: 842




RPr
GTTGCCTGTGGATGACACC
SEQ ID NO: 843





FRP1
NM_003012.2
FPr
TTGGTACCTGTGGGTTAGCA
SEQ ID NO: 844




Probe
TCCCCAGGGTAGAATTCAATCAGAGC
SEQ ID NO: 845




RPr
CACATCCAAATGCAAACTGG
SEQ ID NO: 846





FST
NM_006350.2
FPr
GTAAGTCGGATGAGCCTGTCTGT
SEQ ID NO: 847




Probe
CCAGTGACAATGCCACTTATGCCAGC
SEQ ID NO: 848




RPr
CAGCTTCCTTCATGGCACACT
SEQ ID NO: 849





Furin
NM_002569.1
FPr
AAGTCCTCGATACGCACTATAGCA
SEQ ID NO: 850




Probe
CCCGGATGGTCTCCACGTCAT
SEQ ID NO: 851




RPr
CTGGCATGTGGCACATGAG
SEQ ID NO: 852





FUS
NM_004960.1
FPr
GGATAATTCAGACAACAACACCATCT
SEQ ID NO: 853




Probe
TCAATTGTAACATTCTCACCCAGGCCTTG
SEQ ID NO: 854




RPr
TGAAGTAATCAGCCACAGACTCAAT
SEQ ID NO: 855





FUT1
NM_000148.1
FPr
CCGTGCTCATTGCTAACCA
SEQ ID NO: 856




Probe
TCTGTCCCTGAACTCCCAGAACCA
SEQ ID NO: 857




RPr
CTGCCCAAAGCCAGATGTA
SEQ ID NO: 858





FUT3
NM_000149.1
FPr
CAGTTCGGTCCAACAGAGAA
SEQ ID NO: 859




Probe
AGCAGGCAACCACCATGTCATTTG
SEQ ID NO: 860




RPr
TGCGAATTATATCCCGATGA
SEQ ID NO: 861





FUT6
NM_000150.1
FPr
CGTGTGTCTCAAGACGATCC
SEQ ID NO: 862




Probe
TGTGTACCCTAATGGGTCCCGCTT
SEQ ID NO: 863




RPr
GGTCCCTGTGCTGTCTGG
SEQ ID NO: 864





FXYD5
NM_014164.4
FPr
AGAGCACCAAAGCAGCTCAT
SEQ ID NO: 865




Probe
CACTGATGACACCACGACGCTCTC
SEQ ID NO: 866




RPr
GTGCTTGGGGATGGTCTCT
SEQ ID NO: 867





FYN
NM_002037.3
FPr
GAAGCGCAGATCATGAAGAA
SEQ ID NO: 868




Probe
CTGAAGCACGACAAGCTGGTCCAG
SEQ ID NO: 869




RPr
CTCCTCAGACACCACTGCAT
SEQ ID NO: 870





FZD1
NM_003505.1
FPr
GGTGCACCAGTTCTACCCTC
SEQ ID NO: 871




Probe
ACTTGAGCTCAGCGGAACACTGCA
SEQ ID NO: 872




RPr
GCGTACATGGAGCACAGGA
SEQ ID NO: 873





FZD2
NM_001466.2
FPr
TGGATCCTCACCTGGTCG
SEQ ID NO: 874




Probe
TGCGCTTCCACCTTCTTCACTGTC
SEQ ID NO: 875




RPr
GCGCTGCATGTCTACCAA
SEQ ID NO: 876





FZD6
NM_003506.2
FPr
AATGAGAGAGGTGAAAGCGG
SEQ ID NO: 877




Probe
CGGAGCTAGCACCCCCAGGTTAAG
SEQ ID NO: 878




RPr
AGGTTCACCACAGTCCTGTTC
SEQ ID NO: 879





G-Catenin
NM_002230.1
FPr
TCAGCAGCAAGGGCATCAT
SEQ ID NO: 880




Probe
CGCCCGCAGGCCTCATCCT
SEQ ID NO: 881




RPr
GGTGGTTTTCTTGAGCGTGTACT
SEQ ID NO: 882





G1P2
NM_005101.1
FPr
CAACGAATTCCAGGTGTCC
SEQ ID NO: 883




Probe
CTGAGCAGCTCCATGTCGGTGTC
SEQ ID NO: 884




RPr
GATCTGCGCCTTCAGCTC
SEQ ID NO: 885





GADD45
NM_001924.2
FPr
GTGCTGGTGACGAATCCA
SEQ ID NO: 886




Probe
TTCATCTCAATGGAAGGATCCTGCC
SEQ ID NO: 887




RPr
CCCGGCAAAAACAAATAAGT
SEQ ID NO: 888





GADD45B
NM_015675.1
FPr
ACCCTCGACAAGACCACACT
SEQ ID NO: 889




Probe
AACTTCAGCCCCAGCTCCCAAGTC
SEQ ID NO: 890




RPr
TGGGAGTTCATGGGTACAGA
SEQ ID NO: 891





GADD45G
NM_006705.2
FPr
CGCGCTGCAGATCCATTT
SEQ ID NO: 892




Probe
CGCTGATCCAGGCTTTCTGCTGC
SEQ ID NO: 893




RPr
CGCACTATGTCGATGTCGTTCT
SEQ ID NO: 894





GAGE4
NM_001474.1
FPr
GGAACAGGGTCACCCACAGA
SEQ ID NO: 895




Probe
TCAGGACCATCTTCACACTCACACCCA
SEQ ID NO: 896




RPr
GATTTGGCGGGTCCATCTC
SEQ ID NO: 897





GBP1
NM_002053.1
FPr
TTGGGAAATATTTGGGCATT
SEQ ID NO: 898




Probe
TTGGGACATTGTAGACTTGGCCAGAC
SEQ ID NO: 899




RPr
AGAAGCTAGGGTGGTTGTCC
SEQ ID NO: 900





GBP2
NM_004120.2
FPr
GCATGGGAACCATCAACCA
SEQ ID NO: 901




Probe
CCATGGACCAACTTCACTATGTGACAGA
SEQ ID NO: 902





GC




RPr
TGAGGAGTTTGCCTTGATTCG
SEQ ID NO: 903





GCLC
NM_001498.1
FPr
CTGTTGCAGGAAGGCATTGA
SEQ ID NO: 904




Probe
CATCTCCTGGCCCAGCATGTT
SEQ ID NO: 905




RPr
GTCAGTGGGTCTCTAATAAAGAGATGAG
SEQ ID NO: 906





GCLM
NM_002061.1
FPr
TGTAGAATCAAACTCTTCATCATCAACT
SEQ ID NO: 907





AG




Probe
TGCAGTTGACATGGCCTGTTCAGTCC
SEQ ID NO: 908




RPr
CACAGAATCCAGCTGTGCAACT
SEQ ID NO: 909





GCNT1
NM_001490.3
FPr
TGGTGCTTGGAGCATAGAAG
SEQ ID NO: 910




Probe
TGCCCTTCACAAAGGAAATCCCTG
SEQ ID NO: 911




RPr
GCAACGTCCTCAGCATTTC
SEQ ID NO: 912





GDF15
NM_004864.1
FPr
CGCTCCAGACCTATGATGACT
SEQ ID NO: 913




Probe
TGTTAGCCAAAGACTGCCACTGCA
SEQ ID NO: 914




RPr
ACAGTGGAAGGACCAGGACT
SEQ ID NO: 915





GIT1
NM_014030.2
FPr
GTGTATGACGAGGTGGATCG
SEQ ID NO: 916




Probe
AGCCAGCCACACTGCATCATTTTC
SEQ ID NO: 917




RPr
ACCAGAGTGCTGTGGTTTTG
SEQ ID NO: 918





GJA1
NM_000165.2
FPr
GTTCACTGGGGGTGTATGG
SEQ ID NO: 919




Probe
ATCCCCTCCCTCTCCACCCATCTA
SEQ ID NO: 920




RPr
AAATACCAACATGCACCTCTCTT
SEQ ID NO: 921





GJB2
NM_004004.3
FPr
TGTCATGTACGACGGCTTCT
SEQ ID NO: 922




Probe
AGGCGTTGCACTTCACCAGCC
SEQ ID NO: 923




RPr
AGTCCACAGTGTTGGGACAA
SEQ ID NO: 924





GPX1
NM_000581.2
FPr
GCTTATGACCGACCCCAA
SEQ ID NO: 925




Probe
CTCATCACCTGGTCTCCGGTGTGT
SEQ ID NO: 926




RPr
AAAGTTCCAGGCAACATCGT
SEQ ID NO: 927





GPX2
NM_002083.1
FPr
CACACAGATCTCCTACTCCATCCA
SEQ ID NO: 928




Probe
CATGCTGCATCCTAAGGCTCCTCAGG
SEQ ID NO: 929




RPr
GGTCCAGCAGTGTCTCCTGAA
SEQ ID NO: 930





Grb10
NM_005311.2
FPr
CTTCGCCTTTGCTGATTGC
SEQ ID NO: 931




Probe
CTCCAAACGCCTGCCTGACGACTG
SEQ ID NO: 932




RPr
CCATAACGCACATGCTCCAA
SEQ ID NO: 933





GRB14
NM_004490.1
FPr
TCCCACTGAAGCCCTTTCAG
SEQ ID NO: 934




Probe
CCTCCAAGCGAGTCCTTCTTCAACCG
SEQ ID NO: 935




RPr
AGTGCCCAGGCGTAAACATC
SEQ ID NO: 936





GRB2
NM_002086.2
FPr
GTCCATCAGTGCATGACGTT
SEQ ID NO: 937




Probe
AGGCCACGTATAGTCCTAGCTGACGC
SEQ ID NO: 938




RPr
AGCCCACTTGGTTTCTTGTT
SEQ ID NO: 939





GRB7
NM_005310.1
FPr
CCATCTGCATCCATCTTGTT
SEQ ID NO: 940




Probe
CTCCCCACCCTTGAGAAGTGCCT
SEQ ID NO: 941




RPr
GGCCACCAGGGTATTATCTG
SEQ ID NO: 942





GRIK1
NM_000830.2
FPr
GTTGGGTGCATCTCTCGG
SEQ ID NO: 943




Probe
AATTCATGCCGAGATACAGCCGCT
SEQ ID NO: 944




RPr
CGTGCTCCATCTTCCTAGCTT
SEQ ID NO: 945





GRO1
NM_001511.1
FPr
CGAAAAGATGCTGAACAGTGACA
SEQ ID NO: 946




Probe
CTTCCTCCTCCCTTCTGGTCAGTTGGAT
SEQ ID NO: 947




RPr
TCAGGAACAGCCACCAGTGA
SEQ ID NO: 948





GRP
NM_002091.1
FPr
CTGGGTCTCATAGAAGCAAAGGA
SEQ ID NO: 949




Probe
AGAAACCACCAGCCACCTCAACCCA
SEQ ID NO: 950




RPr
CCACGAAGGCTGCTGATTG
SEQ ID NO: 951





GRPR
NM_005314.1
FPr
ATGCTGCTGGCCATTCCA
SEQ ID NO: 952




Probe
CCGTGTTTTCTGACCTCCATCCCTTCC
SEQ ID NO: 953




RPr
AGGTCTGGTTGGTGCTTTCCT
SEQ ID NO: 954





GSK3B
NM_002093.2
FPr
GACAAGGACGGCAGCAAG
SEQ ID NO: 955




Probe
CCAGGAGTTGCCACCACTGTTGTC
SEQ ID NO: 956




RPr
TTGTGGCCTGTCTGGACC
SEQ ID NO: 957





GSTA3
NM_000847.3
FPr
TCTCCAACTTCCCTCTGCTG
SEQ ID NO: 958




Probe
AGGCCCTGAAAACCAGAATCAGCA
SEQ ID NO: 959




RPr
ACTTCTTCACCGTGGGCA
SEQ ID NO: 960





GSTM1
NM_000561.1
FPr
AAGCTATGAGGAAAAGAAGTACACGAT
SEQ ID NO: 961




Probe
TCAGCCACTGGCTTCTGTCATAATCAGG
SEQ ID NO: 962





AG




RPr
GGCCCAGCTTGAATTTTTCA
SEQ ID NO: 963





GSTM3
NM_000849.3
FPr
CAATGCCATCTTGCGCTACAT
SEQ ID NO: 964




Probe
CTCGCAAGCACAACATGTGTGGTGAGA
SEQ ID NO: 965




RPr
GTCCACTCGAATCTTTTCTTCTTCA
SEQ ID NO: 966





GSTp
NM_000852.2
FPr
GAGACCCTGCTGTCCCAGAA
SEQ ID NO: 967




Probe
TCCCACAATGAAGGTCTTGCCTCCCT
SEQ ID NO: 968




RPr
GGTTGTAGTCAGCGAAGGAGATC
SEQ ID NO: 969





GSTT1
NM_000853.1
FPr
CACCATCCCCACCCTGTCT
SEQ ID NO: 970




Probe
CACAGCCGCCTGAAAGCCACAAT
SEQ ID NO: 971




RPr
GGCCTCAGTGTGCATCATTCT
SEQ ID NO: 972





H2AFZ
NM_002106.2
FPr
CCGGAAAGGCCAAGACAA
SEQ ID NO: 973




Probe
CCCGCTCGCAGAGAGCCGG
SEQ ID NO: 974




RPr
AATACGGCCCACTGGGAACT
SEQ ID NO: 975





HB-EGF
NM_001945.1
FPr
GACTCCTTCGTCCCCAGTTG
SEQ ID NO: 976




Probe
TTGGGCCTCCCATAATTGCTTTGCC
SEQ ID NO: 977




RPr
TGGCACTTGAAGGCTCTGGTA
SEQ ID NO: 978





hCRA a
U78556.1
FPr
TGACACCCTTACCTTCCTGAGAA
SEQ ID NO: 979




Probe
TCTGCTTTCCGCGCTCCCAGG
SEQ ID NO: 980




RPr
AAAAACACGAGTCAAAAATAGAAGTCA
SEQ ID NO: 981





CT





HDAC1
NM_004964.2
FPr
CAAGTACCACAGCGATGACTACATTAA
SEQ ID NO: 982




Probe
TTCTTGCGCTCCATCCGTCCAGA
SEQ ID NO: 983




RPr
GCTTGCTGTACTCCGACATGTT
SEQ ID NO: 984





HDAC2
NM_001527.1
FPr
GGTGGCTACACAATCCGTAA
SEQ ID NO: 985




Probe
TGCAGTCTCATATGTCCAACATCGAGC
SEQ ID NO: 986




RPr
TGGGAATCTCACAATCAAGG
SEQ ID NO: 987





HDGF
NM_004494.1
FPr
TCCTAGGCATTCTGGACCTC
SEQ ID NO: 988




Probe
CATTCCTACCCCTGATCCCAACCC
SEQ ID NO: 989




RPr
GCTGTTGATGCTCCATCCTT
SEQ ID NO: 990





hENT1
NM_004955.1
FPr
AGCCGTGACTGTTGAGGTC
SEQ ID NO: 991




Probe
AAGTCCAGCATCGCAGGCAGC
SEQ ID NO: 992




RPr
AAGTAACGTTCCCAGGTGCT
SEQ ID NO: 993





Hepsin
NM_002151.1
FPr
AGGCTGCTGGAGGTCATCTC
SEQ ID NO: 994




Probe
CCAGAGGCCGTTTCTTGGCCG
SEQ ID NO: 995




RPr
CTTCCTGCGGCCACAGTCT
SEQ ID NO: 996





HER2
NM_004448.1
FPr
CGGTGTGAGAAGTGCAGCAA
SEQ ID NO: 997




Probe
CCAGACCATAGCACACTCGGGCAC
SEQ ID NO: 998




RPr
CCTCTCGCAAGTGCTCCAT
SEQ ID NO: 999





Herstatin
AF177761.2
FPr
CACCCTGTCCTATCCTTCCT
SEQ ID NO: 1000




Probe
CCCTCTTGGGACCTAGTCTCTGCCT
SEQ ID NO: 1001




RPr
GGCCAGGGGTAGAGAGTAGA
SEQ ID NO: 1002





HES6
NM_018645.3
FPr
TTAGGGACCCTGCAGCTCT
SEQ ID NO: 1003




Probe
TAGCTCCCTCCCTCCACCCACTC
SEQ ID NO: 1004




RPr
CTACAAAATTCTTCCTCCTGCC
SEQ ID NO: 1005





HGF
M29145.1
FPr
CCGAAATCCAGATGATGATG
SEQ ID NO: 1006




Probe
CTCATGGACCCTGGTGCTACACG
SEQ ID NO: 1007




RPr
CCCAAGGAATGAGTGGATTT
SEQ ID NO: 1008





HIF1A
NM_001530.1
FPr
TGAACATAAAGTCTGCAACATGGA
SEQ ID NO: 1009




Probe
TTGCACTGCACAGGCCACATTCAC
SEQ ID NO: 1010




RPr
TGAGGTTGGTTACTGTTGGTATCATATA
SEQ ID NO: 1011





HK1
NM_000188.1
FPr
TACGCACAGAGGCAAGCA
SEQ ID NO: 1012




Probe
TAAGAGTCCGGGATCCCCAGCCTA
SEQ ID NO: 1013




RPr
GAGAGAAGTGCTGGAGAGGC
SEQ ID NO: 1014





HLA-DPB1
NM_002121.4
FPr
TCCATGATGGTTCTGCAGGTT
SEQ ID NO: 1015




Probe
CCCCGGACAGTGGCTCTGACG
SEQ ID NO: 1016




RPr
TGAGCAGCACCATCAGTAACG
SEQ ID NO: 1017





HLA-DRA
NM_019111.3
FPr
GACGATTTGCCAGCTTTGAG
SEQ ID NO: 1018




Probe
TCAAGGTGCATTGGCCAACATAGC
SEQ ID NO: 1019




RPr
TCCAGGTTGGCTTTGTCC
SEQ ID NO: 1020





HLA-DRB1
NM_002124.1
FPr
GCTTTCTCAGGACCTGGTTG
SEQ ID NO: 1021




Probe
CATTTTCTGCAGTTGCCGAACCAG
SEQ ID NO: 1022




RPr
AGGAAGCCACAAGGGAGG
SEQ ID NO: 1023





HLA-G
NM_002127.2
FPr
CCTGCGCGGCTACTACAAC
SEQ ID NO: 1024




Probe
CGAGGCCAGTTCTCACACCCTCCAG
SEQ ID NO: 1025




RPr
CAGGTCGCAGCCAATCATC
SEQ ID NO: 1026





HMGB1
NM_002128.3
FPr
TGGCCTGTCCATTGGTGAT
SEQ ID NO: 1027




Probe
TTCCACATCTCTCCCAGTTTCTTCGCAA
SEQ ID NO: 1028




RPr
GCTTGTCATCTGCAGCAGTGTT
SEQ ID NO: 1029





hMLH
NM_000249.2
FPr
CTACTTCCAGCAACCCCAGA
SEQ ID NO: 1030




Probe
TCCACATCAGAATCTTCCCG
SEQ ID NO: 1031




RPr
CTTTCGGGAATCATCTTCCA
SEQ ID NO: 1032





HNRPAB
NM_004499.2
FPr
CAAGGGAGCGACCAACTGA
SEQ ID NO: 1033




Probe
CTCCATATCCAAACAAAGCATGTGTGCG
SEQ ID NO: 1034




RPr
GTTTGCCAAGTTAAATTTGGTACATAAT
SEQ ID NO: 1035





HNRPD
NM_031370.2
FPr
GCCAGTAAGAACGAGGAGGA
SEQ ID NO: 1036




Probe
AAGGCCATTCAAACTCCTCCCCAC
SEQ ID NO: 1037




RPr
CGTCGCTGCTTCAGAGTGT
SEQ ID NO: 1038





HoxA1
NM_005522.3
FPr
AGTGACAGATGGACAATGCAAGA
SEQ ID NO: 1039




Probe
TGAACTCCTTCCTGGAATACCCCA
SEQ ID NO: 1040




RPr
CCGAGTCGCCACTGCTAAGT
SEQ ID NO: 1041





HoxA5
NM_019102.2
FPr
TCCCTTGTGTTCCTTCTGTGAA
SEQ ID NO: 1042




Probe
AGCCCTGTTCTCGTTGCCCTAATTCATC
SEQ ID NO: 1043




RPr
GGCAATAAACAGGCTCATGATTAA
SEQ ID NO: 1044





HOXB13
NM_006361.2
FPr
CGTGCCTTATGGTTACTTTGG
SEQ ID NO: 1045




Probe
ACACTCGGCAGGAGTAGTACCCGC
SEQ ID NO: 1046




RPr
CACAGGGTTTCAGCGAGC
SEQ ID NO: 1047





HOXB7
NM_004502.2
FPr
CAGCCTCAAGTTCGGTTTTC
SEQ ID NO: 1048




Probe
ACCGGAGCCTTCCCAGAACAAACT
SEQ ID NO: 1049




RPr
GTTGGAAGCAAACGCACA
SEQ ID NO: 1050





HRAS
NM_005343.2
FPr
GGACGAATACGACCCCACT
SEQ ID NO: 1051




Probe
ACCACCTGCTTCCGGTAGGAATCC
SEQ ID NO: 1052




RPr
GCACGTCTCCCCATCAAT
SEQ ID NO: 1053





HSBP1
NM_001537.1
FPr
GGAGATGGCCGAGACTGAC
SEQ ID NO: 1054




Probe
CAAGACCGTGCAGGACCTCACCT
SEQ ID NO: 1055




RPr
CTGCAGGAGTGTCTGCACC
SEQ ID NO: 1056





HSD17B1
NM_000413.1
FPr
CTGGACCGCACGGACATC
SEQ ID NO: 1057




Probe
ACCGCTTCTACCAATACCTCGCCCA
SEQ ID NO: 1058




RPr
CGCCTCGCGAAAGACTTG
SEQ ID NO: 1059





HSD17B2
NM_002153.1
FPr
GCTTTCCAAGTGGGGAATTA
SEQ ID NO: 1060




Probe
AGTTGCTTCCATCCAACCTGGAGG
SEQ ID NO: 1061




RPr
TGCCTGCGATATTTGTTAGG
SEQ ID NO: 1062





HSPA1A
NM_005345.4
FPr
CTGCTGCGACAGTCCACTA
SEQ ID NO: 1063




Probe
AGAGTGACTCCCGTTGTCCCAAGG
SEQ ID NO: 1064




RPr
CAGGTTCGCTCTGGGAAG
SEQ ID NO: 1065





HSPA1B
NM_005346.3
FPr
GGTCCGCTTCGTCTTTCGA
SEQ ID NO: 1066




Probe
TGACTCCCGCGGTCCCAAGG
SEQ ID NO: 1067




RPr
GCACAGGTTCGCTCTGGAA
SEQ ID NO: 1068





HSPA4
NM_002154.3
FPr
TTCAGTGTGTCCAGTGCATC
SEQ ID NO: 1069




Probe
CATTTTCCTCAGACTTGTGAACCTCCACT
SEQ ID NO: 1070




RPr
ATCTGTTTCCATTGGCTCCT
SEQ ID NO: 1071





HSPA5
NM_005347.2
FPr
GGCTAGTAGAACTGGATCCCAACA
SEQ ID NO: 1072




Probe
TAATTAGACCTAGGCCTCAGCTGCACTG
SEQ ID NO: 1073





CC




RPr
GGTCTGCCCAAATGCTTTTC
SEQ ID NO: 1074





HSPA8
NM_006597.3
FPr
CCTCCCTCTGGTGGTGCTT
SEQ ID NO: 1075




Probe
CTCAGGGCCCACCATTGAAGAGGTTG
SEQ ID NO: 1076




RPr
GCTACATCTACACTTGGTTGGCTTAA
SEQ ID NO: 1077





HSPB1
NM_001540.2
FPr
CCGACTGGAGGAGCATAAA
SEQ ID NO: 1078




Probe
CGCACTTTTCTGAGCAGACGTCCA
SEQ ID NO: 1079




RPr
ATGCTGGCTGACTCTGCTC
SEQ ID NO: 1080





HSPCA
NM_005348.2
FPr
CAAAAGGCAGAGGCTGATAA
SEQ ID NO: 1081




Probe
TGACCAGATCCTTCACAGACTTGTCGT
SEQ ID NO: 1082




RPr
AGCGCAGTTTCATAAAGCAA
SEQ ID NO: 1083





HSPE1
NM_002157.1
FPr
GCAAGCAACAGTAGTCGCTG
SEQ ID NO: 1084




Probe
TCTCCACCCTTTCCTTTAGAACCCG
SEQ ID NO: 1085




RPr
CCAACTTTCACGCTAACTGGT
SEQ ID NO: 1086





HSPG2
NM_005529.2
FPr
GAGTACGTGTGCCGAGTGTT
SEQ ID NO: 1087




Probe
CAGCTCCGTGCCTCTAGAGGCCT
SEQ ID NO: 1088




RPr
CTCAATGGTGACCAGGACA
SEQ ID NO: 1089





ICAM1
NM_000201.1
FPr
GCAGACAGTGACCATCTACAGCTT
SEQ ID NO: 1090




Probe
CCGGCGCCCAACGTGATTCT
SEQ ID NO: 1091




RPr
CTTCTGAGACCTCTGGCTTCGT
SEQ ID NO: 1092





ICAM2
NM_000873.2
FPr
GGTCATCCTGACACTGCAAC
SEQ ID NO: 1093




Probe
TTGCCCACAGCCACCAAAGTG
SEQ ID NO: 1094




RPr
TGCACTCAATGGTGAAGGAC
SEQ ID NO: 1095





ID1
NM_002165.1
FPr
AGAACCGCAAGGTGAGCAA
SEQ ID NO: 1096




Probe
TGGAGATTCTCCAGCACGTCATCGAC
SEQ ID NO: 1097




RPr
TCCAACTGAAGGTCCCTGATG
SEQ ID NO: 1098





ID2
NM_002166.1
FPr
AACGACTGCTACTCCAAGCTCAA
SEQ ID NO: 1099




Probe
TGCCCAGCATCCCCCAGAACAA
SEQ ID NO: 1100




RPr
GGATTTCCATCTTGCTCACCTT
SEQ ID NO: 1101





ID3
NM_002167.2
FPr
CTTCACCAAATCCCTTCCTG
SEQ ID NO: 1102




Probe
TCACAGTCCTTCGCTCCTGAGCAC
SEQ ID NO: 1103




RPr
CTCTGGCTCTTCAGGCTACA
SEQ ID NO: 1104





ID4
NM_001546.2
FPr
TGGCCTGGCTCTTAATTTG
SEQ ID NO: 1105




Probe
CTTTTGTTTTGCCCAGTATAGACTCGGAAG
SEQ ID NO: 1106




RPr
TGCAATCATGCAAGACCAC
SEQ ID NO: 1107





IFIT1
NM_001548.1
FPr
TGACAACCAAGCAAATGTGA
SEQ ID NO: 1108




Probe
AAGTTGCCCCAGGTCACCAGACTC
SEQ ID NO: 1109




RPr
CAGTCTGCCCATGTGGTAAT
SEQ ID NO: 1110





IGF1
NM_000618.1
FPr
TCCGGAGCTGTGATCTAAGGA
SEQ ID NO: 1111




Probe
TGTATTGCGCACCCCTCAAGCCTG
SEQ ID NO: 1112




RPr
CGGACAGAGCGAGCTGACTT
SEQ ID NO: 1113





IGF1R
NM_000875.2
FPr
GCATGGTAGCCGAAGATTTCA
SEQ ID NO: 1114




Probe
CGCGTCATACCAAAATCTCCGATTTTGA
SEQ ID NO: 1115




RPr
TTTCCGGTAATAGTCTGTCTCATAGATATC
SEQ ID NO: 1116





IGF2
NM_000612.2
FPr
CCGTGCTTCCGGACAACTT
SEQ ID NO: 1117




Probe
TACCCCGTGGGCAAGTTCTTCCAA
SEQ ID NO: 1118




RPr
TGGACTGCTTCCAGGTGTCA
SEQ ID NO: 1119





IGFBP2
NM_000597.1
FPr
GTGGACAGCACCATGAACA
SEQ ID NO: 1120




Probe
CTTCCGGCCAGCACTGCCTC
SEQ ID NO: 1121




RPr
CCTTCATACCCGACTTGAGG
SEQ ID NO: 1122





IGFBP3
NM_000598.1
FPr
ACGCACCGGGTGTCTGA
SEQ ID NO: 1123




Probe
CCCAAGTTCCACCCCCTCCATTCA
SEQ ID NO: 1124




RPr
TGCCCTTTCTTGATGATGATTATC
SEQ ID NO: 1125





IGFBP5
NM_000599.1
FPr
TGGACAAGTACGGGATGAAGCT
SEQ ID NO: 1126




Probe
CCCGTCAACGTACTCCATGCCTGG
SEQ ID NO: 1127




RPr
CGAAGGTGTGGCACTGAAAGT
SEQ ID NO: 1128





IGFBP6
NM_002178.1
FPr
TGAACCGCAGAGACCAACAG
SEQ ID NO: 1129




Probe
ATCCAGGCACCTCTACCACGCCCTC
SEQ ID NO: 1130




RPr
GTCTTGGACACCCGCAGAAT
SEQ ID NO: 1131





IGFBP7
NM_001553
FPr
GGGTCACTATGGAGTTCAAAGGA
SEQ ID NO: 1132




Probe
CCCGGTCACCAGGCAGGAGTTCT
SEQ ID NO: 1133




RPr
GGGTCTGAATGGCCAGGTT
SEQ ID NO: 1134





IHH
NM_002181.1
FPr
AAGGACGAGGAGAACACAGG
SEQ ID NO: 1135




Probe
ATGACCCAGCGCTGCAAGGAC
SEQ ID NO: 1136




RPr
AGATAGCCAGCGAGTTCAGG
SEQ ID NO: 1137





IL-8
NM_000584.2
FPr
AAGGAACCATCTCACTGTGTGTAAAC
SEQ ID NO: 1138




Probe
TGACTTCCAAGCTGGCCGTGGC
SEQ ID NO: 1139




RPr
ATCAGGAAGGCTGCCAAGAG
SEQ ID NO: 1140





IL10
NM_000572.1
FPr
GGCGCTGTCATCGATTTCTT
SEQ ID NO: 1141




Probe
CTGCTCCACGGCCTTGCTCTTG
SEQ ID NO: 1142




RPr
TGGAGCTTATTAAAGGCATTCTTCA
SEQ ID NO: 1143





IL1B
NM_000576.2
FPr
AGCTGAGGAAGATGCTGGTT
SEQ ID NO: 1144




Probe
TGCCCACAGACCTTCCAGGAGAAT
SEQ ID NO: 1145




RPr
GGAAAGAAGGTGCTCAGGTC
SEQ ID NO: 1146





IL6
NM_000600.1
FPr
CCTGAACCTTCCAAAGATGG
SEQ ID NO: 1147




Probe
CCAGATTGGAAGCATCCATCTTTTTCA
SEQ ID NO: 1148




RPr
ACCAGGCAAGTCTCCTCATT
SEQ ID NO: 1149





IL6ST
NM_002184.2
FPr
GGCCTAATGTTCCAGATCCT
SEQ ID NO: 1150




Probe
CATATTGCCCAGTGGTCACCTCACA
SEQ ID NO: 1151




RPr
AAAATTGTGCCTTGGAGGAG
SEQ ID NO: 1152





ILT-2
NM_006669.1
FPr
AGCCATCACTCTCAGTGCAG
SEQ ID NO: 1153




Probe
CAGGTCCTATCGTGGCCCCTGA
SEQ ID NO: 1154




RPr
ACTGCAGAGTCAGGGTCTCC
SEQ ID NO: 1155





IMP-1
NM_006546.2
FPr
GAAAGTGTTTGCGGAGCAC
SEQ ID NO: 1156




Probe
CTCCTACAGCGGCCAGTTCTTGGT
SEQ ID NO: 1157




RPr
GAAGGCGTAGCCGGATTT
SEQ ID NO: 1158





IMP2
NM_006548.3
FPr
CAATCTGATCCCAGGGTTGAA
SEQ ID NO: 1159




Probe
CTCAGCGCACTTGGCATCTTTTCAACA
SEQ ID NO: 1160




RPr
GGCCCTGCTGGTGGAGATA
SEQ ID NO: 1161





ING1L
NM_001564.1
FPr
TGTTTCCAAGATCCTGCTGA
SEQ ID NO: 1162




Probe
CCATCTTTGCTTTATCTGAGGCTCGTTC
SEQ ID NO: 1163




RPr
TCTTTCTGGTTGGCTGGAAT
SEQ ID NO: 1164





ING5
NM_032329.4
FPr
CCTACAGCAAGTGCAAGGAA
SEQ ID NO: 1165




Probe
CCAGCTGCACTTTGTCGTCACTGT
SEQ ID NO: 1166




RPr
CATCTCGTAGGTCTGCATGG
SEQ ID NO: 1167





INHA
NM_002191.2
FPr
CCTCCCAGTTTCATCTTCCACTA
SEQ ID NO: 1168




Probe
ATGTGCAGCCCACAACCACCATGA
SEQ ID NO: 1169




RPr
AGGGACTGGAAGGGACAGGTT
SEQ ID NO: 1170





INHBA
NM_002192.1
FPr
GTGCCCGAGCCATATAGCA
SEQ ID NO: 1171




Probe
ACGTCCGGGTCCTCACTGTCCTTCC
SEQ ID NO: 1172




RPr
CGGTAGTGGTTGATGACTGTTGA
SEQ ID NO: 1173





INHBB
NM_002193.1
FPr
AGCCTCCAGGATACCAGCAA
SEQ ID NO: 1174




Probe
AGCTAAGCTGCCATTTGTCACCG
SEQ ID NO: 1175




RPr
TCTCCGACTGACAGGCATTTG
SEQ ID NO: 1176





IRS1
NM_005544.1
FPr
CCACAGCTCACCTTCTGTCA
SEQ ID NO: 1177




Probe
TCCATCCCAGCTCCAGCCAG
SEQ ID NO: 1178




RPr
CCTCAGTGCCAGTCTCTTCC
SEQ ID NO: 1179





ITGA3
NM_002204.1
FPr
CCATGATCCTCACTCTGCTG
SEQ ID NO: 1180




Probe
CACTCCAGACCTCGCTTAGCATGG
SEQ ID NO: 1181




RPr
GAAGCTTTGTAGCCGGTGAT
SEQ ID NO: 1182





ITGA4
NM_000885.2
FPr
CAACGCTTCAGTGATCAATCC
SEQ ID NO: 1183




Probe
CGATCCTGCATCTGTAAATCGCCC
SEQ ID NO: 1184




RPr
GTCTGGCCGGGATTCTTT
SEQ ID NO: 1185





ITGA5
NM_002205.1
FPr
AGGCCAGCCCTACATTATCA
SEQ ID NO: 1186




Probe
TCTGAGCCTTGTCCTCTATCCGGC
SEQ ID NO: 1187




RPr
GTCTTCTCCACAGTCCAGCA
SEQ ID NO: 1188





ITGA6
NM_000210.1
FPr
CAGTGACAAACAGCCCTTCC
SEQ ID NO: 1189




Probe
TCGCCATCTTTTGTGGGATTCCTT
SEQ ID NO: 1190




RPr
GTTTAGCCTCATGGGCGTC
SEQ ID NO: 1191





ITGA7
NM_002206.1
FPr
GATATGATTGGTCGCTGCTTTG
SEQ ID NO: 1192




Probe
CAGCCAGGACCTGGCCATCCG
SEQ ID NO: 1193




RPr
AGAACTTCCATTCCCCACCAT
SEQ ID NO: 1194





ITGAV
NM_002210.2
FPr
ACTCGGACTGCACAAGCTATT
SEQ ID NO: 1195




Probe
CCGACAGCCACAGAATAACCCAAA
SEQ ID NO: 1196




RPr
TGCCATCACCATTGAAATCT
SEQ ID NO: 1197





ITGB1
NM_002211.2
FPr
TCAGAATTGGATTTGGCTCA
SEQ ID NO: 1198




Probe
TGCTAATGTAAGGCATCACAGTCTTTTCCA
SEQ ID NO: 1199




RPr
CCTGAGCTTAGCTGGTGTTG
SEQ ID NO: 1200





ITGB3
NM_000212.1
FPr
ACCGGGAGCCCTACATGAC
SEQ ID NO: 1201




Probe
AAATACCTGCAACCGTTACTGCCGTGAC
SEQ ID NO: 1202




RPr
CCTTAAGCTCTTTCACTGACTCAATCT
SEQ ID NO: 1203





ITGB4
NM_000213.2
FPr
CAAGGTGCCCTCAGTGGA
SEQ ID NO: 1204




Probe
CACCAACCTGTACCCGTATTGCGA
SEQ ID NO: 1205




RPr
GCGCACACCTTCATCTCAT
SEQ ID NO: 1206





ITGB5
NM_002213.3
FPr
TCGTGAAAGATGACCAGGAG
SEQ ID NO: 1207




Probe
TGCTATGTTTCTACAAAACCGCCAAGG
SEQ ID NO: 1208




RPr
GGTGAACATCATGACGCAGT
SEQ ID NO: 1209





K-ras
NM_033360.2
FPr
GTCAAAATGGGGAGGGACTA
SEQ ID NO: 1210




Probe
TGTATCTTGTTGAGCTATCCAAACTGCCC
SEQ ID NO: 1211




RPr
CAGGACCACCACAGAGTGAG
SEQ ID NO: 1212





KCNH2 iso
NM_000238.2
FPr
GAGCGCAAAGTGGAAATCG
SEQ ID NO: 1213


a/b




Probe
TAGGAAGCAGCTCCCATCTTTCCGGTA
SEQ ID NO: 1214




RPr
TCTTCACGGGCACCACATC
SEQ ID NO: 1215





KCNH2 iso
NM_172057.1
FPr
TCCTGCTGCTGGTCATCTAC
SEQ ID NO: 1216


a/c




Probe
TGTCTTCACACCCTACTCGGCTGC
SEQ ID NO: 1217




RPr
CCTTCTTCCGTCTCCTTCAG
SEQ ID NO: 1218





KCNK4
NM_016611.2
FPr
CCTATCAGCCGCTGGTGT
SEQ ID NO: 1219




Probe
ATCCTGCTCGGCCTGGCTTACTTC
SEQ ID NO: 1220




RPr
TGGTGGTGAGCACTGAGG
SEQ ID NO: 1221





KDR
NM_002253.1
FPr
GAGGACGAAGGCCTCTACAC
SEQ ID NO: 1222




Probe
CAGGCATGCAGTGTTCTTGGCTGT
SEQ ID NO: 1223




RPr
AAAAATGCCTCCACTTTTGC
SEQ ID NO: 1224





Ki-67
NM_002417.1
FPr
CGGACTTTGGGTGCGACTT
SEQ ID NO: 1225




Probe
CCACTTGTCGAACCACCGCTCGT
SEQ ID NO: 1226




RPr
TTACAACTCTTCCACTGGGACGAT
SEQ ID NO: 1227





KIAA0125
NM_014792.2
FPr
GTGTCCTGGTCCATGTGGT
SEQ ID NO: 1228




Probe
CACGTGTCTCCACCTCCAAGGAGA
SEQ ID NO: 1229




RPr
GGGAGGTGCACACTGAGG
SEQ ID NO: 1230





KIF22
NM_007317.1
FPr
CTAAGGCACTTGCTGGAAGG
SEQ ID NO: 1231




Probe
TCCATAGGCAAGCACACTGGCATT
SEQ ID NO: 1232




RPr
TCTTCCCAGCTCCTGTGG
SEQ ID NO: 1233





KIF2C
NM_006845.2
FPr
AATTCCTGCTCCAAAAGAAAGTCTT
SEQ ID NO: 1234




Probe
AAGCCGCTCCACTCGCATGTCC
SEQ ID NO: 1235




RPr
CGTGATGCGAAGCTCTGAGA
SEQ ID NO: 1236





KIFC1
XM_371813.1
FPr
CCACAGGGTTGAAGAACCAG
SEQ ID NO: 1237




Probe
AGCCAGTTCCTGCTGTTCCTGTCC
SEQ ID NO: 1238




RPr
CACCTGATGTGCCAGACTTC
SEQ ID NO: 1239





Kitlng
NM_000899.1
FPr
GTCCCCGGGATGGATGTT
SEQ ID NO: 1240




Probe
CATCTCGCTTATCCAACAATGACTTGGCA
SEQ ID NO: 1241




RPr
GATCAGTCAAGCTGTCTGACAATTG
SEQ ID NO: 1242





KLF5
NM_001730.3
FPr
GTGCAACCGCAGCTTCTC
SEQ ID NO: 1243




Probe
CTCTGACCACCTGGCCCTGCATAT
SEQ ID NO: 1244




RPr
CGGGCAGTGCTCAGTTCT
SEQ ID NO: 1245





KLF6
NM_001300.4
FPr
CACGAGACCGGCTACTTCTC
SEQ ID NO: 1246




Probe
AGTACTCCTCCAGAGACGGCAGCG
SEQ ID NO: 1247




RPr
GCTCTAGGCAGGTCTGTTGC
SEQ ID NO: 1248





KLK10
NM_002776.1
FPr
GCCCAGAGGCTCCATCGT
SEQ ID NO: 1249




Probe
CCTCTTCCTCCCCAGTCGGCTGA
SEQ ID NO: 1250




RPr
CAGAGGTTTGAACAGTGCAGACA
SEQ ID NO: 1251





KLK6
NM_002774.2
FPr
GACGTGAGGGTCCTGATTCT
SEQ ID NO: 1252




Probe
TTACCCCAGCTCCATCCTTGCATC
SEQ ID NO: 1253




RPr
TCCTCACTCATCACGTCCTC
SEQ ID NO: 1254





KLRK1
NM_007360.1
FPr
TGAGAGCCAGGCTTCTTGTA
SEQ ID NO: 1255




Probe
TGTCTCAAAATGCCAGCCTTCTGAA
SEQ ID NO: 1256




RPr
ATCCTGGTCCTCTTTGCTGT
SEQ ID NO: 1257





KNTC2
NM_006101.1
FPr
ATGTGCCAGTGAGCTTGAGT
SEQ ID NO: 1258




Probe
CCTTGGAGAAACACAAGCACCTGC
SEQ ID NO: 1259




RPr
TGAGCCCCTGGTTAACAGTA
SEQ ID NO: 1260





KRAS2
NM_004985.3
FPr
GAGACCAAGGTTGCAAGGC
SEQ ID NO: 1261




Probe
AAGCTCAAAGGTTCACACAGGGCC
SEQ ID NO: 1262




RPr
CAGTCCATGCTGTGAAACTCTC
SEQ ID NO: 1263





KRT19
NM_002276.1
FPr
TGAGCGGCAGAATCAGGAGTA
SEQ ID NO: 1264




Probe
CTCATGGACATCAAGTCGCGGCTG
SEQ ID NO: 1265




RPr
TGCGGTAGGTGGCAATCTC
SEQ ID NO: 1266





KRT8
NM_002273.1
FPr
GGATGAAGCTTACATGAACAAGGTAGA
SEQ ID NO: 1267




Probe
CGTCGGTCAGCCCTTCCAGGC
SEQ ID NO: 1268




RPr
CATATAGCTGCCTGAGGAAGTTGAT
SEQ ID NO: 1269





LAMA3
NM_000227.2
FPr
CAGATGAGGCACATGGAGAC
SEQ ID NO: 1270




Probe
CTGATTCCTCAGGTCCTTGGCCTG
SEQ ID NO: 1271




RPr
TTGAAATGGCAGAACGGTAG
SEQ ID NO: 1272





LAMB3
NM_000228.1
FPr
ACTGACCAAGCCTGAGACCT
SEQ ID NO: 1273




Probe
CCACTCGCCATACTGGGTGCAGT
SEQ ID NO: 1274




RPr
GTCACACTTGCAGCATTTCA
SEQ ID NO: 1275





LAMC2
NM_005562.1
FPr
ACTCAAGCGGAAATTGAAGCA
SEQ ID NO: 1276




Probe
AGGTCTTATCAGCACAGTCTCCGCCTCC
SEQ ID NO: 1277




RPr
ACTCCCTGAAGCCGAGACACT
SEQ ID NO: 1278





LAT
NM_014387.2
FPr
GTGAACGTTCCGGAGAGC
SEQ ID NO: 1279




Probe
ATCCAGAGACGCTTCTGCGCTCTC
SEQ ID NO: 1280




RPr
ACATTCACATACTCCCGGCT
SEQ ID NO: 1281





LCN2
NM_005564.2
FPr
CGCTGGGCAACATTAAGAG
SEQ ID NO: 1282




Probe
TCACCACTCGGACGAGGTAACTCG
SEQ ID NO: 1283




RPr
AGCATGCTGGTTGTAGTTGGT
SEQ ID NO: 1284





LDLRAP1
NM_015627.1
FPr
CAGTGCCTCTCGCCTGTC
SEQ ID NO: 1285




Probe
ACTGGGACAAGCCTGACAGCAGC
SEQ ID NO: 1286




RPr
TGAAGAGGTCATCCTGCTCTG
SEQ ID NO: 1287





LEF
NM_016269.2
FPr
GATGACGGAAAGCATCCAG
SEQ ID NO: 1288




Probe
TGGAGGCCTCTACAACAAGGGACC
SEQ ID NO: 1289




RPr
CCCGGAATAACTCGAGTAGGA
SEQ ID NO: 1290





LGALS3
NM_002306.1
FPr
AGCGGAAAATGGCAGACAAT
SEQ ID NO: 1291




Probe
ACCCAGATAACGCATCATGGAGCGA
SEQ ID NO: 1292




RPr
CTTGAGGGTTTGGGTTTCCA
SEQ ID NO: 1293





LGMN
NM_001008530.1
FPr
TTGGTGCCGTTCCTATAGATG
SEQ ID NO: 1294




Probe
CAGTGCTTGCCTCCATCTTCAGGA
SEQ ID NO: 1295




RPr
GAACCTGCCACGATCACC
SEQ ID NO: 1296





LILRB3
NM_006864.1
FPr
CACCTGGTCTGGGAAGATACC
SEQ ID NO: 1297




Probe
ACCGAGACCCCAATCAAAACCTCC
SEQ ID NO: 1298




RPr
AAGAGCAGCAGGACGAAGG
SEQ ID NO: 1299





LMNB1
NM_005573.1
FPr
TGCAAACGCTGGTGTCACA
SEQ ID NO: 1300




Probe
CAGCCCCCCAACTGACCTCATC
SEQ ID NO: 1301




RPr
CCCCACGAGTTCTGGTTCTTC
SEQ ID NO: 1302





LMYC
NM_012421.1
FPr
CCCATCCAGAACACTGATTG
SEQ ID NO: 1303




Probe
TGACCTCCATCCCTTTCACTTGAATG
SEQ ID NO: 1304




RPr
CTGCTTTCTATGCACCCTTTC
SEQ ID NO: 1305





LOX
NM_002317.3
FPr
CCAATGGGAGAACAACGG
SEQ ID NO: 1306




Probe
CAGGCTCAGCAAGCTGAACACCTG
SEQ ID NO: 1307




RPr
CGCTGAGGCTGGTACTGTG
SEQ ID NO: 1308





LOXL2
NM_002318.1
FPr
TCAGCGGGCTCTTAAACAA
SEQ ID NO: 1309




Probe
CAGCTGTCCCCGCAGTAAAGAAGC
SEQ ID NO: 1310




RPr
AAGACAGGAGTTGACCACGC
SEQ ID NO: 1311





LRP5
NM_002335.1
FPr
CGACTATGACCCACTGGACA
SEQ ID NO: 1312




Probe
CGCCCATCCACCCAGTAGATGAAC
SEQ ID NO: 1313




RPr
CTTGGCTCGCTTGATGTTC
SEQ ID NO: 1314





LRP6
NM_002336.1
FPr
GGATGTAGCCATCTCTGCCT
SEQ ID NO: 1315




Probe
ATAGACCTCAGGGCCTTCGCTGTG
SEQ ID NO: 1316




RPr
AGTTCAAAGCCAATAGGGCA
SEQ ID NO: 1317





LY6D
NM_003695.2
FPr
AATGCTGATGACTTGGAGCAG
SEQ ID NO: 1318




Probe
CACAGACCCCACAGAGGATGAAGC
SEQ ID NO: 1319




RPr
CTGCATCCTCTGTGGGGT
SEQ ID NO: 1320





MAD
NM_002357.1
FPr
TGGTTCTGATTAGGTAACGTATTGGA
SEQ ID NO: 1321




Probe
CTGCCCACAACTCCCTTGCACGTAA
SEQ ID NO: 1322




RPr
GGTCAAGGTGGGACACTGAAG
SEQ ID NO: 1323





MAD1L1
NM_003550.1
FPr
AGAAGCTGTCCCTGCAAGAG
SEQ ID NO: 1324




Probe
CATGTTCTTCACAATCGCTGCATCC
SEQ ID NO: 1325




RPr
AGCCGTACCAGCTCAGACTT
SEQ ID NO: 1326





MAD2L1
NM_002358.2
FPr
CCGGGAGCAGGGAATCAC
SEQ ID NO: 1327




Probe
CGGCCACGATTTCGGCGCT
SEQ ID NO: 1328




RPr
ATGCTGTTGATGCCGAATGA
SEQ ID NO: 1329





MADH2
NM_005901.2
FPr
GCTGCCTTTGGTAAGAACATGTC
SEQ ID NO: 1330




Probe
TCCATCTTGCCATTCACGCCGC
SEQ ID NO: 1331




RPr
ATCCCAGCAGTCTCTTCACAACT
SEQ ID NO: 1332





MADH4
NM_005359.3
FPr
GGACATTACTGGCCTGTTCACA
SEQ ID NO: 1333




Probe
TGCATTCCAGCCTCCCATTTCCA
SEQ ID NO: 1334




RPr
ACCAATACTCAGGAGCAGGATGA
SEQ ID NO: 1335





MADH7
NM_005904.1
FPr
TCCATCAAGGCTTTCGACTA
SEQ ID NO: 1336




Probe
CTGCAGGCTGTACGCCTTCTCG
SEQ ID NO: 1337




RPr
CTGCTGCATAAACTCGTGGT
SEQ ID NO: 1338





MAP2
NM_031846.1
FPr
CGGACCACCAGGTCAGAG
SEQ ID NO: 1339




Probe
CCACTCTTCCCTGCTCTGCGAATT
SEQ ID NO: 1340




RPr
CAGGGGTAGTGGGTGTTGAG
SEQ ID NO: 1341





MAP2K1
NM_002755.2
FPr
GCCTTTCTTACCCAGAAGCAGAA
SEQ ID NO: 1342




Probe
TCTCAAAGTCGTCATCCTTCAGTTCTCCCA
SEQ ID NO: 1343




RPr
CAGCCCCCAGCTCACTGAT
SEQ ID NO: 1344





MAP3K1
XM_042066.8
FPr
GGTTGGCATCAAAAGGAACT
SEQ ID NO: 1345




Probe
AATTGTCCCTGAAACTCTCCTGCACC
SEQ ID NO: 1346




RPr
TGCCATAAATGCAATTGTCC
SEQ ID NO: 1347





MAPK14
NM_139012.1
FPr
TGAGTGGAAAAGCCTGACCTATG
SEQ ID NO: 1348




Probe
TGAAGTCATCAGCTTTGTGCCACCACC
SEQ ID NO: 1349




RPr
GGACTCCATCTCTTCTTGGTCAA
SEQ ID NO: 1350





Maspin
NM_002639.1
FPr
CAGATGGCCACTTTGAGAACATT
SEQ ID NO: 1351




Probe
AGCTGACAACAGTGTGAACGACCAGACC
SEQ ID NO: 1352




RPr
GGCAGCATTAACCACAAGGATT
SEQ ID NO: 1353





MAX
NM_002382.3
FPr
CAAACGGGCTCATCATAATGC
SEQ ID NO: 1354




Probe
TGATGTGGTCCCTACGTTTTCGTTCCA
SEQ ID NO: 1355




RPr
TCCCGCAAACTGTGAAAGCT
SEQ ID NO: 1356





MCM2
NM_004526.1
FPr
GACTTTTGCCCGCTACCTTTC
SEQ ID NO: 1357




Probe
ACAGCTCATTGTTGTCACGCCGGA
SEQ ID NO: 1358




RPr
GCCACTAACTGCTTCAGTATGAAGAG
SEQ ID NO: 1359





MCM3
NM_002388.2
FPr
GGAGAACAATCCCCTTGAGA
SEQ ID NO: 1360




Probe
TGGCCTTTCTGTCTACAAGGATCACCA
SEQ ID NO: 1361




RPr
ATCTCCTGGATGGTGATGGT
SEQ ID NO: 1362





MCM6
NM_005915.2
FPr
TGATGGTCCTATGTGTCACATTCA
SEQ ID NO: 1363




Probe
CAGGTTTCATACCAACACAGGCTTCAGC
SEQ ID NO: 1364





AC




RPr
TGGGACAGGAAACACACCAA
SEQ ID NO: 1365





MCP1
NM_002982.1
FPr
CGCTCAGCCAGATGCAATC
SEQ ID NO: 1366




Probe
TGCCCCAGTCACCTGCTGTTA
SEQ ID NO: 1367




RPr
GCACTGAGATCTTCCTATTGGTGAA
SEQ ID NO: 1368





MDK
NM_002391.2
FPr
GGAGCCGACTGCAAGTACA
SEQ ID NO: 1369




Probe
ATCACACGCACCCCAGTTCTCAAA
SEQ ID NO: 1370




RPr
GACTTTGGTGCCTGTGCC
SEQ ID NO: 1371





MDM2
NM_002392.1
FPr
CTACAGGGACGCCATCGAA
SEQ ID NO: 1372




Probe
CTTACACCAGCATCAAGATCCGG
SEQ ID NO: 1373




RPr
ATCCAACCAATCACCTGAATGTT
SEQ ID NO: 1374





MGAT5
NM_002410.2
FPr
GGAGTCGAAGGTGGACAATC
SEQ ID NO: 1375




Probe
AATGGCACCGGAACAAACTCAACC
SEQ ID NO: 1376




RPr
TGGGAACAGCTGTAGTGGAGT
SEQ ID NO: 1377





MGMT
NM_002412.1
FPr
GTGAAATGAAACGCACCACA
SEQ ID NO: 1378




Probe
CAGCCCTTTGGGGAAGCTGG
SEQ ID NO: 1379




RPr
GACCCTGCTCACAACCAGAC
SEQ ID NO: 1380





mGST1
NM_020300.2
FPr
ACGGATCTACCACACCATTGC
SEQ ID NO: 1381




Probe
TTTGACACCCCTTCCCCAGCCA
SEQ ID NO: 1382




RPr
TCCATATCCAACAAAAAAACTCAAAG
SEQ ID NO: 1383





MMP1
NM_002421.2
FPr
GGGAGATCATCGGGACAACTC
SEQ ID NO: 1384




Probe
AGCAAGATTTCCTCCAGGTCCATCAAAA
SEQ ID NO: 1385





GG




RPr
GGGCCTGGTTGAAAAGCAT
SEQ ID NO: 1386





MMP12
NM_002426.1
FPr
CCAACGCTTGCCAAATCCT
SEQ ID NO: 1387




Probe
AACCAGCTCTCTGTGACCCCAATT
SEQ ID NO: 1388




RPr
ACGGTAGTGACAGCATCAAAACTC
SEQ ID NO: 1389





MMP2
NM_004530.1
FPr
CCATGATGGAGAGGCAGACA
SEQ ID NO: 1390




Probe
CTGGGAGCATGGCGATGGATACCC
SEQ ID NO: 1391




RPr
GGAGTCCGTCCTTACCGTCAA
SEQ ID NO: 1392





MMP7
NM_002423.2
FPr
GGATGGTAGCAGTCTAGGGATTAACT
SEQ ID NO: 1393




Probe
CCTGTATGCTGCAACTCATGAACTTGGC
SEQ ID NO: 1394




RPr
GGAATGTCCCATACCCAAAGAA
SEQ ID NO: 1395





MMP9
NM_004994.1
FPr
GAGAACCAATCTCACCGACA
SEQ ID NO: 1396




Probe
ACAGGTATTCCTCTGCCAGCTGCC
SEQ ID NO: 1397




RPr
CACCCGAGTGTAACCATAGC
SEQ ID NO: 1398





MRP1
NM_004996.2
FPr
TCATGGTGCCCGTCAATG
SEQ ID NO: 1399




Probe
ACCTGATACGTCTTGGTCTTCATCGCCAT
SEQ ID NO: 1400




RPr
CGATTGTCTTTGCTCTTCATGTG
SEQ ID NO: 1401





MRP2
NM_000392.1
FPr
AGGGGATGACTTGGACACAT
SEQ ID NO: 1402




Probe
CTGCCATTCGACATGACTGCAATTT
SEQ ID NO: 1403




RPr
AAAACTGCATGGCTTTGTCA
SEQ ID NO: 1404





MRP3
NM_003786.2
FPr
TCATCCTGGCGATCTACTTCCT
SEQ ID NO: 1405




Probe
TCTGTCCTGGCTGGAGTCGCTTTCAT
SEQ ID NO: 1406




RPr
CCGTTGAGTGGAATCAGCAA
SEQ ID NO: 1407





MRP4
NM_005845.1
FPr
AGCGCCTGGAATCTACAACT
SEQ ID NO: 1408




Probe
CGGAGTCCAGTGTTTTCCCACTTG
SEQ ID NO: 1409




RPr
AGAGCCCCTGGAGAGAAGAT
SEQ ID NO: 1410





MRPL40
NM_003776.2
FPr
ACTTGCAGGCTGCTATCCTT
SEQ ID NO: 1411




Probe
TTCCTACTCTCAGGGGCAGCATGTT
SEQ ID NO: 1412




RPr
AGCAGACTTGAACCCTGGTC
SEQ ID NO: 1413





MSH2
NM_000251.1
FPr
GATGCAGAATTGAGGCAGAC
SEQ ID NO: 1414




Probe
CAAGAAGATTTACTTCGTCGATTCCCAGA
SEQ ID NO: 1415




RPr
TCTTGGCAAGTCGGTTAAGA
SEQ ID NO: 1416





MSH3
NM_002439.1
FPr
TGATTACCATCATGGCTCAGA
SEQ ID NO: 1417




Probe
TCCCAATTGTCGCTTCTTCTGCAG
SEQ ID NO: 1418




RPr
CTTGTGAAAATGCCATCCAC
SEQ ID NO: 1419





MSH6
NM_000179.1
FPr
TCTATTGGGGGATTGGTAGG
SEQ ID NO: 1420




Probe
CCGTTACCAGCTGGAAATTCCTGAGA
SEQ ID NO: 1421




RPr
CAAATTGCGAGTGGTGAAAT
SEQ ID NO: 1422





MT3
NM_005954.1
FPr
GTGTGAGAAGTGTGCCAAGG
SEQ ID NO: 1423




Probe
CTCTCCGCCTTTGCACACACAGT
SEQ ID NO: 1424




RPr
CTGCACTTCTCTGCTTCTGC
SEQ ID NO: 1425





MTA1
NM_004689.2
FPr
CCGCCCTCACCTGAAGAGA
SEQ ID NO: 1426




Probe
CCCAGTGTCCGCCAAGGAGCG
SEQ ID NO: 1427




RPr
GGAATAAGTTAGCCGCGCTTCT
SEQ ID NO: 1428





MUC1
NM_002456.1
FPr
GGCCAGGATCTGTGGTGGTA
SEQ ID NO: 1429




Probe
CTCTGGCCTTCCGAGAAGGTACC
SEQ ID NO: 1430




RPr
CTCCACGTCGTGGACATTGA
SEQ ID NO: 1431





MUC2
NM_002457.1
FPr
CTATGAGCCATGTGGGAACC
SEQ ID NO: 1432




Probe
AGCTTCGAGACCTGCAGGACCATC
SEQ ID NO: 1433




RPr
ATGTTGGAGTGGATGCCG
SEQ ID NO: 1434





MUC5B
XM_039877.11
FPr
TGCCCTTGCACTGTCCTAA
SEQ ID NO: 1435




Probe
TCAGCCATCCTGCACACCTACACC
SEQ ID NO: 1436




RPr
CAGCCACACTCATCCACG
SEQ ID NO: 1437





MUTYH
NM_012222.1
FPr
GTACGACCAAGAGAAACGGG
SEQ ID NO: 1438




Probe
TCTGCCCGTCTTCTCCATGGTAGG
SEQ ID NO: 1439




RPr
CCTGTCCAGGTCCATCTCA
SEQ ID NO: 1440





MVP
NM_017458.1
FPr
ACGAGAACGAGGGCATCTATGT
SEQ ID NO: 1441




Probe
CGCACCTTTCCGGTCTTGACATCCT
SEQ ID NO: 1442




RPr
GCATGTAGGTGCTTCCAATCAC
SEQ ID NO: 1443





MX1
NM_002462.2
FPr
GAAGGAATGGGAATCAGTCATGA
SEQ ID NO: 1444




Probe
TCACCCTGGAGATCAGCTCCCGA
SEQ ID NO: 1445




RPr
GTCTATTAGAGTCAGATCCGGGACAT
SEQ ID NO: 1446





MXD4
NM_006454.2
FPr
AGAAACTGGAGGAGCAGGAC
SEQ ID NO: 1447




Probe
TGCAGCTGCTCCTTGATGCTCAGT
SEQ ID NO: 1448




RPr
CTTCAGGAAACGATGCTCCT
SEQ ID NO: 1449





MYBL2
NM_002466.1
FPr
GCCGAGATCGCCAAGATG
SEQ ID NO: 1450




Probe
CAGCATTGTCTGTCCTCCCTGGCA
SEQ ID NO: 1451




RPr
CTTTTGATGGTAGAGTTCCAGTGATTC
SEQ ID NO: 1452





MYH11
NM_002474.1
FPr
CGGTACTTCTCAGGGCTAATATATACG
SEQ ID NO: 1453




Probe
CTCTTCTGCGTGGTGGTCAACCCCTA
SEQ ID NO: 1454




RPr
CCGAGTAGATGGGCAGGTGTT
SEQ ID NO: 1455





MYLK
NM_053025.1
FPr
TGACGGAGCGTGAGTGCAT
SEQ ID NO: 1456




Probe
CCCTCCGAGATCTGCCGCATGTACT
SEQ ID NO: 1457




RPr
ATGCCCTGCTTGTGGATGTAC
SEQ ID NO: 1458





NAT2
NM_000015.1
FPr
TAACTGACATTCTTGAGCACCAGAT
SEQ ID NO: 1459




Probe
CGGGCTGTTCCCTTTGAGAACCTTAACA
SEQ ID NO: 1460




RPr
ATGGCTTGCCCACAATGC
SEQ ID NO: 1461





NAV2
NM_182964.3
FPr
CTCTCCCAGCACAGCTTGA
SEQ ID NO: 1462




Probe
CCTCACTGAGTCAACCAGCCTGGA
SEQ ID NO: 1463




RPr
CACCAGTGTCATCCAGCAAC
SEQ ID NO: 1464





NCAM1
NM_000615.1
FPr
TAGTTCCCAGCTGACCATCA
SEQ ID NO: 1465




Probe
CTCAGCCTCGTCGTTCTTATCCACC
SEQ ID NO: 1466




RPr
CAGCCTTGTTCTCAGCAATG
SEQ ID NO: 1467





NDE1
NM_017668.1
FPr
CTACTGCGGAAAGTCGGG
SEQ ID NO: 1468




Probe
CTGGAGTCCAAACTCGCTTCCTGC
SEQ ID NO: 1469




RPr
GGACTGATCGTACACGAGGTT
SEQ ID NO: 1470





NDRG1
NM_006096.2
FPr
AGGGCAACATTCCACAGC
SEQ ID NO: 1471




Probe
CTGCAAGGACACTCATCACAGCCA
SEQ ID NO: 1472




RPr
CAGTGCTCCTACTCCGGC
SEQ ID NO: 1473





NDUFS3
NM_004551.1
FPr
TATCCATCCTGATGGCGTC
SEQ ID NO: 1474




Probe
CCCAGTGCTGACTTTCCTCAGGGA
SEQ ID NO: 1475




RPr
TTGAACTGTGCATTGGTGTG
SEQ ID NO: 1476





NEDD8
NM_006156.1
FPr
TGCTGGCTACTGGGTGTTAGT
SEQ ID NO: 1477




Probe
TGCAGTCCTGTGTGCTTCCCTCTC
SEQ ID NO: 1478




RPr
GACAACCAGGGACACAGTCA
SEQ ID NO: 1479





NEK2
NM_002497.1
FPr
GTGAGGCAGCGCGACTCT
SEQ ID NO: 1480




Probe
TGCCTTCCCGGGCTGAGGACT
SEQ ID NO: 1481




RPr
TGCCAATGGTGTACAACACTTCA
SEQ ID NO: 1482





NF2
NM_000268.2
FPr
ACTCCAGAGCTGACCTCCAC
SEQ ID NO: 1483




Probe
CTACAATGACTTCCCAGGCTGGGC
SEQ ID NO: 1484




RPr
TCAGGGCTTCAGTGTCTCAC
SEQ ID NO: 1485





NFKBp50
NM_003998.1
FPr
CAGACCAAGGAGATGGACCT
SEQ ID NO: 1486




Probe
AAGCTGTAAACATGAGCCGCACCA
SEQ ID NO: 1487




RPr
AGCTGCCAGTGCTATCCG
SEQ ID NO: 1488





NFKBp65
NM_021975.1
FPr
CTGCCGGGATGGCTTCTAT
SEQ ID NO: 1489




Probe
CTGAGCTCTGCCCGGACCGCT
SEQ ID NO: 1490




RPr
CCAGGTTCTGGAAACTGTGGAT
SEQ ID NO: 1491





NISCH
NM_007184.1
FPr
CCAAGGAATCATGTTCGTTCAG
SEQ ID NO: 1492




Probe
TGGCCAGCAGCCTCTCGTCCAC
SEQ ID NO: 1493




RPr
TGGTGCTCGGGAGTCAGACT
SEQ ID NO: 1494





Nkd-1
NM_033119.3
FPr
GAGAGAGTGAGCGAACCCTG
SEQ ID NO: 1495




Probe
CCAGGCTCCAAGAAGCAGCTGAAG
SEQ ID NO: 1496




RPr
CGTCGCACTGGAGCTCTT
SEQ ID NO: 1497





NMB
NM_021077.1
FPr
GGCTGCTGGTACAAATACTGC
SEQ ID NO: 1498




Probe
TGTCTGCCCCTATTATTGGTGTCATTTCT
SEQ ID NO: 1499




RPr
CAATCTAAGCCACGCTGTTG
SEQ ID NO: 1500





NMBR
NM_002511.1
FPr
TGATCCATCTCTAGGCCACA
SEQ ID NO: 1501




Probe
TTGTCACCTTAGTTGCCCGGGTTC
SEQ ID NO: 1502




RPr
GAGCAAATGGGTTGACACAA
SEQ ID NO: 1503





NME1
NM_000269.1
FPr
CCAACCCTGCAGACTCCAA
SEQ ID NO: 1504




Probe
CCTGGGACCATCCGTGGAGACTTCT
SEQ ID NO: 1505




RPr
ATGTATAATGTTCCTGCCAACTTGTATG
SEQ ID NO: 1506





NOS3
NM_000603.2
FPr
ATCTCCGCCTCGCTCATG
SEQ ID NO: 1507




Probe
TTCACTCGCTTCGCCATCACCG
SEQ ID NO: 1508




RPr
TCGGAGCCATACAGGATTGTC
SEQ ID NO: 1509





NOTCH1
NM_017617.2
FPr
CGGGTCCACCAGTTTGAATG
SEQ ID NO: 1510




Probe
CCGCTCTGCAGCCGGGACA
SEQ ID NO: 1511




RPr
GTTGTATTGGTTCGGCACCAT
SEQ ID NO: 1512





NOTCH2
NM_024408.2
FPr
CACTTCCCTGCTGGGATTAT
SEQ ID NO: 1513




Probe
CCGTGTTGCACAGCTCATCACACT
SEQ ID NO: 1514




RPr
AGTTGTCAAACAGGCACTCG
SEQ ID NO: 1515





NPM1
NM_002520.2
FPr
AATGTTGTCCAGGTTCTATTGC
SEQ ID NO: 1516




Probe
AACAGGCATTTTGGACAACACATTCTTG
SEQ ID NO: 1517




RPr
CAAGCAAAGGGTGGAGTTC
SEQ ID NO: 1518





NR4A1
NM_002135.2
FPr
CACAGCTTGCTTGTCGATGTC
SEQ ID NO: 1519




Probe
CCTTCGCCTGCCTCTCTGCCC
SEQ ID NO: 1520




RPr
ATGCCGGTCGGTGATGAG
SEQ ID NO: 1521





NRG1
NM_013957.1
FPr
CGAGACTCTCCTCATAGTGAAAGGTAT
SEQ ID NO: 1522




Probe
ATGACCACCCCGGCTCGTATGTCA
SEQ ID NO: 1523




RPr
CTTGGCGTGTGGAAATCTACAG
SEQ ID NO: 1524





NRP1
NM_003873.1
FPr
CAGCTCTCTCCACGCGATTC
SEQ ID NO: 1525




Probe
CAGGATCTACCCCGAGAGAGCCACTCAT
SEQ ID NO: 1526




RPr
CCCAGCAGCTCCATTCTGA
SEQ ID NO: 1527





NRP2
NM_003872.1
FPr
CTACAGCCTAAACGGCAAGG
SEQ ID NO: 1528




Probe
AGGACCCCAGGACCCAGCAG
SEQ ID NO: 1529




RPr
GTTCCCTTCGAACAGCTTTG
SEQ ID NO: 1530





NTN1
NM_004822.1
FPr
AGAAGGACTATGCCGTCCAG
SEQ ID NO: 1531




Probe
ATCCACATCCTGAAGGCGGACAAG
SEQ ID NO: 1532




RPr
CCGTGAACTTCCACCAGTC
SEQ ID NO: 1533





NUFIP1
NM_012345.1
FPr
GCTTCCACATCGTGGTATTG
SEQ ID NO: 1534




Probe
CTTCTGATAGGTTTCCTCGGCATCAGA
SEQ ID NO: 1535




RPr
AACTGCAGGGTTGAAGGACT
SEQ ID NO: 1536





ODC1
NM_002539.1
FPr
AGAGATCACCGGCGTAATCAA
SEQ ID NO: 1537




Probe
CCAGCGTTGGACAAATACTTTCCGTCA
SEQ ID NO: 1538




RPr
CGGGCTCAGCTATGATTCTCA
SEQ ID NO: 1539





OPN,
NM_000582.1
FPr
CAACCGAAGTTTTCACTCCAGTT
SEQ ID NO: 1540


osteopontin




Probe
TCCCCACAGTAGACACATATGATGGCCG
SEQ ID NO: 1541




RPr
CCTCAGTCCATAAACCACACTATCA
SEQ ID NO: 1542





ORC1L
NM_004153.2
FPr
TCCTTGACCATACCGGAGG
SEQ ID NO: 1543




Probe
TGCATGTACATCTCCGGTGTCCCT
SEQ ID NO: 1544




RPr
CAGTGGCAGTCTTCCCTGTC
SEQ ID NO: 1545





OSM
NM_020530.3
FPr
GTTTCTGAAGGGGAGGTCAC
SEQ ID NO: 1546




Probe
CTGAGCTGGCCTCCTATGCCTCAT
SEQ ID NO: 1547




RPr
AGGTGTCTGGTTTGGGACA
SEQ ID NO: 1548





OSMR
NM_003999.1
FPr
GCTCATCATGGTCATGTGCT
SEQ ID NO: 1549




Probe
CAGGTCTCCTTGATCCACTGACTTTTCA
SEQ ID NO: 1550




RPr
TGTAAGGGTCAGGGATGTCA
SEQ ID NO: 1551





P14ARF
S78535.1
FPr
CCCTCGTGCTGATGCTACT
SEQ ID NO: 1552




Probe
CTGCCCTAGACGCTGGCTCCTC
SEQ ID NO: 1553




RPr
CATCATGACCTGGTCTTCTAGG
SEQ ID NO: 1554





p16-INK4
L27211.1
FPr
GCGGAAGGTCCCTCAGACA
SEQ ID NO: 1555




Probe
CTCAGAGCCTCTCTGGTTCTTTCAATCGG
SEQ ID NO: 1556




RPr
TGATGATCTAAGTTTCCCGAGGTT
SEQ ID NO: 1557





p21
NM_000389.1
FPr
TGGAGACTCTCAGGGTCGAAA
SEQ ID NO: 1558




Probe
CGGCGGCAGACCAGCATGAC
SEQ ID NO: 1559




RPr
GGCGTTTGGAGTGGTAGAAATC
SEQ ID NO: 1560





p27
NM_004064.1
FPr
CGGTGGACCACGAAGAGTTAA
SEQ ID NO: 1561




Probe
CCGGGACTTGGAGAAGCACTGCA
SEQ ID NO: 1562




RPr
GGCTCGCCTCTTCCATGTC
SEQ ID NO: 1563





P53
NM_000546.2
FPr
CTTTGAACCCTTGCTTGCAA
SEQ ID NO: 1564




Probe
AAGTCCTGGGTGCTTCTGACGCACA
SEQ ID NO: 1565




RPr
CCCGGGACAAAGCAAATG
SEQ ID NO: 1566





p53R2
AB036063.1
FPr
CCCAGCTAGTGTTCCTCAGA
SEQ ID NO: 1567




Probe
TCGGCCAGCTTTTTCCAATCTTTG
SEQ ID NO: 1568




RPr
CCGTAAGCCCTTCCTCTATG
SEQ ID NO: 1569





PADI4
NM_012387.1
FPr
AGCAGTGGCTTGCTTTCTTC
SEQ ID NO: 1570




Probe
CCTGTGATGTCCCAGTTTCCCACTC
SEQ ID NO: 1571




RPr
TGCTAGGACCATGTTGGGAT
SEQ ID NO: 1572





PAI1
NM_000602.1
FPr
CCGCAACGTGGTTTTCTCA
SEQ ID NO: 1573




Probe
CTCGGTGTTGGCCATGCTCCAG
SEQ ID NO: 1574




RPr
TGCTGGGTTTCTCCTCCTGTT
SEQ ID NO: 1575





Pak1
NM_002576.3
FPr
GAGCTGTGGGTTGTTATGGA
SEQ ID NO: 1576




Probe
ACATCTGTCAAGGAGCCTCCAGCC
SEQ ID NO: 1577




RPr
CCATGCAAGTTTCTGTCACC
SEQ ID NO: 1578





PARC
NM_015089.1
FPr
GGAGCTGACCTGCTTCCTAC
SEQ ID NO: 1579




Probe
TCCTTATGCATCGAGGCCAGGC
SEQ ID NO: 1580




RPr
AGCAGAGCACCACAGCATAG
SEQ ID NO: 1581





PCAF
NM_003884.3
FPr
AGGTGGCTGTGTTACTGCAA
SEQ ID NO: 1582




Probe
TGCCACAGTTCTGCGACAGTCTACC
SEQ ID NO: 1583




RPr
CACCTGTGTGGTTTCGTACC
SEQ ID NO: 1584





PCNA
NM_002592.1
FPr
GAAGGTGTTGGAGGCACTCAAG
SEQ ID NO: 1585




Probe
ATCCCAGCAGGCCTCGTTGATGAG
SEQ ID NO: 1586




RPr
GGTTTACACCGCTGGAGCTAA
SEQ ID NO: 1587





PDGFA
NM_002607.2
FPr
TTGTTGGTGTGCCCTGGTG
SEQ ID NO: 1588




Probe
TGGTGGCGGTCACTCCCTCTGC
SEQ ID NO: 1589




RPr
TGGGTTCTGTCCAAACACTGG
SEQ ID NO: 1590





PDGFB
NM_002608.1
FPr
ACTGAAGGAGACCCTTGGAG
SEQ ID NO: 1591




Probe
TCTCCTGCCGATGCCCCTAGG
SEQ ID NO: 1592




RPr
TAAATAACCCTGCCCACACA
SEQ ID NO: 1593





PDGFC
NM_016205.1
FPr
AGTTACTAAAAAATACCACGAGGTCCTT
SEQ ID NO: 1594




Probe
CCCTGACACCGGTCTTTGGTCTCAACT
SEQ ID NO: 1595




RPr
GTCGGTGAGTGATTTGTGCAA
SEQ ID NO: 1596





PDGFD
NM_025208.2
FPr
TATCGAGGCAGGTCATACCA
SEQ ID NO: 1597




Probe
TCCAGGTCAACTTTTGACTTCCGGT
SEQ ID NO: 1598




RPr
TAACGCTTGGCATCATCATT
SEQ ID NO: 1599





PDGFRa
NM_006206.2
FPr
GGGAGTTTCCAAGAGATGGA
SEQ ID NO: 1600




Probe
CCCAAGACCCGACCAAGCACTAG
SEQ ID NO: 1601




RPr
CTTCAACCACCTTCCCAAAC
SEQ ID NO: 1602





PDGFRb
NM_002609.2
FPr
CCAGCTCTCCTTCCAGCTAC
SEQ ID NO: 1603




Probe
ATCAATGTCCCTGTCCGAGTGCTG
SEQ ID NO: 1604




RPr
GGGTGGCTCTCACTTAGCTC
SEQ ID NO: 1605





PFN1
NM_005022.2
FPr
GGAAAACGTTCGTCAACATC
SEQ ID NO: 1606




Probe
CAACCAGGACACCCACCTCAGCT
SEQ ID NO: 1607




RPr
AAAACTTGACCGGTCTTTGC
SEQ ID NO: 1608





PFN2
NM_053024.1
FPr
TCTATACGTCGATGGTGACTGC
SEQ ID NO: 1609




Probe
CTCCCCACCTTGACTCTTTGTCCG
SEQ ID NO: 1610




RPr
GCCGACAGCCACATTGTAT
SEQ ID NO: 1611





PGK1
NM_000291.1
FPr
AGAGCCAGTTGCTGTAGAACTCAA
SEQ ID NO: 1612




Probe
TCTCTGCTGGGCAAGGATGTTCTGTTC
SEQ ID NO: 1613




RPr
CTGGGCCTACACAGTCCTTCA
SEQ ID NO: 1614





PI3K
NM_002646.2
FPr
TGCTACCTGGACAGCCCG
SEQ ID NO: 1615




Probe
TCCTCCTGAAACGAGCTGTGTCTGACTT
SEQ ID NO: 1616




RPr
AGGCCGTCCTTCAGTAACCA
SEQ ID NO: 1617





PI3KC2A
NM_002645.1
FPr
ATACCAATCACCGCACAAACC
SEQ ID NO: 1618




Probe
TGCGCTGTGACTGGACTTAACAAATAGC
SEQ ID NO: 1619





CT




RPr
CACACTAGCATTTTCTCCGCATA
SEQ ID NO: 1620





PIK3CA
NM_006218.1
FPr
GTGATTGAAGAGCATGCCAA
SEQ ID NO: 1621




Probe
TCCTGCTTCTCGGGATACAGACCA
SEQ ID NO: 1622




RPr
GTCCTGCGTGGGAATAGC
SEQ ID NO: 1623





PIM1
NM_002648.2
FPr
CTGCTCAAGGACACCGTCTA
SEQ ID NO: 1624




Probe
TACACTCGGGTCCCATCGAAGTCC
SEQ ID NO: 1625




RPr
GGATCCACTCTGGAGGGC
SEQ ID NO: 1626





Pin1
NM_006221.1
FPr
GATCAACGGCTACATCCAGA
SEQ ID NO: 1627




Probe
TCAAAGTCCTCCTCTCCCGACTTGA
SEQ ID NO: 1628




RPr
TGAACTGTGAGGCCAGAGAC
SEQ ID NO: 1629





PKD1
NM_000296.2
FPr
CAGCACCAGCGATTACGAC
SEQ ID NO: 1630




Probe
AGCCATTGTGAGGACTCTCCCAGC
SEQ ID NO: 1631




RPr
CTGAATAGGCCCACGTCC
SEQ ID NO: 1632





PKR2
NM_002654.3
FPr
CCGCCTGGACATTGATTCAC
SEQ ID NO: 1633




Probe
ACCCATCACAGCCCGGAACACTG
SEQ ID NO: 1634




RPr
CTGGGCCAATGGTACAGATGA
SEQ ID NO: 1635





PLA2G2A
NM_000300.2
FPr
GCATCCCTCACCCATCCTA
SEQ ID NO: 1636




Probe
AGGCCAGGCAGGAGCCCTTCTATA
SEQ ID NO: 1637




RPr
GCTGGAAATCTGCTGGATGT
SEQ ID NO: 1638





PLAUR
NM_002659.1
FPr
CCCATGGATGCTCCTCTGAA
SEQ ID NO: 1639




Probe
CATTGACTGCCGAGGCCCCATG
SEQ ID NO: 1640




RPr
CCGGTGGCTACCAGACATTG
SEQ ID NO: 1641





PLK
NM_005030.2
FPr
AATGAATACAGTATTCCCAAGCACAT
SEQ ID NO: 1642




Probe
AACCCCGTGGCCGCCTCC
SEQ ID NO: 1643




RPr
TGTCTGAAGCATCTTCTGGATGA
SEQ ID NO: 1644





PLK3
NM_004073.2
FPr
TGAAGGAGACGTACCGCTG
SEQ ID NO: 1645




Probe
CAAGCAGGTTCACTACACGCTGCC
SEQ ID NO: 1646




RPr
CAGGCAGTGAGAGGCTGG
SEQ ID NO: 1647





PLOD2
NM_000935.2
FPr
CAGGGAGGTGGTTGCAAAT
SEQ ID NO: 1648




Probe
TCCAGCCTTTTCGTGGTGACTCAA
SEQ ID NO: 1649




RPr
TCTCCCAGGATGCATGAAG
SEQ ID NO: 1650





PMS1
NM_000534.2
FPr
CTTACGGTTTTCGTGGAGAAG
SEQ ID NO: 1651




Probe
CCTCAGCTATACAACAAATTGACCCCAAG
SEQ ID NO: 1652




RPr
AGCAGCCGTTCTTGTTGTAA
SEQ ID NO: 1653





PMS2
NM_000535.2
FPr
GATGTGGACTGCCATTCAAA
SEQ ID NO: 1654




Probe
TCGAAATTTACATCCGGTATCTTCCTGG
SEQ ID NO: 1655




RPr
TGCGAGATTAGTTGGCTGAG
SEQ ID NO: 1656





PPARG
NM_005037.3
FPr
TGACTTTATGGAGCCCAAGTT
SEQ ID NO: 1657




Probe
TTCCAGTGCATTGAACTTCACAGCA
SEQ ID NO: 1658




RPr
GCCAAGTCGCTGTCATCTAA
SEQ ID NO: 1659





PPID
NM_005038.1
FPr
TCCTCATTTGGATGGGAAAC
SEQ ID NO: 1660




Probe
TTCCTTTAATTACTTGGCCAAACACCACA
SEQ ID NO: 1661




RPr
CCAATATCCTTGCCACTCCTA
SEQ ID NO: 1662





PPM1D
NM_003620.1
FPr
GCCATCCGCAAAGGCTTT
SEQ ID NO: 1663




Probe
TCGCTTGTCACCTTGCCATGTGG
SEQ ID NO: 1664




RPr
GGCCATTCCGCCAGTTTC
SEQ ID NO: 1665





PPP2R4
NM_178001.1
FPr
GGCTCAGAGCATAAGGCTTC
SEQ ID NO: 1666




Probe
TTGGTCACTTCTCCCAACTTGGGC
SEQ ID NO: 1667




RPr
ACGGGAACTCAGAAAACTGG
SEQ ID NO: 1668





PR
NM_000926.2
FPr
GCATCAGGCTGTCATTATGG
SEQ ID NO: 1669




Probe
TGTCCTTACCTGTGGGAGCTGTAAGGTC
SEQ ID NO: 1670




RPr
AGTAGTTGTGCTGCCCTTCC
SEQ ID NO: 1671





PRDX2
NM_005809.4
FPr
GGTGTCCTTCGCCAGATCAC
SEQ ID NO: 1672




Probe
TTAATGATTTGCCTGTGGGACGCTCC
SEQ ID NO: 1673




RPr
CAGCCGCAGAGCCTCATC
SEQ ID NO: 1674





PRDX3
NM_006793.2
FPr
TGACCCCAATGGAGTCATCA
SEQ ID NO: 1675




Probe
CATTTGAGCGTCAACGATCTCCCAGTG
SEQ ID NO: 1676




RPr
CCAAGCGGAGGGTTTCTTC
SEQ ID NO: 1677





PRDX4
NM_006406.1
FPr
TTACCCATTTGGCCTGGATTAA
SEQ ID NO: 1678




Probe
CCAAGTCCTCCTTGTCTTCGAGGGGT
SEQ ID NO: 1679




RPr
CTGAAAGAAGTGGAATCCTTATTGG
SEQ ID NO: 1680





PRDX6
NM_004905.2
FPr
CTGTGAGCCAGAGGATGTCA
SEQ ID NO: 1681




Probe
CTGCCAATTGTGTTTTCCTGCAGC
SEQ ID NO: 1682




RPr
TGTGATGACACCAGGATGTG
SEQ ID NO: 1683





PRKCA
NM_002737.1
FPr
CAAGCAATGCGTCATCAATGT
SEQ ID NO: 1684




Probe
CAGCCTCTGCGGAATGGATCACACT
SEQ ID NO: 1685




RPr
GTAAATCCGCCCCCTCTTCT
SEQ ID NO: 1686





PRKCB1
NM_002738.5
FPr
GACCCAGCTCCACTCCTG
SEQ ID NO: 1687




Probe
CCAGACCATGGACCGCCTGTACTT
SEQ ID NO: 1688




RPr
CCCATTCACGTACTCCATCA
SEQ ID NO: 1689





PRKCD
NM_006254.1
FPr
CTGACACTTGCCGCAGAGAA
SEQ ID NO: 1690




Probe
CCCTTTCTCACCCACCTCATCTGCAC
SEQ ID NO: 1691




RPr
AGGTGGTCCTTGGTCTGGAA
SEQ ID NO: 1692





PRKR
NM_002759.1
FPr
GCGATACATGAGCCCAGAACA
SEQ ID NO: 1693




Probe
AGGTCCACTTCCTTTCCATAGTCTTGCGA
SEQ ID NO: 1694




RPr
TCAGCAAGAATTAGCCCCAAAG
SEQ ID NO: 1695





pS2
NM_003225.1
FPr
GCCCTCCCAGTGTGCAAAT
SEQ ID NO: 1696




Probe
TGCTGTTTCGACGACACCGTTCG
SEQ ID NO: 1697




RPr
CGTCGATGGTATTAGGATAGAAGCA
SEQ ID NO: 1698





PTCH
NM_000264.2
FPr
CCACGACAAAGCCGACTAC
SEQ ID NO: 1699




Probe
CCTGAAACAAGGCTGAGAATCCCG
SEQ ID NO: 1700




RPr
TACTCGATGGGCTCTGCTG
SEQ ID NO: 1701





PTEN
NM_000314.1
FPr
TGGCTAAGTGAAGATGACAATCATG
SEQ ID NO: 1702




Probe
CCTTTCCAGCTTTACAGTGAATTGCTGCA
SEQ ID NO: 1703




RPr
TGCACATATCATTACACCAGTTCGT
SEQ ID NO: 1704





PTGER3
NM_000957.2
FPr
TAACTGGGGCAACCTTTTCT
SEQ ID NO: 1705




Probe
CCTTTGCCTTCCTGGGGCTCTT
SEQ ID NO: 1706




RPr
TTGCAGGAAAAGGTGACTGT
SEQ ID NO: 1707





PTHLH
NM_002820.1
FPr
AGTGACTGGGAGTGGGCTAGAA
SEQ ID NO: 1708




Probe
TGACACCTCCACAACGTCGCTGGA
SEQ ID NO: 1709




RPr
AAGCCTGTTACCGTGAATCGA
SEQ ID NO: 1710





PTHR1
NM_000316.1
FPr
CGAGGTACAAGCTGAGATCAAGAA
SEQ ID NO: 1711




Probe
CCAGTGCCAGTGTCCAGCGGCT
SEQ ID NO: 1712




RPr
GCGTGCCTTTCGCTTGAA
SEQ ID NO: 1713





PTK2
NM_005607.3
FPr
GACCGGTCGAATGATAAGGT
SEQ ID NO: 1714




Probe
ACCAGGCCCGTCACATTCTCGTAC
SEQ ID NO: 1715




RPr
CTGGACATCTCGATGACAGC
SEQ ID NO: 1716





PTK2B
NM_004103.3
FPr
CAAGCCCAGCCGACCTAAG
SEQ ID NO: 1717




Probe
CTCCGCAAACCAACCTCCTGGCT
SEQ ID NO: 1718




RPr
GAACCTGGAACTGCAGCTTTG
SEQ ID NO: 1719





PTP4A3
NM_007079.2
FPr
CCTGTTCTCGGCACCTTAAA
SEQ ID NO: 1720




Probe
ACCTGACTGCCCCGGGGTCTAATA
SEQ ID NO: 1721




RPr
TATTGCCTTCGGGTGTCC
SEQ ID NO: 1722





PTP4A3 v2
NM_032611.1
FPr
AATATTTGTGCGGGGTATGG
SEQ ID NO: 1723




Probe
CCAAGAGAAACGAGATTTAAAAACCCA
SEQ ID NO: 1724





CC




RPr
AACGAGATCCCTGTGCTTGT
SEQ ID NO: 1725





PTPD1
NM_007039.2
FPr
CGCTTGCCTAACTCATACTTTCC
SEQ ID NO: 1726




Probe
TCCACGCAGCGTGGCACTG
SEQ ID NO: 1727




RPr
CCATTCAGACTGCGCCACTT
SEQ ID NO: 1728





PTPN1
NM_002827.2
FPr
AATGAGGAAGTTTCGGATGG
SEQ ID NO: 1729




Probe
CTGATCCAGACAGCCGACCAGCT
SEQ ID NO: 1730




RPr
CTTCGATCACAGCCAGGTAG
SEQ ID NO: 1731





PTPRF
NM_002840.2
FPr
TGTTTTAGCTGAGGGACGTG
SEQ ID NO: 1732




Probe
CCGACGTCCCCAAACCTAGCTAGG
SEQ ID NO: 1733




RPr
TACCAACCCTGGAATGTTGA
SEQ ID NO: 1734





PTPRJ
NM_002843.2
FPr
AACTTCCGGTACCTCGTTCGT
SEQ ID NO: 1735




Probe
ACTACATGAAGCAGAGTCCTCCCGAATCG
SEQ ID NO: 1736




RPr
AGCACTGCAATGCACCAGAA
SEQ ID NO: 1737





PTPRO
NM_030667.1
FPr
CATGGCCTGATCATGGTGT
SEQ ID NO: 1738




Probe
CCCACAGCAAATGCTGCAGAAAGT
SEQ ID NO: 1739




RPr
CCATGTGTACAAACTGCAGGA
SEQ ID NO: 1740





PTTG1
NM_004219.2
FPr
GGCTACTCTGATCTATGTTGATAAGGAA
SEQ ID NO: 1741




Probe
CACACGGGTGCCTGGTTCTCCA
SEQ ID NO: 1742




RPr
GCTTCAGCCCATCCTTAGCA
SEQ ID NO: 1743





RAB32
NM_006834.2
FPr
CCTGCAGCTGTGGGACAT
SEQ ID NO: 1744




Probe
CGATTTGGCAACATGACCCGAGTA
SEQ ID NO: 1745




RPr
AGCACCAACAGCTTCCTTG
SEQ ID NO: 1746





RAB6C
NM_032144.1
FPr
GCGACAGCTCCTCTAGTTCCA
SEQ ID NO: 1747




Probe
TTCCCGAAGTCTCCGCCCG
SEQ ID NO: 1748




RPr
GGAACACCAGCTTGAATTTCCT
SEQ ID NO: 1749





RAC1
NM_006908.3
FPr
TGTTGTAAATGTCTCAGCCCC
SEQ ID NO: 1750




Probe
CGTTCTTGGTCCTGTCCCTTGGA
SEQ ID NO: 1751




RPr
TTGAGCAAAGCGTACAAAGG
SEQ ID NO: 1752





RAD51C
NM_058216.1
FPr
GAACTTCTTGAGCAGGAGCATACC
SEQ ID NO: 1753




Probe
AGGGCTTCATAATCACCTTCTGTTC
SEQ ID NO: 1754




RPr
TCCACCCCCAAGAATATCATCTAGT
SEQ ID NO: 1755





RAD54L
NM_003579.2
FPr
AGCTAGCCTCAGTGACACACATG
SEQ ID NO: 1756




Probe
ACACAACGTCGGCAGTGCAACCTG
SEQ ID NO: 1757




RPr
CCGGATCTGACGGCTGTT
SEQ ID NO: 1758





RAF1
NM_002880.1
FPr
CGTCGTATGCGAGAGTCTGT
SEQ ID NO: 1759




Probe
TCCAGGATGCCTGTTAGTTCTCAGCA
SEQ ID NO: 1760




RPr
TGAAGGCGTGAGGTGTAGAA
SEQ ID NO: 1761





RALBP1
NM_006788.2
FPr
GGTGTCAGATATAAATGTGCAAATGC
SEQ ID NO: 1762




Probe
TGCTGTCCTGTCGGTCTCAGTACGTTCA
SEQ ID NO: 1763




RPr
TTCGATATTGCCAGCAGCTATAAA
SEQ ID NO: 1764





RANBP2
NM_006267.3
FPr
TCCTTCAGCTTTCACACTGG
SEQ ID NO: 1765




Probe
TCCAGAAGAGTCATGCAACTTCATTTCTG
SEQ ID NO: 1766




RPr
AAATCCTGTTCCCACCTGAC
SEQ ID NO: 1767





ranBP7
NM_006391.1
FPr
AACATGATTATCCAAGCCGC
SEQ ID NO: 1768




Probe
AAGCCAATTTTGTCCACAATGGCA
SEQ ID NO: 1769




RPr
GCCAACAAGCACTGTTATCG
SEQ ID NO: 1770





RANBP9
NM_005493.2
FPr
CAAGTCAGTTGAGACGCCAGTT
SEQ ID NO: 1771




Probe
TTCTATGGCGGCCTGACTTCCTCCA
SEQ ID NO: 1772




RPr
TGCAGCTCTCGTCCAAAGTG
SEQ ID NO: 1773





RAP1GDS1
NM_021159.3
FPr
TGTGGATGCTGGATTGATTT
SEQ ID NO: 1774




Probe
CCACTGGTGCAGCTGCTAAATAGCA
SEQ ID NO: 1775




RPr
AAGCAGCACTTCCTGGTCTT
SEQ ID NO: 1776





RARA
NM_000964.1
FPr
AGTCTGTGAGAAACGACCGAAAC
SEQ ID NO: 1777




Probe
TCGGGCTTGGGCACCTCCTTCTT
SEQ ID NO: 1778




RPr
CGGCGTCAGCGTGTAGCT
SEQ ID NO: 1779





RARB
NM_016152.2
FPr
TGCCTGGACATCCTGATTCT
SEQ ID NO: 1780




Probe
TGCACCAGGTATACCCCAGAACAAGA
SEQ ID NO: 1781




RPr
AAGGCCGTCTGAGAAAGTCA
SEQ ID NO: 1782





RASSF1
NM_007182.3
FPr
AGTGGGAGACACCTGACCTT
SEQ ID NO: 1783




Probe
TTGATCTTCTGCTCAATCTCAGCTTGAGA
SEQ ID NO: 1784




RPr
TGATCTGGGCATTGTACTCC
SEQ ID NO: 1785





RBM5
NM_005778.1
FPr
CGAGAGGGAGAGCAAGACCAT
SEQ ID NO: 1786




Probe
CTGCGCGGCCTTCCCATCA
SEQ ID NO: 1787




RPr
TCTCGAATATCGCTCTCTGTGATG
SEQ ID NO: 1788





RBX1
NM_014248.2
FPr
GGAACCACATTATGGATCTTTGC
SEQ ID NO: 1789




Probe
TAGAATGTCAAGCTAACCAGGCGTCCGC
SEQ ID NO: 1790




RPr
CATGCGACAGTACACTCTTCTGAA
SEQ ID NO: 1791





RCC1
NM_001269.2
FPr
GGGCTGGGTGAGAATGTG
SEQ ID NO: 1792




Probe
ATACCAGGGCCGGCTTCTTCCTCT
SEQ ID NO: 1793




RPr
CACAACATCCTCCGGAATG
SEQ ID NO: 1794





REG4
NM_032044.2
FPr
TGCTAACTCCTGCACAGCC
SEQ ID NO: 1795




Probe
TCCTCTTCCTTTCTGCTAGCCTGGC
SEQ ID NO: 1796




RPr
TGCTAGGTTTCCCCTCTGAA
SEQ ID NO: 1797





RFC
NM_003056.1
FPr
TCAAGACCATCATCACTTTCATTGT
SEQ ID NO: 1798




Probe
CCTCCCGGTCCGCAAGCAGTT
SEQ ID NO: 1799




RPr
GGATCAGGAAGTACACGGAGTATAACT
SEQ ID NO: 1800





RhoB
NM_004040.2
FPr
AAGCATGAACAGGACTTGACC
SEQ ID NO: 1801




Probe
CTTTCCAACCCCTGGGGAAGACAT
SEQ ID NO: 1802




RPr
CCTCCCCAAGTCAGTTGC
SEQ ID NO: 1803





rhoC
NM_175744.1
FPr
CCCGTTCGGTCTGAGGAA
SEQ ID NO: 1804




Probe
TCCGGTTCGCCATGTCCCG
SEQ ID NO: 1805




RPr
GAGCACTCAAGGTAGCCAAAGG
SEQ ID NO: 1806





RIZ1
NM_012231.1
FPr
CCAGACGAGCGATTAGAAGC
SEQ ID NO: 1807




Probe
TGTGAGGTGAATGATTTGGGGGA
SEQ ID NO: 1808




RPr
TCCTCCTCTTCCTCCTCCTC
SEQ ID NO: 1809





RNF11
NM_014372.3
FPr
ACCCTGGAAGAGATGGATCA
SEQ ID NO: 1810




Probe
CCATCATACAGATCACACACTCCCGG
SEQ ID NO: 1811




RPr
ATTGGGTCCCCATAAACAAA
SEQ ID NO: 1812





ROCK1
NM_005406.1
FPr
TGTGCACATAGGAATGAGCTTC
SEQ ID NO: 1813




Probe
TCACTCTCTTTGCTGGCCAACTGC
SEQ ID NO: 1814




RPr
GTTTAGCACGCAATTGCTCA
SEQ ID NO: 1815





ROCK2
NM_004850.3
FPr
GATCCGAGACCCTCGCTC
SEQ ID NO: 1816




Probe
CCCATCAACGTGGAGAGCTTGCT
SEQ ID NO: 1817




RPr
AGGACCAAGGAATTTAAGCCA
SEQ ID NO: 1818





RPLPO
NM_001002.2
FPr
CCATTCTATCATCAACGGGTACAA
SEQ ID NO: 1819




Probe
TCTCCACAGACAAGGCCAGGACTCG
SEQ ID NO: 1820




RPr
TCAGCAAGTGGGAAGGTGTAATC
SEQ ID NO: 1821





RPS13
NM_001017.2
FPr
CAGTCGGCTTTACCCTATCG
SEQ ID NO: 1822




Probe
CAACTTCAACCAAGTGGGGACGCT
SEQ ID NO: 1823




RPr
TCTGCTCCTTCACGTCGTC
SEQ ID NO: 1824





RRM1
NM_001033.1
FPr
GGGCTACTGGCAGCTACATT
SEQ ID NO: 1825




Probe
CATTGGAATTGCCATTAGTCCCAGC
SEQ ID NO: 1826




RPr
CTCTCAGCATCGGTACAAGG
SEQ ID NO: 1827





RRM2
NM_001034.1
FPr
CAGCGGGATTAAACAGTCCT
SEQ ID NO: 1828




Probe
CCAGCACAGCCAGTTAAAAGATGCA
SEQ ID NO: 1829




RPr
ATCTGCGTTGAAGCAGTGAG
SEQ ID NO: 1830





RTN4
NM_007008.1
FPr
GACTGGAGTGGTGTTTGGTG
SEQ ID NO: 1831




Probe
CCAGCCTATTCCTGCTGCTTTCATTG
SEQ ID NO: 1832




RPr
CTGTTACGCTCACAATGCTG
SEQ ID NO: 1833





RUNX1
NM_001754.2
FPr
AACAGAGACATTGCCAACCA
SEQ ID NO: 1834




Probe
TTGGATCTGCTTGCTGTCCAAACC
SEQ ID NO: 1835




RPr
GTGATTTGCCCAGGAAGTTT
SEQ ID NO: 1836





RXRA
NM_002957.3
FPr
GCTCTGTTGTGTCCTGTTGC
SEQ ID NO: 1837




Probe
TCAGTCACAGGAAGGCCAGAGCC
SEQ ID NO: 1838




RPr
GTACGGAGAAGCCACTTCACA
SEQ ID NO: 1839





S100A1
NM_006271.1
FPr
TGGACAAGGTGATGAAGGAG
SEQ ID NO: 1840




Probe
CCTCCCCGTCTCCATTCTCGTCTA
SEQ ID NO: 1841




RPr
AGCACCACATACTCCTGGAA
SEQ ID NO: 1842





S100A2
NM_005978.2
FPr
TGGCTGTGCTGGTCACTACCT
SEQ ID NO: 1843




Probe
CACAAGTACTCCTGCCAAGAGGGCGAC
SEQ ID NO: 1844




RPr
TCCCCCTTACTCAGCTTGAACT
SEQ ID NO: 1845





S100A4
NM_002961.2
FPr
GACTGCTGTCATGGCGTG
SEQ ID NO: 1846




Probe
ATCACATCCAGGGCCTTCTCCAGA
SEQ ID NO: 1847




RPr
CGAGTACTTGTGGAAGGTGGAC
SEQ ID NO: 1848





S100A8
NM_002964.3
FPr
ACTCCCTGATAAAGGGGAATTT
SEQ ID NO: 1849




Probe
CATGCCGTCTACAGGGATGACCTG
SEQ ID NO: 1850




RPr
TGAGGACACTCGGTCTCTAGC
SEQ ID NO: 1851





S100A9
NM_002965.2
FPr
CTTTGGGACAGAGTGCAAGA
SEQ ID NO: 1852




Probe
CGATGACTTGCAAAATGTCGCAGC
SEQ ID NO: 1853




RPr
TGGTCTCTATGTTGCGTTCC
SEQ ID NO: 1854





S100P
NM_005980.2
FPr
AGACAAGGATGCCGTGGATAA
SEQ ID NO: 1855




Probe
TTGCTCAAGGACCTGGACGCCAA
SEQ ID NO: 1856




RPr
GAAGTCCACCTGGGCATCTC
SEQ ID NO: 1857





SAT
NM_002970.1
FPr
CCTTTTACCACTGCCTGGTT
SEQ ID NO: 1858




Probe
TCCAGTGCTCTTTCGGCACTTCTG
SEQ ID NO: 1859




RPr
ACAATGCTGTGTCCTTCCG
SEQ ID NO: 1860





SBA2
NM_018639.3
FPr
GGACTCAACGATGGGCAG
SEQ ID NO: 1861




Probe
CCCTGTCTGCACCTCCCAGATCTT
SEQ ID NO: 1862




RPr
CGGAAAGATTCAAAAGCAGG
SEQ ID NO: 1863





SDC1
NM_002997.1
FPr
GAAATTGACGAGGGGTGTCT
SEQ ID NO: 1864




Probe
CTCTGAGCGCCTCCATCCAAGG
SEQ ID NO: 1865




RPr
AGGAGCTAACGGAGAACCTG
SEQ ID NO: 1866





SEMA3B
NM_004636.1
FPr
GCTCCAGGATGTGTTTCTGTTG
SEQ ID NO: 1867




Probe
TCGCGGGACCACCGGACC
SEQ ID NO: 1868




RPr
ACGTGGAGAAGACGGCATAGA
SEQ ID NO: 1869





SEMA3F
NM_004186.1
FPr
CGCGAGCCCCTCATTATACA
SEQ ID NO: 1870




Probe
CTCCCCACAGCGCATCGAGGAA
SEQ ID NO: 1871




RPr
CACTCGCCGTTGACATCCT
SEQ ID NO: 1872





SEMA4B
NM_020210.1
FPr
TTCCAGCCCAACACAGTGAA
SEQ ID NO: 1873




Probe
ACTTTGGCCTGCCCGCTCCTCT
SEQ ID NO: 1874




RPr
GAGTCGGGTCGCCAGGTT
SEQ ID NO: 1875





SFRP2
NM_003013.2
FPr
CAAGCTGAACGGTGTGTCC
SEQ ID NO: 1876




Probe
CAGCACCGATTTCTTCAGGTCCCT
SEQ ID NO: 1877




RPr
TGCAAGCTGTCTTTGAGCC
SEQ ID NO: 1878





SFRP4
NM_003014.2
FPr
TACAGGATGAGGCTGGGC
SEQ ID NO: 1879




Probe
CCTGGGACAGCCTATGTAAGGCCA
SEQ ID NO: 1880




RPr
GTTGTTAGGGCAAGGGGC
SEQ ID NO: 1881





SGCB
NM_000232.1
FPr
CAGTGGAGACCAGTTGGGTAGTG
SEQ ID NO: 1882




Probe
CACACATGCAGAGCTTGTAGCGTACCCA
SEQ ID NO: 1883




RPr
CCTTGAAGAGCGTCCCATCA
SEQ ID NO: 1884





SHC1
NM_003029.3
FPr
CCAACACCTTCTTGGCTTCT
SEQ ID NO: 1885




Probe
CCTGTGTTCTTGCTGAGCACCCTC
SEQ ID NO: 1886




RPr
CTGTTATCCCAACCCAAACC
SEQ ID NO: 1887





SHH
NM_000193.2
FPr
GTCCAAGGCACATATCCACTG
SEQ ID NO: 1888




Probe
CACCGAGTTCTCTGCTTTCACCGA
SEQ ID NO: 1889




RPr
GAAGCAGCCTCCCGATTT
SEQ ID NO: 1890





SI
NM_001041.1
FPr
AACGGACTCCCTCAATTTGT
SEQ ID NO: 1891




Probe
TGTCCATGGTCATGCAAATCTTGC
SEQ ID NO: 1892




RPr
GAAATTGCAGGGTCCAAGAT
SEQ ID NO: 1893





Siah-1
NM_003031.2
FPr
TTGGCATTGGAACTACATTCA
SEQ ID NO: 1894




Probe
TCCGCGGTATCCTCGGATTAGTTC
SEQ ID NO: 1895




RPr
GGTATGGAGAAGGGGGTCC
SEQ ID NO: 1896





SIAT4A
NM_003033.2
FPr
AACCACAGTTGGAGGAGGAC
SEQ ID NO: 1897




Probe
CAGAGACAGTTTCCCTCCCCGCT
SEQ ID NO: 1898




RPr
CGAAGGAAGGGTGTTGGTAT
SEQ ID NO: 1899





SIAT7B
NM_006456.1
FPr
TCCAGCCCAAATCCTCCT
SEQ ID NO: 1900




Probe
TGGCACATCCTACCCCAGATGCTA
SEQ ID NO: 1901




RPr
GGTGTCCTGGAGTCCTTGAA
SEQ ID NO: 1902





SIM2
NM_005069.2
FPr
GATGGTAGGAAGGGATGTGC
SEQ ID NO: 1903




Probe
CGCCTCTCCACGCACTCAGCTAT
SEQ ID NO: 1904




RPr
CACAAGGAGCTGTGAATGAGG
SEQ ID NO: 1905





SIN3A
NM_015477.1
FPr
CCAGAGTCATGCTCATCCAG
SEQ ID NO: 1906




Probe
CTGTCCCTGCACTGGTGCAACTG
SEQ ID NO: 1907




RPr
CCACCTTCAGCCTCTGAAAT
SEQ ID NO: 1908





SIR2
NM_012238.3
FPr
AGCTGGGGTGTCTGTTTCAT
SEQ ID NO: 1909




Probe
CCTGACTTCAGGTCAAGGGATGG
SEQ ID NO: 1910




RPr
ACAGCAAGGCGAGCATAAAT
SEQ ID NO: 1911





SKP1A
NM_006930.2
FPr
CCATTGCCTTTGCTTTGTTCAT
SEQ ID NO: 1912




Probe
TCCCATGGTTTTTATTCTGCCCTGCTG
SEQ ID NO: 1913




RPr
TTCCGGATTTCCTTTCTTTGC
SEQ ID NO: 1914





SKP2
NM_005983.2
FPr
AGTTGCAGAATCTAAGCCTGGAA
SEQ ID NO: 1915




Probe
CCTGCGGCTTTCGGATCCCA
SEQ ID NO: 1916




RPr
TGAGTTTTTTGCGAGAGTATTGACA
SEQ ID NO: 1917





SLC25A3
NM_213611.1
FPr
TCTGCCAGTGCTGAATTCTT
SEQ ID NO: 1918




Probe
TGCTGACATTGCCCTGGCTCCTAT
SEQ ID NO: 1919




RPr
TTCGAACCTTAGCAGCTTCC
SEQ ID NO: 1920





SLC2A1
NM_006516.1
FPr
GCCTGAGTCTCCTGTGCC
SEQ ID NO: 1921




Probe
ACATCCCAGGCTTCACCCTGAATG
SEQ ID NO: 1922




RPr
AGTCTCCACCCTCAGGCAT
SEQ ID NO: 1923





SLC31A1
NM_001859.2
FPr
CCGTTCGAAGAGTCGTGAG
SEQ ID NO: 1924




Probe
TCTCCGAATCTTAACCCGTCACCC
SEQ ID NO: 1925




RPr
AGTCCAGCCACTAGCACCTC
SEQ ID NO: 1926





SLC5A8
NM_145913.2
FPr
CCTGCTTTCAACCACATTGA
SEQ ID NO: 1927




Probe
TCCCATTGCTCTTGCCACTCTGAT
SEQ ID NO: 1928




RPr
AGAGCAGCTTCACAAACGAG
SEQ ID NO: 1929





SLC7A5
NM_003486.4
FPr
GCGCAGAGGCCAGTTAAA
SEQ ID NO: 1930




Probe
AGATCACCTCCTCGAACCCACTCC
SEQ ID NO: 1931




RPr
AGCTGAGCTGTGGGTTGC
SEQ ID NO: 1932





SLPI
NM_003064.2
FPr
ATGGCCAATGTTTGATGCT
SEQ ID NO: 1933




Probe
TGGCCATCCATCTCACAGAAATTGG
SEQ ID NO: 1934




RPr
ACACTTCAAGTCACGCTTGC
SEQ ID NO: 1935





SMARCA3
NM_003071.2
FPr
AGGGACTGTCCTGGCACAT
SEQ ID NO: 1936




Probe
AGCAAAAGACCCAGGACATCTGCA
SEQ ID NO: 1937




RPr
CAACAAATTTGCCGCAGTC
SEQ ID NO: 1938





SNAI1
NM_005985.2
FPr
CCCAATCGGAAGCCTAACTA
SEQ ID NO: 1939




Probe
TCTGGATTAGAGTCCTGCAGCTCGC
SEQ ID NO: 1940




RPr
GTAGGGCTGCTGGAAGGTAA
SEQ ID NO: 1941





SNAI2
NM_003068.3
FPr
GGCTGGCCAAACATAAGCA
SEQ ID NO: 1942




Probe
CTGCACTGCGATGCCCAGTCTAGAAAATC
SEQ ID NO: 1943




RPr
TCCTTGTCACAGTATTTACAGCTGAA
SEQ ID NO: 1944





SNRPF
NM_003095.1
FPr
GGCTGGTCGGCAGAGAGTAG
SEQ ID NO: 1945




Probe
AAACTCATGTAAACCACGGCCGAATGTTG
SEQ ID NO: 1946




RPr
TGAGGAAAGGTTTGGGATTGA
SEQ ID NO: 1947





SOD1
NM_000454.3
FPr
TGAAGAGAGGCATGTTGGAG
SEQ ID NO: 1948




Probe
TTTGTCAGCAGTCACATTGCCCAA
SEQ ID NO: 1949




RPr
AATAGACACATCGGCCACAC
SEQ ID NO: 1950





SOD2
NM_000636.1
FPr
GCTTGTCCAAATCAGGATCCA
SEQ ID NO: 1951




Probe
AACAACAGGCCTTATTCCACTGCTGGG
SEQ ID NO: 1952




RPr
AGCGTGCTCCCACACATCA
SEQ ID NO: 1953





SOS1
NM_005633.2
FPr
TCTGCACCAAATTCTCCAAG
SEQ ID NO: 1954




Probe
AACACCGTTAACACCTCCGCCTG
SEQ ID NO: 1955




RPr
GTGGTACTGGAAGCACCAGA
SEQ ID NO: 1956





SOX17
NM_022454.2
FPr
TCGTGTGCAAGCCTGAGA
SEQ ID NO: 1957




Probe
CTCCCCTACCAGGGGCATGACTC
SEQ ID NO: 1958




RPr
CTGTCGGGGAGATTCACAC
SEQ ID NO: 1959





SPARC
NM_003118.1
FPr
TCTTCCCTGTACACTGGCAGTTC
SEQ ID NO: 1960




Probe
TGGACCAGCACCCCATTGACGG
SEQ ID NO: 1961




RPr
AGCTCGGTGTGGGAGAGGTA
SEQ ID NO: 1962





SPINT2
NM_021102.1
FPr
AGGAATGCAGCGGATTCCT
SEQ ID NO: 1963




Probe
CCCAAGTGCTCCCAGAAGGCAGG
SEQ ID NO: 1964




RPr
TCGCTGGAGTGGTCTTCAGA
SEQ ID NO: 1965





SPRY1
AK026960.1
FPr
CAGACCAGTCCCTGGTCATAGG
SEQ ID NO: 1966




Probe
CTGGGTCCGGATTGCCCTTTCAG
SEQ ID NO: 1967




RPr
CCTTCAAGTCATCCACAATCAGTT
SEQ ID NO: 1968





SPRY2
NM_005842.1
FPr
TGTGGCAAGTGCAAATGTAA
SEQ ID NO: 1969




Probe
CAGAGGCCTTGGGTAGGTGCACTC
SEQ ID NO: 1970




RPr
GTCGCAGATCCAGTCTGATG
SEQ ID NO: 1971





SR-A1
NM_021228.1
FPr
AGATGGAAGAAGCCAACCTG
SEQ ID NO: 1972




Probe
CTGGATCAGCTCCTGGGCCTTC
SEQ ID NO: 1973




RPr
CTGTGGCTGAGGATCTGGT
SEQ ID NO: 1974





ST14
NM_021978.2
FPr
TGACTGCACATGGAACATTG
SEQ ID NO: 1975




Probe
AGGTGCCCAACAACCAGCATGT
SEQ ID NO: 1976




RPr
AAGAATTTGAAGCGCACCTT
SEQ ID NO: 1977





STAT1
NM_007315.1
FPr
GGGCTCAGCTTTCAGAAGTG
SEQ ID NO: 1978




Probe
TGGCAGTTTTCTTCTGTCACCAAAA
SEQ ID NO: 1979




RPr
ACATGTTCAGCTGGTCCACA
SEQ ID NO: 1980





STAT3
NM_003150.1
FPr
TCACATGCCACTTTGGTGTT
SEQ ID NO: 1981




Probe
TCCTGGGAGAGATTGACCAGCA
SEQ ID NO: 1982




RPr
CTTGCAGGAAGCGGCTATAC
SEQ ID NO: 1983





STAT5A
NM_003152.1
FPr
GAGGCGCTCAACATGAAATTC
SEQ ID NO: 1984




Probe
CGGTTGCTCTGCACTTCGGCCT
SEQ ID NO: 1985




RPr
GCCAGGAACACGAGGTTCTC
SEQ ID NO: 1986





STAT5B
NM_012448.1
FPr
CCAGTGGTGGTGATCGTTCA
SEQ ID NO: 1987




Probe
CAGCCAGGACAACAATGCGACGG
SEQ ID NO: 1988




RPr
GCAAAAGCATTGTCCCAGAGA
SEQ ID NO: 1989





STC1
NM_003155.1
FPr
CTCCGAGGTGAGGAGGACT
SEQ ID NO: 1990




Probe
CACATCAAACGCACATCCCATGAG
SEQ ID NO: 1991




RPr
ACCTCTCCCTGGTTATGCAC
SEQ ID NO: 1992





STK11
NM_000455.3
FPr
GGACTCGGAGACGCTGTG
SEQ ID NO: 1993




Probe
TTCTTGAGGATCTTGACGGCCCTC
SEQ ID NO: 1994




RPr
GGGATCCTTCGCAACTTCTT
SEQ ID NO: 1995





STK15
NM_003600.1
FPr
CATCTTCCAGGAGGACCACT
SEQ ID NO: 1996




Probe
CTCTGTGGCACCCTGGACTACCTG
SEQ ID NO: 1997




RPr
TCCGACCTTCAATCATTTCA
SEQ ID NO: 1998





STMN1
NM_005563.2
FPr
AATACCCAACGCACAAATGA
SEQ ID NO: 1999




Probe
CACGTTCTCTGCCCCGTTTCTTG
SEQ ID NO: 2000




RPr
GGAGACAATGCAAACCACAC
SEQ ID NO: 2001





STMY3
NM_005940.2
FPr
CCTGGAGGCTGCAACATACC
SEQ ID NO: 2002




Probe
ATCCTCCTGAAGCCCTTTTCGCAGC
SEQ ID NO: 2003




RPr
TACAATGGCTTTGGAGGATAGCA
SEQ ID NO: 2004





STS
NM_000351.2
FPr
GAAGATCCCTTTCCTCCTACTGTTC
SEQ ID NO: 2005




Probe
CTTCGTGGCTCTCGGCTTCCCA
SEQ ID NO: 2006




RPr
GGATGATGTTCGGCCTTGAT
SEQ ID NO: 2007





SURV
NM_001168.1
FPr
TGTTTTGATTCCCGGGCTTA
SEQ ID NO: 2008




Probe
TGCCTTCTTCCTCCCTCACTTCTCACCT
SEQ ID NO: 2009




RPr
CAAAGCTGTCAGCTCTAGCAAAAG
SEQ ID NO: 2010





TAGLN
NM_003186.2
FPr
GATGGAGCAGGTGGCTCAGT
SEQ ID NO: 2011




Probe
CCCAGAGTCCTCAGCCGCCTTCAG
SEQ ID NO: 2012




RPr
AGTCTGGAACATGTCAGTCTTGATG
SEQ ID NO: 2013





TBP
NM_003194.1
FPr
GCCCGAAACGCCGAATATA
SEQ ID NO: 2014




Probe
TACCGCAGCAAACCGCTTGGG
SEQ ID NO: 2015




RPr
CGTGGCTCTCTTATCCTCATGAT
SEQ ID NO: 2016





TCF-1
NM_000545.3
FPr
GAGGTCCTGAGCACTGCC
SEQ ID NO: 2017




Probe
CTGGGTTCACAGGCTCCTTTGTCC
SEQ ID NO: 2018




RPr
GATGTGGGACCATGCTTGT
SEQ ID NO: 2019





TCF-7
NM_003202.2
FPr
GCAGCTGCAGTCAACAGTTC
SEQ ID NO: 2020




Probe
AAGTCATGGCCCAAATCCAGTGTG
SEQ ID NO: 2021




RPr
CTGTGAATGGGGAGGGGT
SEQ ID NO: 2022





TCF7L1
NM_031283.1
FPr
CCGGGACACTTTCCAGAAG
SEQ ID NO: 2023




Probe
TCTCACTTCGGCGAAATAGTCCCG
SEQ ID NO: 2024




RPr
AGAACGCGCTGTCCTGAG
SEQ ID NO: 2025





TCF7L2
NM_030756.1
FPr
CCAATCACGACAGGAGGATT
SEQ ID NO: 2026




Probe
AGACACCCCTACCCCACAGCTCTG
SEQ ID NO: 2027




RPr
TGGACACGGAAGCATTGAC
SEQ ID NO: 2028





TCFL4
NM_170607.2
FPr
CTGACTGCTCTGCTTAAAGGTGAA
SEQ ID NO: 2029




Probe
TAGCAGGAACAACAACAAAAGCCAACC
SEQ ID NO: 2030





AA




RPr
ATGTCTTGCACTGGCTACCTTGT
SEQ ID NO: 2031





TEK
NM_000459.1
FPr
ACTTCGGTGCTACTTAACAACTTACATC
SEQ ID NO: 2032




Probe
AGCTCGGACCACGTACTGCTCCCTG
SEQ ID NO: 2033




RPr
CCTGGGCCTTGGTGTTGAC
SEQ ID NO: 2034





TERC
U86046.1
FPr
AAGAGGAACGGAGCGAGTC
SEQ ID NO: 2035




Probe
CACGTCCCACAGCTCAGGGAATC
SEQ ID NO: 2036




RPr
ATGTGTGAGCCGAGTCCTG
SEQ ID NO: 2037





TERT
NM_003219.1
FPr
GACATGGAGAACAAGCTGTTTGC
SEQ ID NO: 2038




Probe
ACCAAACGCAGGAGCAGCCCG
SEQ ID NO: 2039




RPr
GAGGTGTCACCAACAAGAAATCAT
SEQ ID NO: 2040





TFF3
NM_003226.1
FPr
AGGCACTGTTCATCTCAGTTTTTCT
SEQ ID NO: 2041




Probe
CAGAAAGCTTGCCGGGAGCAAAGG
SEQ ID NO: 2042




RPr
CATCAGGCTCCAGATATGAACTTTC
SEQ ID NO: 2043





TGFA
NM_003236.1
FPr
GGTGTGCCACAGACCTTCCT
SEQ ID NO: 2044




Probe
TTGGCCTGTAATCACCTGTGCAGCCTT
SEQ ID NO: 2045




RPr
ACGGAGTTCTTGACAGAGTTTTGA
SEQ ID NO: 2046





TGFB2
NM_003238.1
FPr
ACCAGTCCCCCAGAAGACTA
SEQ ID NO: 2047




Probe
TCCTGAGCCCGAGGAAGTCCC
SEQ ID NO: 2048




RPr
CCTGGTGCTGTTGTAGATGG
SEQ ID NO: 2049





TGFB3
NM_003239.1
FPr
GGATCGAGCTCTTCCAGATCCT
SEQ ID NO: 2050




Probe
CGGCCAGATGAGCACATTGCC
SEQ ID NO: 2051




RPr
GCCACCGATATAGCGCTGTT
SEQ ID NO: 2052





TGFBI
NM_000358.1
FPr
GCTACGAGTGCTGTCCTGG
SEQ ID NO: 2053




Probe
CCTTCTCCCCAGGGACCTTTTCAT
SEQ ID NO: 2054




RPr
AGTGGTAGGGCTGCTGGAC
SEQ ID NO: 2055





TGFBR1
NM_004612.1
FPr
GTCATCACCTGGCCTTGG
SEQ ID NO: 2056




Probe
AGCAATGACAGCTGCCAGTTCCAC
SEQ ID NO: 2057




RPr
GCAGACGAAGCACACTGGT
SEQ ID NO: 2058





TGFBR2
NM_003242.2
FPr
AACACCAATGGGTTCCATCT
SEQ ID NO: 2059




Probe
TTCTGGGCTCCTGATTGCTCAAGC
SEQ ID NO: 2060




RPr
CCTCTTCATCAGGCCAAACT
SEQ ID NO: 2061





THBS1
NM_003246.1
FPr
CATCCGCAAAGTGACTGAAGAG
SEQ ID NO: 2062




Probe
CCAATGAGCTGAGGCGGCCTCC
SEQ ID NO: 2063




RPr
GTACTGAACTCCGTTGTGATAGCATAG
SEQ ID NO: 2064





THY1
NM_006288.2
FPr
GGACAAGACCCTCTCAGGCT
SEQ ID NO: 2065




Probe
CAAGCTCCCAAGAGCTTCCAGAGC
SEQ ID NO: 2066




RPr
TTGGAGGCTGTGGGTCAG
SEQ ID NO: 2067





TIMP1
NM_003254.1
FPr
TCCCTGCGGTCCCAGATAG
SEQ ID NO: 2068




Probe
ATCCTGCCCGGAGTGGAACTGAAGC
SEQ ID NO: 2069




RPr
GTGGGAACAGGGTGGACACT
SEQ ID NO: 2070





TIMP2
NM_003255.2
FPr
TCACCCTCTGTGACTTCATCGT
SEQ ID NO: 2071




Probe
CCCTGGGACACCCTGAGCACCA
SEQ ID NO: 2072




RPr
TGTGGTTCAGGCTCTTCTTCTG
SEQ ID NO: 2073





TIMP3
NM_000362.2
FPr
CTACCTGCCTTGCTTTGTGA
SEQ ID NO: 2074




Probe
CCAAGAACGAGTGTCTCTGGACCG
SEQ ID NO: 2075




RPr
ACCGAAATTGGAGAGCATGT
SEQ ID NO: 2076





TJP1
NM_003257.1
FPr
ACTTTGCTGGGACAAAGGTC
SEQ ID NO: 2077




Probe
CTCGGGCCTGCCCACTTCTTC
SEQ ID NO: 2078




RPr
CACATGGACTCCTCAGCATC
SEQ ID NO: 2079





TK1
NM_003258.1
FPr
GCCGGGAAGACCGTAATTGT
SEQ ID NO: 2080




Probe
CAAATGGCTTCCTCTGGAAGGTCCCA
SEQ ID NO: 2081




RPr
CAGCGGCACCAGGTTCAG
SEQ ID NO: 2082





TLN1
NM_006289.2
FPr
AAGCAGAAGGGAGAGCGTAAGA
SEQ ID NO: 2083




Probe
CTTCCAGGCACACAAGAATTGTGGGC
SEQ ID NO: 2084




RPr
CCTTGGCCTCAATCTCACTCA
SEQ ID NO: 2085





TMEPAI
NM_020182.3
FPr
CAGAAGGATGCCTGTGGC
SEQ ID NO: 2086




Probe
ATTCCGTTGCCTGACACTGTGCTC
SEQ ID NO: 2087




RPr
GTAGACCTGCGGCTCTGG
SEQ ID NO: 2088





TMSB10
NM_021103.2
FPr
GAAATCGCCAGCTTCGATAA
SEQ ID NO: 2089




Probe
CGTCTCCGTTTTCTTCAGCTTGGC
SEQ ID NO: 2090




RPr
GTCGGCAGGGTGTTCTTTT
SEQ ID NO: 2091





TMSB4X
NM_021109.2
FPr
CACATCAAAGAACTACTGACAACGAA
SEQ ID NO: 2092




Probe
CCGCGCCTGCCTTTCCCA
SEQ ID NO: 2093




RPr
CCTGCCAGCCAGATAGATAGACA
SEQ ID NO: 2094





TNC
NM_002160.1
FPr
AGCTCGGAACCTCACCGT
SEQ ID NO: 2095




Probe
CAGCCTTCGGGCTGTGGACATAC
SEQ ID NO: 2096




RPr
GTAGCAGCCTTGAGGCCC
SEQ ID NO: 2097





TNF
NM_000594.1
FPr
GGAGAAGGGTGACCGACTCA
SEQ ID NO: 2098




Probe
CGCTGAGATCAATCGGCCCGACTA
SEQ ID NO: 2099




RPr
TGCCCAGACTCGGCAAAG
SEQ ID NO: 2100





TNFRSF5
NM_001250.3
FPr
TCTCACCTCGCTATGGTTCGT
SEQ ID NO: 2101




Probe
TGCCTCTGCAGTGCGTCCTCTGG
SEQ ID NO: 2102




RPr
GATGGACAGCGGTCAGCAA
SEQ ID NO: 2103





TNFRSF6B
NM_003823.2
FPr
CCTCAGCACCAGGGTACCA
SEQ ID NO: 2104




Probe
TGACGGCACGCTCACACTCCTCAG
SEQ ID NO: 2105




RPr
TGTCCTGGAAAGCCACAAAGT
SEQ ID NO: 2106





TNFSF4
NM_003326.2
FPr
CTTCATCTTCCCTCTACCCAGA
SEQ ID NO: 2107




Probe
CAGGGGTTGGACCCTTTCCATCTT
SEQ ID NO: 2108




RPr
GCTGCATTTCCCACATTCTC
SEQ ID NO: 2109





TOP2A
NM_001067.1
FPr
AATCCAAGGGGGAGAGTGAT
SEQ ID NO: 2110




Probe
CATATGGACTTTGACTCAGCTGTGGC
SEQ ID NO: 2111




RPr
GTACAGATTTTGCCCGAGGA
SEQ ID NO: 2112





TOP2B
NM_001068.1
FPr
TGTGGACATCTTCCCCTCAGA
SEQ ID NO: 2113




Probe
TTCCCTACTGAGCCACCTTCTCTG
SEQ ID NO: 2114




RPr
CTAGCCCGACCGGTTCGT
SEQ ID NO: 2115





TP
NM_001953.2
FPr
CTATATGCAGCCAGAGATGTGACA
SEQ ID NO: 2116




Probe
ACAGCCTGCCACTCATCACAGCC
SEQ ID NO: 2117




RPr
CCACGAGTTTCTTACTGAGAATGG
SEQ ID NO: 2118





TP53BP1
NM_005657.1
FPr
TGCTGTTGCTGAGTCTGTTG
SEQ ID NO: 2119




Probe
CCAGTCCCCAGAAGACCATGTCTG
SEQ ID NO: 2120




RPr
CTTGCCTGGCTTCACAGATA
SEQ ID NO: 2121





TP53BP2
NM_005426.1
FPr
GGGCCAAATATTCAGAAGC
SEQ ID NO: 2122




Probe
CCACCATAGCGGCCATGGAG
SEQ ID NO: 2123




RPr
GGATGGGTATGATGGGACAG
SEQ ID NO: 2124





TP53I3
NM_004881.2
FPr
GCGGACTTAATGCAGAGACA
SEQ ID NO: 2125




Probe
CAGTATGACCCACCTCCAGGAGCC
SEQ ID NO: 2126




RPr
TCAAGTCCCAAAATGTTGCT
SEQ ID NO: 2127





TRAG3
NM_004909.1
FPr
GACGCTGGTCTGGTGAAGATG
SEQ ID NO: 2128




Probe
CCAGGAAACCACGAGCCTCCAGC
SEQ ID NO: 2129




RPr
TGGGTGGTTGTTGGACAATG
SEQ ID NO: 2130





TRAIL
NM_003810.1
FPr
CTTCACAGTGCTCCTGCAGTCT
SEQ ID NO: 2131




Probe
AAGTACACGTAAGTTACAGCCACACA
SEQ ID NO: 2132




RPr
CATCTGCTTCAGCTCGTTGGT
SEQ ID NO: 2133





TS
NM_001071.1
FPr
GCCTCGGTGTGCCTTTCA
SEQ ID NO: 2134




Probe
CATCGCCAGCTACGCCCTGCTC
SEQ ID NO: 2135




RPr
CGTGATGTGCGCAATCATG
SEQ ID NO: 2136





TST
NM_003312.4
FPr
GGAGCCGGATGCAGTAGGA
SEQ ID NO: 2137




Probe
ACCACGGATATGGCCCGAGTCCA
SEQ ID NO: 2138




RPr
AAGTCCATGAAAGGCATGTTGA
SEQ ID NO: 2139





TUBA1
NM_006000.1
FPr
TGTCACCCCGACTCAACGT
SEQ ID NO: 2140




Probe
AGACGCACCGCCCGGACTCAC
SEQ ID NO: 2141




RPr
ACGTGGACTGAGATGCATTCAC
SEQ ID NO: 2142





TUBB
NM_001069.1
FPr
CGAGGACGAGGCTTAAAAAC
SEQ ID NO: 2143




Probe
TCTCAGATCAATCGTGCATCCTTAGTGAA
SEQ ID NO: 2144




RPr
ACCATGCTTGAGGACAACAG
SEQ ID NO: 2145





TUFM
NM_003321.3
FPr
GTATCACCATCAATGCGGC
SEQ ID NO: 2146




Probe
CATGTGGAGTATAGCACTGCCGCC
SEQ ID NO: 2147




RPr
CAGTCTGTGTGGGCGTAGTG
SEQ ID NO: 2148





TULP3
NM_003324.2
FPr
TGTGTATAGTCCTGCCCCTCAA
SEQ ID NO: 2149




Probe
CCGGATTATCCGACATCTTACTGTGA
SEQ ID NO: 2150




RPr
CCCGATCCATTCCCCTTTTA
SEQ ID NO: 2151





tusc4
NM_006545.4
FPr
GGAGGAGCTAAATGCCTCAG
SEQ ID NO: 2152




Probe
ACTCATCAATGGGCAGAGTGCACC
SEQ ID NO: 2153




RPr
CCTTCAAGTGGATGGTGTTG
SEQ ID NO: 2154





UBB
NM_018955.1
FPr
GAGTCGACCCTGCACCTG
SEQ ID NO: 2155




Probe
AATTAACAGCCACCCCTCAGGCG
SEQ ID NO: 2156




RPr
GCGAATGCCATGACTGAA
SEQ ID NO: 2157





UBC
NM_021009.2
FPr
ACGCACCCTGTCTGACTACA
SEQ ID NO: 2158




Probe
CATCCAGAAAGAGTCCACCCTGCA
SEQ ID NO: 2159




RPr
ACCTCTAAGACGGAGCACCA
SEQ ID NO: 2160





UBE2C
NM_007019.2
FPr
TGTCTGGCGATAAAGGGATT
SEQ ID NO: 2161




Probe
TCTGCCTTCCCTGAATCAGACAACC
SEQ ID NO: 2162




RPr
ATGGTCCCTACCCATTTGAA
SEQ ID NO: 2163





UBE2M
NM_003969.1
FPr
CTCCATAATTTATGGCCTGCAGTA
SEQ ID NO: 2164




Probe
TCTTCTTGGAGCCCAACCCCGAG
SEQ ID NO: 2165




RPr
TGCGGCCTCCTTGTTCAG
SEQ ID NO: 2166





UBL1
NM_003352.3
FPr
GTGAAGCCACCGTCATCATG
SEQ ID NO: 2167




Probe
CTGACCAGGAGGCAAAACCTTCAACTGA
SEQ ID NO: 2168




RPr
CCTTCCTTCTTATCCCCCAAGT
SEQ ID NO: 2169





UCP2
NM_003355.2
FPr
ACCATGCTCCAGAAGGAGG
SEQ ID NO: 2170




Probe
CCCCGAGCCTTCTACAAAGGGTTC
SEQ ID NO: 2171




RPr
AACCCAAGCGGAGAAAGG
SEQ ID NO: 2172





UGT1A1
NM_000463.2
FPr
CCATGCAGCCTGGAATTTG
SEQ ID NO: 2173




Probe
CTACCCAGTGCCCCAACCCATTCTC
SEQ ID NO: 2174




RPr
GAGAGGCCTGGGCACGTA
SEQ ID NO: 2175





UMPS
NM_000373.1
FPr
TGCGGAAATGAGCTCCAC
SEQ ID NO: 2176




Probe
CCCTGGCCACTGGGGACTACACTA
SEQ ID NO: 2177




RPr
CCTCAGCCATTCTAACCGC
SEQ ID NO: 2178





UNC5A
XM_030300.7
FPr
GACAGCTGATCCAGGAGCC
SEQ ID NO: 2179




Probe
CGGGTCCTGCACTTCAAGGACAGT
SEQ ID NO: 2180




RPr
ATGGATAGGCGCAGGTTG
SEQ ID NO: 2181





UNC5B
NM_170744.2
FPr
AGAACGGAGGCCGTGACT
SEQ ID NO: 2182




Probe
CGGGACGCTGCTCGACTCTAAGAA
SEQ ID NO: 2183




RPr
CATGCACAGCCCATCTGT
SEQ ID NO: 2184





UNC5C
NM_003728.2
FPr
CTGAACACAGTGGAGCTGGT
SEQ ID NO: 2185




Probe
ACCTGCCGCACACAGAGTTTGC
SEQ ID NO: 2186




RPr
CTGGAAGATCTGCCCTTCTC
SEQ ID NO: 2187





upa
NM_002658.1
FPr
GTGGATGTGCCCTGAAGGA
SEQ ID NO: 2188




Probe
AAGCCAGGCGTCTACACGAGAGTCTCAC
SEQ ID NO: 2189




RPr
CTGCGGATCCAGGGTAAGAA
SEQ ID NO: 2190





UPP1
NM_003364.2
FPr
ACGGGTCCTGCCTCAGTT
SEQ ID NO: 2191




Probe
TCAGCTTTCTCTGCATTGGCTCCC
SEQ ID NO: 2192




RPr
CGGGGCAATCATTGTGAC
SEQ ID NO: 2193





VCAM1
NM_001078.2
FPr
TGGCTTCAGGAGCTGAATACC
SEQ ID NO: 2194




Probe
CAGGCACACACAGGTGGGACACAAAT
SEQ ID NO: 2195




RPr
TGCTGTCGTGATGAGAAAATAGTG
SEQ ID NO: 2196





VCL
NM_003373.2
FPr
GATACCACAACTCCCATCAAGCT
SEQ ID NO: 2197




Probe
AGTGGCAGCCACGGCGCC
SEQ ID NO: 2198




RPr
TCCCTGTTAGGCGCATCAG
SEQ ID NO: 2199





VCP
NM_007126.2
FPr
GGCTTTGGCAGCTTCAGAT
SEQ ID NO: 2200




Probe
AGCTCCACCCTGGTTCCCTGAAG
SEQ ID NO: 2201




RPr
CTCCACTGCCCTGACTGG
SEQ ID NO: 2202





VDAC1
NM_003374.1
FPr
GCTGCGACATGGATTTCGA
SEQ ID NO: 2203




Probe
TTGCTGGGCCTTCCATCCGG
SEQ ID NO: 2204




RPr
CCAGCCCTCGTAACCTAGCA
SEQ ID NO: 2205





VDAC2
NM_003375.2
FPr
ACCCACGGACAGACTTGC
SEQ ID NO: 2206




Probe
CGCGTCCAATGTGTATTCCTCCAT
SEQ ID NO: 2207




RPr
AGCTTTGCCAAGGTCAGC
SEQ ID NO: 2208





VDR
NM_000376.1
FPr
GCCCTGGATTTCAGAAAGAG
SEQ ID NO: 2209




Probe
CAAGTCTGGATCTGGGACCCTTTCC
SEQ ID NO: 2210




RPr
AGTTACAAGCCAGGGAAGGA
SEQ ID NO: 2211





VEGF
NM_003376.3
FPr
CTGCTGTCTTGGGTGCATTG
SEQ ID NO: 2212




Probe
TTGCCTTGCTGCTCTACCTCCACCA
SEQ ID NO: 2213




RPr
GCAGCCTGGGACCACTTG
SEQ ID NO: 2214





VEGF_altsplice1
AF486837.1
FPr
TGTGAATGCAGACCAAAGAAAGA
SEQ ID NO: 2215




Probe
AGAGCAAGACAAGAAAATCCCTGTGGGC
SEQ ID NO: 2216




RPr
GCTTTCTCCGCTCTGAGCAA
SEQ ID NO: 2217





VEGF_altsplice2
AF214570.1
FPr
AGCTTCCTACAGCACAACAAAT
SEQ ID NO: 2218




Probe
TGTCTTGCTCTATCTTTCTTTGGTCTGCA
SEQ ID NO: 2219




RPr
CTCGGCTTGTCACATTTTTC
SEQ ID NO: 2220





VEGFB
NM_003377.2
FPr
TGACGATGGCCTGGAGTGT
SEQ ID NO: 2221




Probe
CTGGGCAGCACCAAGTCCGGA
SEQ ID NO: 2222




RPr
GGTACCGGATCATGAGGATCTG
SEQ ID NO: 2223





VEGFC
NM_005429.2
FPr
CCTCAGCAAGACGTTATTTGAAATT
SEQ ID NO: 2224




Probe
CCTCTCTCTCAAGGCCCCAAACCAGT
SEQ ID NO: 2225




RPr
AAGTGTGATTGGCAAAACTGATTG
SEQ ID NO: 2226





VIM
NM_003380.1
FPr
TGCCCTTAAAGGAACCAATGA
SEQ ID NO: 2227




Probe
ATTTCACGCATCTGGCGTTCCA
SEQ ID NO: 2228




RPr
GCTTCAACGGCAAAGTTCTCTT
SEQ ID NO: 2229





WIF
NM_007191.2
FPr
TACAAGCTGAGTGCCCAGG
SEQ ID NO: 2230




Probe
TACAAAAGCCTCCATTTCGGCACC
SEQ ID NO: 2231




RPr
CACTCGCAGATGCGTCTTT
SEQ ID NO: 2232





WISP1
NM_003882.2
FPr
AGAGGCATCCATGAACTTCACA
SEQ ID NO: 2233




Probe
CGGGCTGCATCAGCACACGC
SEQ ID NO: 2234




RPr
CAAACTCCACAGTACTTGGGTTGA
SEQ ID NO: 2235





Wnt-3a
NM_033131.2
FPr
ACAAAGCTACCAGGGAGTCG
SEQ ID NO: 2236




Probe
TTTGTCCACGCCATTGCCTCAG
SEQ ID NO: 2237




RPr
TGAGCGTGTCACTGCAAAG
SEQ ID NO: 2238





Wnt-5a
NM_003392.2
FPr
GTATCAGGACCACATGCAGTACATC
SEQ ID NO: 2239




Probe
TTGATGCCTGTCTTCGCGCCTTCT
SEQ ID NO: 2240




RPr
TGTCGGAATTGATACTGGCATT
SEQ ID NO: 2241





Wnt-5b
NM_032642.2
FPr
TGTCTTCAGGGTCTTGTCCA
SEQ ID NO: 2242




Probe
TTCCGTAAGAGGCCTGGTGCTCTC
SEQ ID NO: 2243




RPr
GTGCACGTGGATGAAAGAGT
SEQ ID NO: 2244





WNT2
NM_003391.1
FPr
CGGTGGAATCTGGCTCTG
SEQ ID NO: 2245




Probe
CTCCCTCTGCTCTTGACCTGGCTC
SEQ ID NO: 2246




RPr
CCATGAAGAGTTGACCTCGG
SEQ ID NO: 2247





WWOX
NM_016373.1
FPr
ATCGCAGCTGGTGGGTGTA
SEQ ID NO: 2248




Probe
CTGCTGTTTACCTTGGCGAGGCCTTT
SEQ ID NO: 2249




RPr
AGCTCCCTGTTGCATGGACTT
SEQ ID NO: 2250





XPA
NM_000380.2
FPr
GGGTAGAGGGAAAAGGGTTC
SEQ ID NO: 2251




Probe
CAAAGGCTGAACTGGATTCTTAACCAAGA
SEQ ID NO: 2252




RPr
TGCACCACCATTGCTATTATT
SEQ ID NO: 2253





XPC
NM_004628.2
FPr
GATACATCGTCTGCGAGGAA
SEQ ID NO: 2254




Probe
TTCAAAGACGTGCTCCTGACTGCC
SEQ ID NO: 2255




RPr
CTTTCAATGACTGCCTGCTC
SEQ ID NO: 2256





XRCC1
NM_006297.1
FPr
GGAGATGAAGCCCCCAAG
SEQ ID NO: 2257




Probe
AGAAGCAACCCCAGACCAAAACCA
SEQ ID NO: 2258




RPr
GTCCAGCTGCCTGAGTGG
SEQ ID NO: 2259





YB-1
NM_004559.1
FPr
AGACTGTGGAGTTTGATGTTGTTGA
SEQ ID NO: 2260




Probe
TTGCTGCCTCCGCACCCTTTTCT
SEQ ID NO: 2261




RPr
GGAACACCACCAGGACCTGTAA
SEQ ID NO: 2262





YWHAH
NM_003405.2
FPr
CATGGCCTCCGCTATGAA
SEQ ID NO: 2263




Probe
AGGTTCATTCAGCTCTGTCACCGC
SEQ ID NO: 2264




RPr
GGAGATTTCGATCTTCATTGGA
SEQ ID NO: 2265





zbtb7
NM_015898.2
FPr
CTGCGTTCACACCCCAGT
SEQ ID NO: 2266




Probe
TCTCTCCAGAACAGCTCGCCCTGT
SEQ ID NO: 2267




RPr
CTCAGCCACGACAGATGGT
SEQ ID NO: 2268





ZG16
NM_152338.1
FPr
TGCTGAGCCTCCTCTCCTT
SEQ ID NO: 2269




Probe
TACTCCTCATCACAGTGCCCCTGC
SEQ ID NO: 2270




RPr
GGATGGGGGTTAGTGATAAGG
SEQ ID NO: 2271




















TABLE B








SEQ






ID


Gene
Locus Link
Sequence
NO







A-Catenin
NM_001903.1
CGTTCCGATCCTCTATACTGCATCCCAGGCATGCCTACAGCACCCTGATGTCGCAGCCTATA
SEQ ID





AGGCCAACAGGGACCT
NO:





2272





ABCB1
NM_000927.2
AAACACCACTGGAGCATTGACTACCAGGCTCGCCAATGATGCTGCTCAAGTTAAAGGGGCT
SEQ ID




ATAGGTTCCAGGCTTG
NO:





2273





ABCC5
NM_005688.1
TGCAGACTGTACCATGCTGACCATTGCCCATCGCCTGCACACGGTTCTAGGCTCCGATAGGA
SEQ ID




TTATGGTGCTGGCC
NO:





2274





ABCC6
NM_001171.2
GGATGAACCTCGACCTGCTGCAGGAGCACTCGGACGAGGCTATCTGGGCAGCCCTGGAGAC
SEQ ID




GGTGCAGCTC
NO:





2275





ACP1
NM_004300.2
GCTACCAAGTCCGTGCTGTTTGTGTGTCTGGGTAACATTTGTCGATCACCCATTGCAGAAGC
SEQ ID




AGTTTTC
NO:





2276





ADAM10
NM_001110.1
CCCATCAACTTGTGCCAGTACAGGGTCTGTGCAGTGGAGTAGGCACTTCAGTGGTCGAACCA
SEQ ID




TCACC
NO:





2277





ADAM17
NM_003183.3
GAAGTGCCAGGAGGCGATTAATGCTACTTGCAAAGGCGTGTCCTACTGCACAGGTAATAGC
SEQ ID




AGTGAGTGCCCG
NO:





2278





ADAMTS12
NM_030955.2
GGAGAAGGGTGGAGTGCAGCACCCAGATGGATTCTGACTGTGCGGCCATCCAGAGACCTGA
SEQ ID




CCCTG
NO:





2279





ADPRT
NM_001618.2
TTGACAACCTGCTGGACATCGAGGTGGCCTACAGTCTGCTCAGGGGAGGGTCTGATGATAGC
SEQ ID




AGCAAGGATCCCAT
NO:





2280





AGXT
NM_000030.1
CTTTTCCCTCCAGTGGCACCTCCTGGAAACAGTCCACTTGGGCGCAAAACCCAGTGCCTTCC
SEQ ID




AAAT
NO:





2281





AKAP12
NM_005100.2
TAGAGAGCCCCTGACAATCCTGAGGCTTCATCAGGAGCTAGAGCCATTTAACATTTCCTCTT
SEQ ID




TCCAAGACCAACC
NO:





2282





AKT1
NM_005163.1
CGCTTCTATGGCGCTGAGATTGTGTCAGCCCTGGACTACCTGCACTCGGAGAAGAACGTGGT
SEQ ID




GTACCGGGA
NO:





2283





AKT2
NM_001626.2
TCCTGCCACCCTTCAAACCTCAGGTCACGTCCGAGGTCGACACAAGGTACTTCGATGATGAA
SEQ ID




TTTACCGCC
NO:





2284





AKT3
NM_005465.1
TTGTCTCTGCCTTGGACTATCTACATTCCGGAAAGATTGTGTACCGTGATCTCAAGTTGGAGA
SEQ ID




ATCTAATGCTGG
NO:





2285





AL137428
AL137428.1
CAAGAAGAGGCTCTACCCTGGGACTGGGAATTTCCAAGGCCACCTTTGAGGATCGCAGAGC
SEQ ID




TCATTT
NO:





2286





ALCAM
NM_001627.1
GAGGAATATGGAATCCAAGGGGGCCAGTTCCTGCCGTCTGCTCTTCTGCCTCTTGATCTCCG
SEQ ID




CCAC
NO:





2287





ALDH1A1
NM_000689.1
GAAGGAGATAAGGAGGATGTTGACAAGGCAGTGAAGGCCGCAAGACAGGCTTTTCAGATTG
SEQ ID




GATCTCCGTGGCG
NO:





2288





ALDOA
NM_000034.2
GCCTGTACGTGCCAGCTCCCCGACTGCCAGAGCCTCAACTGTCTCTGCTTCGAGATCAAGCT
SEQ ID




CCGATGA
NO:





2289





AMFR
NM_001144.2
GATGGTTCAGCTCTGCAAGGATCGATTTGAATATCTTTCCTTCTCGCCCACCACGCCGATGA
SEQ ID




GCAGCCACGGTCGA
NO:





2290





ANGPT2
NM_001147.1
CCGTGAAAGCTGCTCTGTAAAAGCTGACACAGCCCTCCCAAGTGAGCAGGACTGTTCTTCCC
SEQ ID




ACTGCAA
NO:





2291





ANTXR1
NM_032208.1
CTCCAGGTGTACCTCCAACCCTAGCCTTCTCCCACAGCTGCCTACAACAGAGTCTCCCAGCC
SEQ ID




TTCTC
NO:





2292





ANXA1
NM_000700.1
GCCCCTATCCTACCTTCAATCCATCCTCGGATGTCGCTGCCTTGCATAAGGCCATAATGGTTA
SEQ ID




AAGG
NO:





2293





ANXA2
NM_004039.1
CAAGACACTAAGGGCGACTACCAGAAAGCGCTGCTGTACCTGTGTGGTGGAGATGACTGAA
SEQ ID




GCCCGACACG
NO:





2294





ANXA5
NM_001154.2
GCTCAAGCCTGGAAGATGACGTGGTGGGGGACACTTCAGGGTACTACCAGCGGATGTTGGT
SEQ ID




GGTTCT
NO:





2295





AP-1 (JUN
NM_002228.2
GACTGCAAAGATGGAAACGACCTTCTATGACGATGCCCTCAACGCCTCGTTCCTCCCGTCCG
SEQ ID


official)

AGAGCGGACCTTATGGCTA
NO:





2296





APC
NM_000038.1
GGACAGCAGGAATGTGTTTCTCCATACAGGTCACGGGGAGCCAATGGTTCAGAAACAAATC
SEQ ID




GAGTGGGT
NO:





2297





APEX-1
NM_001641.2
GATGAAGCCTTTCGCAAGTTCCTGAAGGGCCTGGCTTCCCGAAAGCCCCTTGTGCTGTGTGG
SEQ ID




AGACCT
NO:





2298





APG-1
NM_014278.2
ACCCCGGCCTGTATATCATTGGGATCAAGAACTCGAGCCATTGGAAATGCAGCAAAGAGCC
SEQ ID




AGATAG
NO:





2299





APN
NM_001150.1
CCACCTTGGACCAAAGTAAAGCGTGGAATCGTTACCGCCTCCCCAACACGCTGAAACCCGAT
SEQ ID


(ANPEP

TCCTACCAGGTGACGCTGAGA
NO:


official)


2300





APOC1
NM_001645.3
GGAAACACACTGGAGGACAAGGCTCGGGAACTCATCAGCCGCATCAAACAGAGTGAACTTT
SEQ ID




CTGCCAAGATGCG
NO:





2301





AREG
NM_001657.1
TGTGAGTGAAATGCCTTCTAGTAGTGAACCGTCCTCGGGAGCCGACTATGACTACTCAGAAG
SEQ ID




AGTATGATAACGAACCACAA
NO:





2302





ARG
NM_005158.2
CGCAGTGCAGCTGAGTATCTGCTCAGCAGTCTAATCAATGGCAGCTTCCTGGTGCGAGAAAG
SEQ ID




TGAGAGTAGCCCTGGGCA
NO:





2303





ARHF
NM_019034.2
ACTGGCCCACTTAGTCCTCAAGCTCCCAACCTGCTGTCCCTCAAGCCCCGCTTCTACCAGCCT
SEQ ID




GTGGAGTTCAG
NO:





2304





ATOH1
NM_005172.1
GCAGCCACCTGCAACTTTGCAGGCGAGAGAGCATCCCGTCTACCCGCCTGAGCTGTCCCTCC
SEQ ID




TGGA
NO:





2305





ATP5A1
NM_004046.3
GATGCTGCCACTCAACAACTTTTGAGTCGTGGCGTGCGTCTAACTGAGTTGCTGAAGCAAGG
SEQ ID




ACA
NO:





2306





ATP5E
NM_006886.2
CCGCTTTCGCTACAGCATGGTGGCCTACTGGAGACAGGCTGGACTCAGCTACATCCGATACT
SEQ ID




CCCA
NO:





2307





AURKB
NM_004217.1
AGCTGCAGAAGAGCTGCACATTTGACGAGCAGCGAACAGCCACGATCATGGAGGAGTTGGC
SEQ ID




AGATGC
NO:





2308





Axin 2
NM_004655.2
GGCTATGTCTTTGCACCAGCCACCAGCGCCAACGACAGTGAGATATCCAGTGATGCGCTGAC
SEQ ID




GGAT
NO:





2309





axin1
NM_003502.2
CCGTGTGACAGCATCGTTGTGGCGTACTACTTCTGCGGGGAACCCATCCCCTACCGCACCCT
SEQ ID




GGTGAG
NO:





2310





B-Catenin
NM_001904.1
GGCTCTTGTGCGTACTGTCCTTCGGGCTGGTGACAGGGAAGACATCACTGAGCCTGCCATCT
SEQ ID




GTGCTCTTCGTCATCTGA
NO:





2311





BAD
NM_032989.1
GGGTCAGGTGCCTCGAGATCGGGCTTGGGCCCAGAGCATGTTCCAGATCCCAGAGTTTGAGC
SEQ ID




CGAGTGAGCAG
NO:





2312





BAG1
NM_004323.2
CGTTGTCAGCACTTGGAATACAAGATGGTTGCCGGGTCATGTTAATTGGGAAAAAGAACAG
SEQ ID




TCCACAGGAAGAGGTTGAAC
NO:





2313





BAG2
NM_004282.2
CTAGGGGCAAAAAGCATGACTGCTTTTTCCTGTCTGGCATGGAATCACGCAGTCACCTTGGG
SEQ ID




CATTTAG
NO:





2314





BAG3
NM_004281.2
GAAAGTAAGCCAGGCCCAGTTGGACCAGAACTCCCTCCTGGACACATCCCAATTCAAGTGA
SEQ ID




TCCGCAAAGAGGT
NO:





2315





Bak
NM_001188.1
CCATTCCCACCATTCTACCTGAGGCCAGGACGTCTGGGGTGTGGGGATTGGTGGGTCTATGT
SEQ ID




TCCC
NO:





2316





Bax
NM_004324.1
CCGCCGTGGACACAGACTCCCCCCGAGAGGTCTTTTTCCGAGTGGCAGCTGACATGTTTTCT
SEQ ID




GACGGCAA
NO:





2317





BBC3
NM_014417.1
CCTGGAGGGTCCTGTACAATCTCATCATGGGACTCCTGCCCTTACCCAGGGGCCACAGAGCC
SEQ ID




CCCGAGATGGAGCCCAATTAG
NO:





2318





BCAS1
NM_003657.1
CCCCGAGACAACGGAGATAAGTGCTGTTGCGGATGCCAACGGAAAGAATCTTGGGAAAGAG
SEQ ID




GCCAAACCCGAG
NO:





2319





Bcl2
NM_000633.1
CAGATGGACCTAGTACCCACTGAGATTTCCACGCCGAAGGACAGCGATGGGAAAAATGCCC
SEQ ID




TTAAATCATAGG
NO:





2320





BCL2L10
NM_020396.2
GCTGGGATGGCTTTTGTCACTTCTTCAGGACCCCCTTTCCACTGGCTTTTTGGAGAAAACAGC
SEQ ID




TGGTCCAGGC
NO:





2321





BCL2L11
NM_138621.1
AATTACCAAGCAGCCGAAGACCACCCACGAATGGTTATCTTACGACTGTTACGTTACATTGT
SEQ ID




CCGCCTG
NO:





2322





BCL2L12
NM_138639.1
AACCCACCCCTGTCTTGGAGCTCCGGGTAGCTCTCAAACTCGAGGCTGCGCACCCCCTTTCC
SEQ ID




CGTCAGCTGAG
NO:





2323





Bclx
NM_001191.1
CTTTTGTGGAACTCTATGGGAACAATGCAGCAGCCGAGAGCCGAAAGGGCCAGGAACGCTT
SEQ ID




CAACCGCTG
NO:





2324





BCRP
NM_004827.1
TGTACTGGCGAAGAATATTTGGTAAAGCAGGGCATCGATCTCTCACCCTGGGGCTTGTGGAA
SEQ ID




GAATCACGTGGC
NO:





2325





BFGF
NM_007083.1
CCAGGAAGAATGCTTAAGATGTGAGTGGATGGATCTCAATGACCTGGCGAAGACTGAAAAT
SEQ ID




ACAACTCCCATCACCA
NO:





2326





BGN
NM_001711.3
GAGCTCCGCAAGGATGACTTCAAGGGTCTCCAGCACCTCTACGCCCTCGTCCTGGTGAACAA
SEQ ID




CAAG
NO:





2327





BID
NM_001196.2
GGACTGTGAGGTCAACAACGGTTCCAGCCTCAGGGATGAGTGCATCACAAACCTACTGGTG
SEQ ID




TTTGGCTTCC
NO:





2328





BIK
NM_001197.3
ATTCCTATGGCTCTGCAATTGTCACCGGTTAACTGTGGCCTGTGCCCAGGAAGAGCCATTCA
SEQ ID




CTCCTGCC
NO:





2329





BIN1
NM_004305.1
CCTGCAAAAGGGAACAAGAGCCCTTCGCCTCCAGATGGCTCCCCTGCCGCCACCCCCGAGAT
SEQ ID




CAGAGTCAACCACG
NO:





2330





BLMH
NM_000386.2
GGTTGCTGCCTCCATCAAAGATGGAGAGGCTGTGTGGTTTGGCTGTGATGTTGGAAAACACT
SEQ ID




TCAATAGCAAGCTGG
NO:





2331





BMP2
NM_001200.1
ATGTGGACGCTCTTTCAATGGACGTGTCCCCGCGTGCTTCTTAGACGGACTGCGGTCTCCTA
SEQ ID




AAGGTCGACCATGGT
NO:





2332





BMP4
NM_001202.2
GGGCTAGCCATTGAGGTGACTCACCTCCATCAGACTCGGACCCACCAGGGCCAGCATGTCA
SEQ ID




GGATTAGC
NO:





2333





BMP7
NM_001719.1
TCGTGGAACATGACAAGGAATTCTTCCACCCACGCTACCACCATCGAGAGTTCCGGTTTGAT
SEQ ID




CTTTCCA
NO:





2334





BMPR1A
NM_004329.2
TTGGTTCAGCGAACTATTGCCAAACAGATTCAGATGGTCCGGCAAGTTGGTAAAGGCCGATA
SEQ ID




TGGAGA
NO:





2335





BRAF
NM_004333.1
CCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGAGACCGATCCTCATCA
SEQ ID




GCTCCCAATGTGCATATAAA
NO:





2336





BRCA1
NM_007295.1
TCAGGGGGCTAGAAATCTGTTGCTATGGGCCCTTCACCAACATGCCCACAGATCAACTGGAA
SEQ ID




TGG
NO:





2337





BRCA2
NM_000059.1
AGTTCGTGCTTTGCAAGATGGTGCAGAGCTTTATGAAGCAGTGAAGAATGCAGCAGACCCA
SEQ ID




GCTTACCTT
NO:





2338





BRK
NM_005975.1
GTGCAGGAAAGGTTCACAAATGTGGAGTGTCTGCGTCCAATACACGCGTGTGCTCCTCTCCT
SEQ ID




TACTCCATCGTGTGTGC
NO:





2339





BTF3
NM_001207.2
CAGTGATCCACTTTAACAACCCTAAAGTTCAGGCATCTCTGGCAGCGAACACTTTCACCATT
SEQ ID




ACAGGCCATGCT
NO:





2340





BTRC
NM_033637.2
GTTGGGACACAGTTGGTCTGCAGTCGGCCCAGGACGGTCTACTCAGCACAACTGACTGCTTCA
SEQ ID





NO:





2341





BUB1
NM_004336.1
CCGAGGTTAATCCAGCACGTATGGGGCCAAGTGTAGGCTCCCAGCAGGAACTGAGAGCGCC
SEQ ID




ATGTCTT
NO:





2342





BUB1B
NM_001211.3
TCAACAGAAGGCTGAACCACTAGAAAGACTACAGTCCCAGCACCGACAATTCCAAGCTCGA
SEQ ID




GTGTCTCGGCAAACTCTGTTG
NO:





2343





BUB3
NM_004725.1
CTGAAGCAGATGGTTCATCATTTCCTGGGCTGTTAAACAAAGCGAGGTTAAGGTTAGACTCT
SEQ ID




TGGGAATCAGC
NO:





2344





c-abl
NM_005157.2
CCATCTCGCTGAGATACGAAGGGAGGGTGTACCATTACAGGATCAACACTGCTTCTGATGGC
SEQ ID




AAGCTCTACGTCT
NO:





2345





c-kit
NM_000222.1
GAGGCAACTGCTTATGGCTTAATTAAGTCAGATGCGGCCATGACTGTCGCTGTAAAGATGCT
SEQ ID




CAAGCCGAGTGCC
NO:





2346





c-myb (MYB
NM_005375.1
AACTCAGACTTGGAAATGCCTTCTTTAACTTCCACCCCCCTCATTGGTCACAAATTGACTGTT
SEQ ID


official)

ACAACACCATTTCATAGAGACCAG
NO:





2347





c-Src
NM_005417.3
TGAGGAGTGGTATTTTGGCAAGATCACCAGACGGGAGTCAGAGCGGTTACTGCTCAATGCA
SEQ ID




GAGAACCCGAGAG
NO:





2348





C20 orf1
NM_012112.2
TCAGCTGTGAGCTGCGGATACCGCCCGGCAATGGGACCTGCTCTTAACCTCAAACCTAGGAC
SEQ ID




CGT
NO:





2349





C20ORF126
NM_030815.2
CCAGCACTGCTCGTTACTGTCTGCCTTCAGTGGTCTGAGGTCCCAGTATGAACTGCCGTGAA
SEQ ID




GTCAA
NO:





2350





C8orf4
NM_020130.2
CTACGAGTCAGCCCATCCATCCATGGCTACCACTTCGACACAGCCTCTCGTAAGAAAGCCGT
SEQ ID




GGGCA
NO:





2351





CA9
NM_001216.1
ATCCTAGCCCTGGTTTTTGGCCTCCTTTTTGCTGTCACCAGCGTCGCGTTCCTTGTGCAGATG
SEQ ID




AGAAGGCAG
NO:





2352





Cad17
NM_004063.2
GAAGGCCAAGAACCGAGTCAAATTATATTCCAGTTTAAGGCCAATCCTCCTGCTGTGACTTT
SEQ ID




TGAACTAACTGGGGA
NO:





2353





CALD1
NM_004342.4
CACTAAGGTTTGAGACAGTTCCAGAAAGAACCCAAGCTCAAGACGCAGGACGAGCTCAGTT
SEQ ID




GTAGAGGGCTAATTCGC
NO:





2354





CAPG
NM_001747.1
GATTGTCACTGATGGGGAGGAGCCTGCTGAGATGATCCAGGTCCTGGGCCCCAAGCCTGCTC
SEQ ID




TGAAGG
NO:





2355





CAPN1
NM_005186.2
CAAGAAGCTGTACGAGCTCATCATCACCCGCTACTCGGAGCCCGACCTGGCGGTCGACTTTG
SEQ ID




ACAATTTCGTTTGCTGC
NO:





2356





CASP8
NM_033357.1
CCTCGGGGATACTGTCTGATCATCAACAATCACAATTTTGCAAAAGCACGGGAGAAAGTGC
SEQ ID




CCAAACTTC
NO:





2357





CASP9
NM_001229.2
TGAATGCCGTGGATTGCACGTGGCCTCTTGAGCAGTGGCTGGTCCAGGGCTAGTGACTTGTG
SEQ ID




TCCCATGATCCCTGT
NO:





2358





CAT
NM_001752.1
ATCCATTCGATCTCACCAAGGTTTGGCCTCACAAGGACTACCCTCTCATCCCAGTTGGTAAA
SEQ ID




CTGGTCTTAAACCGGA
NO:





2359





CAV1
NM_001753.3
GTGGCTCAACATTGTGTTCCCATTTCAGCTGATCAGTGGGCCTCCAAGGAGGGGCTGTAAAA
SEQ ID




TGGAGGCCATTG
NO:





2360





CBL
NM_005188.1
TCATTCACAAACCTGGCAGTTATATCTTCCGGCTGAGCTGTACTCGTCTGGGTCAGTGGGCT
SEQ ID




ATTGGGTATG
NO:





2361





CCL20
NM_004591.1
CCATGTGCTGTACCAAGAGTTTGCTCCTGGCTGCTTTGATGTCAGTGCTGCTACTCCACCTCT
SEQ ID




GCGGCG
NO:





2362





CCL3
NM_002983.1
AGCAGACAGTGGTCAGTCCTTTCTTGGCTCTGCTGACACTCGAGCCCACATTCCGTCACCTG
SEQ ID




CTCAGAATCATGCAG
NO:





2363





CCNA2
NM_001237.2
CCATACCTCAAGTATTTGCCATCAGTTATTGCTGGAGCTGCCTTTCATTTAGCACTCTACACA
SEQ ID




GTCACGGGACAAAGCT
NO:





2364





CCNB1
NM_031966.1
TTCAGGTTGTTGCAGGAGACCATGTACATGACTGTCTCCATTATTGATCGGTTCATGCAGAA
SEQ ID




TAATTGTGTGCCCAAGAAGATG
NO:





2365





CCNB2
NM_004701.2
AGGCTTCTGCAGGAGACTCTGTACATGTGCGTTGGCATTATGGATCGATTTTTACAGGTTCA
SEQ ID




GCCAGTTTCCC
NO:





2366





CCND1
NM_001758.1
GCATGTTCGTGGCCTCTAAGATGAAGGAGACCATCCCCCTGACGGCCGAGAAGCTGTGCATC
SEQ ID




TACACCG
NO:





2367





CCND3
NM_001760.2
CCTCTGTGCTACAGATTATACCTTTGCCATGTACCCGCCATCCATGATCGCCACGGGCAGCA
SEQ ID




TTGGGGCTGCAGTG
NO:





2368





CCNE1
NM_001238.1
AAAGAAGATGATGACCGGGTTTACCCAAACTCAACGTGCAAGCCTCGGATTATTGCACCATC
SEQ ID




CAGAGGCTC
NO:





2369





CCNE2
NM_057749.1
ATGCTGTGGCTCCTTCCTAACTGGGGCTTTCTTGACATGTAGGTTGCTTGGTAATAACCTTTT
SEQ ID




TGTATATCACAATTTGGGT
NO:





2370





CCNE2
NM_057749var1
GGTCACCAAGAAACATCAGTATGAAATTAGGAATTGTTGGCCACCTGTATTATCTGGGGGGA
SEQ ID


variant 1

TCAGTCCTTGCATTATCATTGAA
NO:





2371





CCR7
NM_001838.2
GGATGACATGCACTCAGCTCTTGGCTCCACTGGGATGGGAGGAGAGGACAAGGGAAATGTC
SEQ ID




AGG
NO:





2372





CD105
NM_000118.1
GCAGGTGTCAGCAAGTATGATCAGCAATGAGGCGGTGGTCAATATCCTGTCGAGCTCATCAC
SEQ ID




CACAGCGGAAAAA
NO:





2373





CD134
NM_003327.1
GCCCAGTGCGGAGAACAGGTCCAGCTTGATTCTCGTCTCTGCACTTAAGCTGTTCTCCAGGT
SEQ ID


(TNFRSF4

GCGTGTGATT
NO:


official)


2374





CD18
NM_000211.1
CGTCAGGACCCACCATGTCTGCCCCATCACGCGGCCGAGACATGGCTTGGCCACAGCTCTTG
SEQ ID




AGGATGTCACCAATTAACC
NO:





2375





CD24
NM_013230.1
TCCAACTAATGCCACCACCAAGGCGGCTGGTGGTGCCCTGCAGTCAACAGCCAGTCTCTTCG
SEQ ID




TGGTCTCACTCTCTC
NO:





2376





CD28
NM_006139.1
TGTGAAAGGGAAACACCTTTGTCCAAGTCCCCTATTTCCCGGACCTTCTAAGCCCTTTTGGGT
SEQ ID




GCT
NO:





2377





CD31
NM_000442.1
TGTATTTCAAGACCTCTGTGCACTTATTTATGAACCTGCCCTGCTCCCACAGAACACAGCAAT
SEQ ID




TCCTCAGGCTAA
NO:





2378





CD34
NM_001773.1
CCACTGCACACACCTCAGAGGCTGTTCTTGGGGCCCTACACCTTGAGGAGGGGCAGGTAAA
SEQ ID




CTCCTG
NO:





2379





CD3z
NM_000734.1
AGATGAAGTGGAAGGCGCTTTTCACCGCGGCCATCCTGCAGGCACAGTTGCCGATTACAGA
SEQ ID




GGCA
NO:





2380





CD44E
X55150
ATCACCGACAGCACAGACAGAATCCCTGCTACCAATATGGACTCCAGTCATAGTACAACGCT
SEQ ID




TCAGCCTACTGCAAATCCAAACACAGGT
NO:





2381





CD44s
M59040.1
GACGAAGACAGTCCCTGGATCACCGACAGCACAGACAGAATCCCTGCTACCAGAGACCAAG
SEQ ID




ACACATTCCACCCCAGT
NO:





2382





CD44v3
AJ251595v3
CACACAAAACAGAACCAGGACTGGACCCAGTGGAACCCAAGCCATTCAAATCCGGAAGTGC
SEQ ID




TACTTCAG
NO:





2383





CD44v6
AJ251595v6
CTCATACCAGCCATCCAATGCAAGGAAGGACAACACCAAGCCCAGAGGACAGTTCCTGGAC
SEQ ID




TGATTTCTTCAACCCAA
NO:





2384





CD68
NM_001251.1
TGGTTCCCAGCCCTGTGTCCACCTCCAAGCCCAGATTCAGATTCGAGTCATGTACACAACCC
SEQ ID




AGGGTGGAGGAG
NO:





2385





CD80
NM_005191.2
TTCAGTTGCTTTGCAGGAAGTGTCTAGAGGAATATGGTGGGCACAGAAGTAGCTCTGGTGAC
SEQ ID




CTTGATCAA
NO:





2386





CD82
NM_002231.2
GTGCAGGCTCAGGTGAAGTGCTGCGGCTGGGTCAGCTTCTACAACTGGACAGACAACGCTG
SEQ ID




AGCTCATGAATCGCCCTGAGGTC
NO:





2387





CD8A
NM_171827.1
AGGGTGAGGTGCTTGAGTCTCCAACGGCAAGGGAACAAGTACTTCTTGATACCTGGGATACT
SEQ ID




GTGCCC
NO:





2388





CD9
NM_001769.1
GGGCGTGGAACAGTTTATCTCAGACATCTGCCCCAAGAAGGACGTACTCGAAACCTTCACCG
SEQ ID




TG
NO:





2389





CDC2
NM_001786.2
GAGAGCGACGCGGTTGTTGTAGCTGCCGCTGCGGCCGCCGCGGAATAATAAGCCGGGATCT
SEQ ID




ACCATAC
NO:





2390





CDC20
NM_001255.1
TGGATTGGAGTTCTGGGAATGTACTGGCCGTGGCACTGGACAACAGTGTGTACCTGTGGAGT
SEQ ID




GCAAGC
NO:





2391





cdc25A
NM_001789.1
TCTTGCTGGCTACGCCTCTTCTGTCCCTGTTAGACGTCCTCCGTCCATATCAGAACTGTGCCA
SEQ ID




CAATGCAG
NO:





2392





CDC25B
NM_021874.1
AAACGAGCAGTTTGCCATCAGACGCTTCCAGTCTATGCCGGTGAGGCTGCTGGGCCACAGCC
SEQ ID




CCGTGCTTCGGAACATCACCAAC
NO:





2393





CDC25C
NM_001790.2
GGTGAGCAGAAGTGGCCTATATCGCTCCCCGTCGATGCCAGAGAACTTGAACAGGCCAAGA
SEQ ID




CTGAAG
NO:





2394





CDC4
NM_018315.2
GCAGTCCGCTGTGTTCAATATGATGGCAGGAGGGTTGTTAGTGGAGCATATGATTTTATGGT
SEQ ID




AAAGGTGTGGGATCC
NO:





2395





CDC42
NM_001791.2
TCCAGAGACTGCTGAAAAGCTGGCCCGTGACCTGAAGGCTGTCAAGTATGTGGAGTGTTCTG
SEQ ID




CACTTACACA
NO:





2396





CDC42BPA
NM_003607.2
GAGCTGAAAGACGCACACTGTCAGAGGAAACTGGCCATGCAGGAATTCATGGAGATCAATG
SEQ ID




AGCGGC
NO:





2397





CDC6
NM_001254.2
GCAACACTCCCCATTTACCTCCTTGTTCTCCACCAAAGCAAGGCAAGAAAGAGAATGGTCCC
SEQ ID




CCTCA
NO:





2398





CDCA7 v2
NM_145810.1
AAGACCGTGGATGGCTACATGAATGAAGATGACCTGCCCAGAAGCCGTCGCTCCAGATCAT
SEQ ID




CCGTGACCCT
NO:





2399





CDH1
NM_004360.2
TGAGTGTCCCCCGGTATCTTCCCCGCCCTGCCAATCCCGATGAAATTGGAAATTTTATTGATG
SEQ ID




AAAATCTGAAAGCGGCTG
NO:





2400





CDH11
NM_001797.2
GTCGGCAGAAGCAGGACTTGTACCTTCTGCCCATAGTGATCAGCGATGGCGGCATCCCGCCC
SEQ ID




ATGAGTAG
NO:





2401





CDH3
NM_001793.3
ACCCATGTACCGTCCTCGGCCAGCCAACCCAGATGAAATCGGCAACTTTATAATTGAGAACC
SEQ ID




TGAAGGCGG
NO:





2402





CDK2
NM_001798.2
AATGCTGCACTACGACCCTAACAAGCGGATTTCGGCCAAGGCAGCCCTGGCTCACCCTTTCT
SEQ ID




TCCAGGATGTGACCAA
NO:





2403





CDX1
NM_001804.1
AGCAACACCAGCCTCCTGGCCACCTCCTCTCCAATGCCTGTGAAAGAGGAGTTTCTGCCATA
SEQ ID




GCCC
NO:





2404





Cdx2
NM_001265.2
GGGCAGGCAAGGTTTACACTGCGGAAGCCAAAGGCAGCTAAGATAGAAAGCTGGACTGACC
SEQ ID




AAAGAC
NO:





2405





CEACAM1
NM_001712.2
ACTTGCCTGTTCAGAGCACTCATTCCTTCCCACCCCCAGTCCTGTCCTATCACTCTAATTCGG
SEQ ID




ATTTGCCA
NO:





2406





CEACAM6
NM_002483.2
CACAGCCTCACTTCTAACCTTCTGGAACCCACCCACCACTGCCAAGCTCACTATTGAATCCA
SEQ ID




CGCCATTCAA
NO:





2407





CEBPB
NM_005194.2
GCAACCCACGTGTAACTGTCAGCCGGGCCCTGAGTAATCGCTTAAAGATGTTCCTACGGGCT
SEQ ID




TGT
NO:





2408





CEGP1
NM_020974.1
TGACAATCAGCACACCTGCATTCACCGCTCGGAAGAGGGCCTGAGCTGCATGAATAAGGAT
SEQ ID




CACGGCTGTAGTCACA
NO:





2409





CENPA
NM_001809.2
TAAATTCACTCGTGGTGTGGACTTCAATTGGCAAGCCCAGGCCCTATTGGCCCTACAAGAGGC
SEQ ID





NO:





2410





CENPE
NM_001813.1
GGATGCTGGTGACCTCTTCTTCCCTCACGTTGCAACAGGAATTAAAGGCTAAAAGAAAACGA
SEQ ID




AGAGTTACTTGGTGCCTTGGC
NO:





2411





CENPF
NM_016343.2
CTCCCGTCAACAGCGTTCTTTCCAAACACTGGACCAGGAGTGCATCCAGATGAAGGCCAGAC
SEQ ID




TCACCC
NO:





2412





CES2
NM_003869.4
ACTTTGCGAGAAATGGGAACCCCAATGGCGAGGGTCTGCCACACTGGCCGCTGTTCGACCA
SEQ ID




GGAGGAGCAATACCTG
NO:





2413





CGA
NM_001275.2
CTGAAGGAGCTCCAAGACCTCGCTCTCCAAGGCGCCAAGGAGAGGGCACATCAGCAGAAGA
SEQ ID


(CHGA

AACACAGCGGTTTTG
NO:


official)


2414





CGB
NM_000737.2
CCACCATAGGCAGAGGCAGGCCTTCCTACACCCTACTCCCTGTGCCTCCAGCCTCGACTAGT
SEQ ID




CCCTAGCACTCGACGACT
NO:





2415





CHAF1B
NM_005441.1
GAGGCCAGTGGTGGAAACAGGTGTGGAGCTGATGAGTCTGCCCTACCGCCTGGTGTTTGCTG
SEQ ID




TGGCCTCGGA
NO:





2416





CHD2
NM_001271.1
CTCTGTGCGAGGCTGTCAGCCACACTAGGTATCAGGGATCCCGAGATGGGTACCAGCCCAC
SEQ ID




AGTCCTTACC
NO:





2417





CHFR
NM_018223.1
AAGGAAGTGGTCCCTCTGTGGCAAGTGATGAAGTCTCCAGCTTTGCCTCAGCTCTCCCAGAC
SEQ ID




AGAAAGACTGCGTC
NO:





2418





Chk1
NM_001274.1
GATAAATTGGTACAAGGGATCAGCTTTTCCCAGCCCACATGTCCTGATCATATGCTTTTGAA
SEQ ID




TAGTCAGTTACTTGGCACCC
NO:





2419





Chk2
NM_007194.1
ATGTGGAACCCCCACCTACTTGGCGCCTGAAGTTCTTGTTTCTGTTGGGACTGCTGGGTATAA
SEQ ID




CCGTGCTGTGGACTG
NO:





2420





CIAP1
NM_001166.2
TGCCTGTGGTGGGAAGCTCAGTAACTGGGAACCAAAGGATGATGCTATGTCAGAACACCGG
SEQ ID




AGGCATTTTCC
NO:





2421





cIAP2
NM_001165.2
GGATATTTCCGTGGCTCTTATTCAAACTCTCCATCAAATCCTGTAAACTCCAGAGCAAATCA
SEQ ID




AGATTTTTCTGCCTTGATGAGAAG
NO:





2422





CKS1B
NM_001826.1
GGTCCCTAAAACCCATCTGATGTCTGAATCTGAATGGAGGAATCTTGGCGTTCAGCAGAGTC
SEQ ID




AGGGATGGGTCCATTA
NO:





2423





CKS2
NM_001827.1
GGCTGGACGTGGTTTTGTCTGCTGCGCCCGCTCTTCGCGCTCTCGTTTCATTTTCTGCAGCG
SEQ ID





NO:





2424





Claudin 4
NM_001305.2
GGCTGCTTTGCTGCAACTGTCCACCCCGCACAGACAAGCCTTACTCCGCCAAGTATTCTGCT
SEQ ID




GCCCGCTCTG
NO:





2425





CLDN1
NM_021101.3
TCTGGGAGGTGCCCTACTTTGCTGTTCCTGTCCCCGAAAAACAACCTCTTACCCAACACCAA
SEQ ID




GGCCCTATCCA
NO:





2426





CLDN7
NM_001307.3
GGTCTGCCCTAGTCATCCTGGGAGGTGCACTGCTCTCCTGTTCCTGTCCTGGGAATGAGAGC
SEQ ID




AAGGCTGGGTAC
NO:





2427





CLIC1
NM_001288.3
CGGTACTTGAGCAATGCCTACGCCCGGGAAGAATTCGCTTCCACCTGTCCAGATGATGAGGA
SEQ ID




GATCGA
NO:





2428





CLTC
NM_004859.1
ACCGTATGGACAGCCACAGCCTGGCTTTGGGTACAGCATGTGAGATGAAGCGCTGATCCTGT
SEQ ID




AGTCA
NO:





2429





CLU
NM_001831.1
CCCCAGGATACCTACCACTACCTGCCCTTCAGCCTGCCCCACCGGAGGCCTCACTTCTTCTTT
SEQ ID




CCCAAGTCCCGCA
NO:





2430





cMet
NM_000245.1
GACATTTCCAGTCCTGCAGTCAATGCCTCTCTGCCCCACCCTTTGTTCAGTGTGGCTGGTGCC
SEQ ID




ACGACAAATGTGTGCGATCGGAG
NO:





2431





cMYC
NM_002467.1
TCCCTCCACTCGGAAGGACTATCCTGCTGCCAAGAGGGTCAAGTTGGACAGTGTCAGAGTCC
SEQ ID




TGAGACAGATCAGCAACAACCG
NO:





2432





CNN
NM_001299.2
TCCACCCTCCTGGCTTTGGCCAGCATGGCGAAGACGAAAGGAAACAAGGTGAACGTGGGAG
SEQ ID




TGA
NO:





2433





COL1A1
NM_000088.2
GTGGCCATCCAGCTGACCTTCCTGCGCCTGATGTCCACCGAGGCCTCCCAGAACATCACCTA
SEQ ID




CCACTG
NO:





2434





COL1A2
NM_000089.2
CAGCCAAGAACTGGTATAGGAGCTCCAAGGACAAGAAACACGTCTGGCTAGGAGAAACTAT
SEQ ID




CAATGCTGGCAGCCAGTTT
NO:





2435





COPS3
NM_003653.2
ATGCCCAGTGTTCCTGACTTCGAAACGCTATTCTCACAGGTTCAGCTCTTCATCAGCACTTGT
SEQ ID




AATGGGGAG
NO:





2436





COX2
NM_000963.1
TCTGCAGAGTTGGAAGCACTCTATGGTGACATCGATGCTGTGGAGCTGTATCCTGCCCTTCT
SEQ ID




GGTAGAAAAGCCTCGGC
NO:





2437





COX3
MITO_COX3
TCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTTGTAGCCACAGGCT
SEQ ID




TCCACGGACTTCACGTC
NO:





2438





CP
NM_000096.1
CGTGAGTACACAGATGCCTCCTTCACAAATCGAAAGGAGAGAGGCCCTGAAGAAGAGCATC
SEQ ID




TTGGCATCCTGG
NO:





2439





CRBP
NM_002899.2
TGGTCTGCAAGCAAGTATTCAAGAAGGTGCAGTGAGGCCCAAGCAGACAACCTTGTCCCAA
SEQ ID




CCAATCAGC
NO:





2440





CREBBP
NM_004380.1
TGGGAAGCAGCTGTGTACCATTCCTCGCGATGCTGCCTACTACAGCTATCAGAATAGGTATC
SEQ ID




ATTTCTGTGAGAAGTGTTTC
NO:





2441





CRIP2
NM_001312.1
GTGCTACGCCACCCTGTTCGGACCCAAAGGCGTGAACATCGGGGGCGCGGGCTCCTACATCT
SEQ ID




ACGAGAAGCCCCTG
NO:





2442





cripto
NM_003212.1
GGGTCTGTGCCCCATGACACCTGGCTGCCCAAGAAGTGTTCCCTGTGTAAATGCTGGCACGG
SEQ ID


(TDGF1

TCA
NO:


official)


2443





CRK(a)
NM_016823.2
CTCCCTAACCTCCAGAATGGGCCCATATATGCCAGGGTTATCCAGAAGCGAGTCCCCAATGC
SEQ ID




CTACGACAAGACA
NO:





2444





CRMP1
NM_001313.1
AAGGTTTTTGGATTGCAAGGGGTTTCCAGGGGCATGTATGACGGTCCTGTGTACGAGGTACC
SEQ ID




AGCTACACCC
NO:





2445





CRYAB
NM_001885.1
GATGTGATTGAGGTGCATGGAAAACATGAAGAGCGCCAGGATGAACATGGTTTCATCTCCA
SEQ ID




GGGAGTTC
NO:





2446





CSEL1
NM_001316.2
TTACGCAGCTCATGCTCTTGAACGGCTCTTTACTATGCGAGGGCCTAACAATGCCACTCTCTT
SEQ ID




TACAGCTGC
NO:





2447





CSF1
NM_000757.3
TGCAGCGGCTGATTGACAGTCAGATGGAGACCTCGTGCCAAATTACATTTGAGTTTGTAGAC
SEQ ID




CAGGAACAGTTG
NO:





2448





CSK (SRC)
NM_004383.1
CCTGAACATGAAGGAGCTGAAGCTGCTGCAGACCATCGGGAAGGGGGAGTTCGGAGACGTG
SEQ ID




ATG
NO:





2449





CTAG1B
NM_001327.1
GCTCTCCATCAGCTCCTGTCTCCAGCAGCTTTCCCTGTTGATGTGGATCACGCAGTGCTTTCT
SEQ ID




GCCCGTGTT
NO:





2450





CTGF
NM_001901.1
GAGTTCAAGTGCCCTGACGGCGAGGTCATGAAGAAGAACATGATGTTCATCAAGACCTGTG
SEQ ID




CCTGCCATTACAACT
NO:





2451





CTHRC1
NM_138455.2
GCTCACTTCGGCTAAAATGCAGAAATGCATGCTGTCAGCGTTGGTATTTCACATTCAATGGA
SEQ ID




GCTGA
NO:





2452





CTLA4
NM_005214.2
CACTGAGGTCCGGGTGACAGTGCTTCGGCAGGCTGACAGCCAGGTGACTGAAGTCTGTGCG
SEQ ID




GCAACCTAC
NO:





2453





CTNNBIP1
NM_020248.2
GTTTTCCAGGTCGGAGACGGAAGACCGGAGGCAGTAGCTGCAAAGCCCTTGGAACACCCTG
SEQ ID




GATGCT
NO:





2454





CTSB
NM_001908.1
GGCCGAGATCTACAAAAACGGCCCCGTGGAGGGAGCTTTCTCTGTGTATTCGGACTTCCTGC
SEQ ID





NO:





2455





CTSD
NM_001909.1
GTACATGATCCCCTGTGAGAAGGTGTCCACCCTGCCCGCGATCACACTGAAGCTGGGAGGC
SEQ ID




AAAGGCTACAAGCTGTCCC
NO:





2456





CTSH
NM_004390.1
GCAAGTTCCAACCTGGAAAGGCCATCGGCTTTGTCAAGGATGTAGCCAACATCACAATCTAT
SEQ ID




GACGAGGAAGCGATG
NO:





2457





CTSL
NM_001912.1
GGGAGGCTTATCTCACTGAGTGAGCAGAATCTGGTAGACTGCTCTGGGCCTCAAGGCAATG
SEQ ID




AAGGCTGCAATGG
NO:





2458





CTSL2
NM_001333.2
TGTCTCACTGAGCGAGCAGAATCTGGTGGACTGTTCGCGTCCTCAAGGCAATCAGGGCTGCA
SEQ ID




ATGGT
NO:





2459





CUL1
NM_003592.2
ATGCCCTGGTAATGTCTGCATTCAACAATGACGCTGGCTTTGTGGCTGCTCTTGATAAGGCTT
SEQ ID




GTGGTCGC
NO:





2460





CUL4A
NM_003589.1
AAGCATCTTCCTGTTCTTGGACCGCACCTATGTGCTGCAGAACTCCACGCTGCCCTCCATCTG
SEQ ID




GGATATGGGATT
NO:





2461





CXCL12
NM_000609.3
GAGCTACAGATGCCCATGCCGATTCTTCGAAAGCCATGTTGCCAGAGCCAACGTCAAGCATC
SEQ ID




TCAAA
NO:





2462





CXCR4
NM_003467.1
TGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATCATGGTTGG
SEQ ID




CCTTATCCT
NO:





2463





CYBA
NM_000101.1
GGTGCCTACTCCATTGTGGCGGGCGTGTTTGTGTGCCTGCTGGAGTACCCCCGGGGGAAGAG
SEQ ID




GAAGAAGGGCTCCAC
NO:





2464





CYP1B1
NM_000104.2
CCAGCTTTGTGCCTGTCACTATTCCTCATGCCACCACTGCCAACACCTCTGTCTTGGGCTACC
SEQ ID




ACATTCCC
NO:





2465





CYP2C8
NM_000770.2
CCGTGTTCAAGAGGAAGCTCACTGCCTTGTGGAGGAGTTGAGAAAAACCAAGGCTTCACCC
SEQ ID




TGTGATCCCACT
NO:





2466





CYP3A4
NM_017460.3
AGAACAAGGACAACATAGATCCTTACATATACACACCCTTTGGAAGTGGACCCAGAAACTG
SEQ ID




CATTGGCATGAGGTTTGC
NO:





2467





CYR61
NM_001554.3
TGCTCATTCTTGAGGAGCATTAAGGTATTTCGAAACTGCCAAGGGTGCTGGTGCGGATGGAC
SEQ ID




ACTAATGCAGCCAC
NO:





2468





DAPK1
NM_004938.1
CGCTGACATCATGAATGTTCCTCGACCGGCTGGAGGCGAGTTTGGATATGACAAAGACACAT
SEQ ID




CGTTGCTGAAAGAGA
NO:





2469





DCC
NM_005215.1
AAATGTCCTCCTCGACTGCTCCGCGGAGTCCGACCGAGGAGTTCCAGTGATCAAGTGGAAG
SEQ ID




AAAGATGGCATTCA
NO:





2470





DCC_exons18-23
X76132_18-23
GGTCACCGTTGGTGTCATCACAGTGCTGGTAGTGGTCATCGTGGCTGTGATTTGCACCCGAC
SEQ ID




GCTC
NO:





2471





DCC_exons6-7
X76132_6-7
ATGGAGATGTGGTCATTCCTAGTGATTATTTTCAGATAGTGGGAGGAAGCAACTTACGGATA
SEQ ID




CTTGGGGTGGTG
NO:





2472





DCK
NM_000788.1
GCCGCCACAAGACTAAGGAATGGCCACCCCGCCCAAGAGAAGCTGCCCGTCTTTCTCAGCC
SEQ ID




AGCTCTGAGGGGACCCGCATCAAGAAAATCTCCATCGAAGGGAACATCG
NO:





2473





DDB1
NM_001923.2
TGCGGATCATCCGGAATGGAATTGGAATCCACGAGCATGCCAGCATTGACTTACCAGGCATC
SEQ ID




AAAGGA
NO:





2474





DET1
NM_017996.2
CTTGTGGAGATCACCCAATCAGGTTCTATGCCCGGGACTCGGGCCTGCTCAAGTTTGAGATC
SEQ ID




CAGGCGGG
NO:





2475





DHFR
NM_000791.2
TTGCTATAACTAAGTGCTTCTCCAAGACCCCAACTGAGTCCCCAGCACCTGCTACAGTGAGC
SEQ ID




TGCCATTCCAC
NO:





2476





DHPS
NM_013407.1
GGGAGAACGGGATCAATAGGATCGGAAACCTGCTGGTGCCCAATGAGAATTACTGCAAGTT
SEQ ID




TGAGGACTGGCTGATGC
NO:





2477





DIABLO
NM_019887.1
CACAATGGCGGCTCTGAAGAGTTGGCTGTCGCGCAGCGTAACTTCATTCTTCAGGTACAGAC
SEQ ID




AGTGTTTGTGT
NO:





2478





DIAPH1
NM_005219.2
CAAGCAGTCAAGGAGAACCAGAAGCGGCGGGAGACAGAAGAAAAGATGAGGCGAGCAAA
SEQ ID




ACT
NO:





2479





DICER1
NM_177438.1
TCCAATTCCAGCATCACTGTGGAGAAAAGCTGTTTGTCTCCCCAGCATACTTTATCGCCTTCA
SEQ ID




CTGCC
NO:





2480





DKK1
NM_012242.1
TGACAACTACCAGCCGTACCCGTGCGCAGAGGACGAGGAGTGCGGCACTGATGAGTACTGC
SEQ ID




GCTAGTCCC
NO:





2481





DLC1
NM_006094.3
GATTCAGACGAGGATGAGCCTTGTGCCATCAGTGGCAAATGGACTTTCCAAAGGGACAGCA
SEQ ID




AGAGGTG
NO:





2482





DPYD
NM_000110.2
AGGACGCAAGGAGGGTTTGTCACTGGCAGACTCGAGACTGTAGGCACTGCCATGGCCCCTG
SEQ ID




TGCTCAGTAAGGACTCGGCGGACATC
NO:





2483





DR4
NM_003844.1
TGCACAGAGGGTGTGGGTTACACCAATGCTTCCAACAATTTGTTTGCTTGCCTCCCATGTAC
SEQ ID




AGCTTGTAAATCAGATGAAGA
NO:





2484





DR5
NM_003842.2
CTCTGAGACAGTGCTTCGATGACTTTGCAGACTTGGTGCCCTTTGACTCCTGGGAGCCGCTC
SEQ ID




ATGAGGAAGTTGGGCCTCATGG
NO:





2485





DRG1
NM_004147.3
CCTGGATCTCCCAGGTATCATTGAAGGTGCCAAGGATGGGAAAGGTAGAGGTCGTCAAGTC
SEQ ID




ATTGCA
NO:





2486





DSP
NM_004415.1
TGGCACTACTGCATGATTGACATAGAGAAGATCAGGGCCATGACAATCGCCAAGCTGAAAA
SEQ ID




CAATGCGGCAGG
NO:





2487





DTYMK
NM_012145.1
AAATCGCTGGGAACAAGTGCCGTTAATTAAGGAAAAGTTGAGCCAGGGCGTGACCCTCGTC
SEQ ID




GTGGACAGATACGCATT
NO:





2488





DUSP1
NM_004417.2
AGACATCAGCTCCTGGTTCAACGAGGCCATTGACTTCATAGACTCCATCAAGAATGCTGGAG
SEQ ID




GAAGGGTGTTTGTC
NO:





2489





DUSP2
NM_004418.2
TATCCCTGTGGAGGACAACCAGATGGTGGAGATCAGTGCCTGGTTCCAGGAGGCCATAGGC
SEQ ID




TTCATTGACTGGGTG
NO:





2490





DUT
NM_001948.2
ACACATGGAGTGCTTCTGGAACTATCAGCCCACTTGACCACCCAGTTTGTGGAAGCACAGGC
SEQ ID




AAGAG
NO:





2491





DYRK1B
NM_004714.1
AGCATGACACGGAGATGAAGTACTATATAGTACACCTGAAGCGGCACTTCATGTTCCGGAA
SEQ ID




CCACCTGTGCCTGGTATT
NO:





2492





E2F1
NM_005225.1
ACTCCCTCTACCCTTGAGCAAGGGCAGGGGTCCCTGAGCTGTTCTTCTGCCCCATACTGAAG
SEQ ID




GAACTGAGGCCTG
NO:





2493





EDN1
NM_001955.1
TGCCACCTGGACATCATTTGGGTCAACACTCCCGAGCACGTTGTTCCGTATGGACTTGGAAG
SEQ ID


endothelin

CCCTAGGTCCA
NO:





2494





EFNA1
NM_004428.2
TACATCTCCAAACCCATCCACCAGCATGAAGACCGCTGCTTGAGGTTGAAGGTGACTGTCAG
SEQ ID




TGGCAA
NO:





2495





EFNA3
NM_004952.3
ACTACATCTCCACGCCCACTCACAACCTGCACTGGAAGTGTCTGAGGATGAAGGTGTTCGTC
SEQ ID




TGCTG
NO:





2496





EFNB1
NM_004429.3
GGAGCCCGTATCCTGGAGCTCCCTCAACCCCAAGTTCCTGAGTGGGAAGGGCTTGGTGATCT
SEQ ID




ATCC
NO:





2497





EFNB2
NM_004093.2
TGACATTATCATCCCGCTAAGGACTGCGGACAGCGTCTTCTGCCCTCACTACGAGAAGGTCA
SEQ ID




GCGGGGACTAC
NO:





2498





EFP
NM_005082.2
TTGAACAGAGCCTGACCAAGAGGGATGAGTTCGAGTTTCTGGAGAAAGCATCAAAACTGCG
SEQ ID




AGGAATCTCAACA
NO:





2499





EGFR
NM_005228.1
TGTCGATGGACTTCCAGAACCACCTGGGCAGCTGCCAAAAGTGTGATCCAAGCTGTCCCAAT
SEQ ID





NO:





2500





EGLN1
NM_022051.1
TCAATGGCCGGACGAAAGCCATGGTTGCTTGTTATCCGGGCAATGGAACGGGTTATGTACGT
SEQ ID




CATGTTGATAATCCAAA
NO:





2501





EGLN3
NM_022073.2
GCTGGTCCTCTACTGCGGGAGCCGGCTGGGCAAATACTACGTCAAGGAGAGGTCTAAGGCA
SEQ ID




ATGGTGG
NO:





2502





EGR1
NM_001964.2
GTCCCCGCTGCAGATCTCTGACCCGTTCGGATCCTTTCCTCACTCGCCCACCATGGACAACTA
SEQ ID




CCCTAAGCTGGAG
NO:





2503





EGR3
NM_004430.2
CCATGTGGATGAATGAGGTGTCTCCTTTCCATACCCAGTCTCACCTTCTCCCCACCCTACCTC
SEQ ID




ACCTCTTCTCAGGCA
NO:





2504





EI24
NM_004879.2
AAAGTGGTGAATGCCATTTGGTTTCAGGATATAGCTGACCTGGCATTTGAGGTATCAGGGAG
SEQ ID




GAAGCCTCAC
NO:





2505





EIF4E
NM_001968.1
GATCTAAGATGGCGACTGTCGAACCGGAAACCACCCCTACTCCTAATCCCCCGACTACAGAA
SEQ ID




GAGGAGAAAACGGAATCTAA
NO:





2506





EIF4EL3
NM_004846.1
AAGCCGCGGTTGAATGTGCCATGACCCTCTCCCTCTCTGGATGGCACCATCATTGAAGCTGG
SEQ ID




CGTCA
NO:





2507





ELAVL1
NM_001419.2
GACAGGAGGCCTCTATCCTGTCCCTCCACCCCACCCTCCACCTCAATCCCCTCCCATCTTCCC
SEQ ID




CAGACCTACCTCAC
NO:





2508





EMP1
NM_001423.1
GCTAGTACTTTGATGCTCCCTTGATGGGGTCCAGAGAGCCTCCCTGCAGCCACCAGACTTGG
SEQ ID




CCTCCAGCTGTTC
NO:





2509





EMR3
NM_032571.2
TGGCCTACCTCTTCACCATCATCAACAGCCTCCAAGGCTTCTTCATCTTCTTGGTCTACTGCC
SEQ ID




TCCTCA
NO:





2510





EMS1
NM_005231.2
GGCAGTGTCACTGAGTCCTTGAAATCCTCCCCTGCCCCGCGGGTCTCTGGATTGGGACGCAC
SEQ ID




AGTGCA
NO:





2511





ENO1
NM_001428.2
CAAGGCCGTGAACGAGAAGTCCTGCAACTGCCTCCTGCTCAAAGTCAACCAGATTGGCTCCG
SEQ ID




TGACCG
NO:





2512





EP300
NM_001429.1
AGCCCCAGCAACTACAGTCTGGGATGCCAAGGCCAGCCATGATGTCAGTGGCCCAGCATGG
SEQ ID




TCAACCTTTGAACA
NO:





2513





EPAS1
NM_001430.3
AAGCCTTGGAGGGTTTCATTGCCGTGGTGACCCAAGATGGCGACATGATCTTTCTGTCAGAA
SEQ ID




AACATCAGCA
NO:





2514





EpCAM
NM_002354.1
GGGCCCTCCAGAACAATGATGGGCTTTATGATCCTGACTGCGATGAGAGCGGGCTCTTTAAG
SEQ ID




GCCAAGCAGTGCA
NO:





2515





EPHA2
NM_004431.2
CGCCTGTTCACCAAGATTGACACCATTGCGCCCGATGAGATCACCGTCAGCAGCGACTTCGA
SEQ ID




GGCACGCCAC
NO:





2516





EPHB2
NM_004442.4
CAACCAGGCAGCTCCATCGGCAGTGTCCATCATGCATCAGGTGAGCCGCACCGTGGACAGC
SEQ ID




ATTAC
NO:





2517





EPHB4
NM_004444.3
TGAACGGGGTATCCTCCTTAGCCACGGGGCCCGTCCCATTTGAGCCTGTCAATGTCACCACT
SEQ ID




GACCGAGAGGTACCT
NO:





2518





EphB6
NM_004445.1
ACTGGTCCTCCATCGGCTCCCCAGGAGCTTTGGTTTGAGGTGCAAGGCTCAGCACTCATGCT
SEQ ID




ACACTGG
NO:





2519





EPM2A
NM_005670.2
ACTGTGGCACTTAGGGGAGATGACATTTGCTTTGGGCAGAGGCAGCTAGCCAGGACACATTT
SEQ ID




CCACT
NO:





2520





ErbB3
NM_001982.1
CGGTTATGTCATGCCAGATACACACCTCAAAGGTACTCCCTCCTCCCGGGAAGGCACCCTTT
SEQ ID




CTTCAGTGGGTCTCAGTTC
NO:





2521





ERCC1
NM_001983.1
GTCCAGGTGGATGTGAAAGATCCCCAGCAGGCCCTCAAGGAGCTGGCTAAGATGTGTATCC
SEQ ID




TGGCCG
NO:





2522





ERCC2
NM_000400.2
TGGCCTTCTTCACCAGCTACCAGTACATGGAGAGCACCGTGGCCTCCTGGTATGAGCAGGGG
SEQ ID




ATCCTTG
NO:





2523





EREG
NM_001432.1
ATAACAAAGTGTAGCTCTGACATGAATGGCTATTGTTTGCATGGACAGTGCATCTATCTGGT
SEQ ID




GGACATGAGTCAAAACTACTGCAGGTGTG
NO:





2524





ERK1
Z11696.1
ACGGATCACAGTGGAGGAAGCGCTGGCTCACCCCTACCTGGAGCAGTACTATGACCCGACG
SEQ ID




GATGAG
NO:





2525





ERK2
NM_002745.1
AGTTCTTGACCCCTGGTCCTGTCTCCAGCCCGTCTTGGCTTATCCACTTTGACTCCTTTGAGC
SEQ ID




CGTTT
NO:





2526





ESPL1
NM_012291.1
ACCCCCAGACCGGATCAGGCAAGCTGGCCCTCATGTCCCCTTCACGGTGTTTGAGGAAGTCT
SEQ ID




GCCCTACA
NO:





2527





EstR1
NM_000125.1
CGTGGTGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCA
SEQ ID




CTAGCC
NO:





2528





ETV4
NM_001986.1
TCCAGTGCCTATGACCCCCCCAGACAAATCGCCATCAAGTCCCCTGCCCCTGGTGCCCTTGG
SEQ ID




ACAGT
NO:





2529





F3
NM_001993.2
GTGAAGGATGTGAAGCAGACGTACTTGGCACGGGTCTTCTCCTACCCGGCAGGGAATGTGG
SEQ ID




AGAGCACCGGTT
NO:





2530





FABP4
NM_001442.1
GCTTTGCCACCAGGAAAGTGGCTGGCATGGCCAAACCTAACATGATCATCAGTGTGAATGG
SEQ ID




GGATG
NO:





2531





FAP
NM_004460.2
CTGACCAGAACCACGGCTTATCCGGCCTGTCCACGAACCACTTATACACCCACATGACCCAC
SEQ ID




TTCC
NO:





2532





fas
NM_000043.1
GGATTGCTCAACAACCATGCTGGGCATCTGGACCCTCCTACCTCTGGTTCTTACGTCTGTTGC
SEQ ID




TAGATTATCGTCCAAAAGTGTTAATGCC
NO:





2533





fasI
NM_000639.1
GCACTTTGGGATTCTTTCCATTATGATTCTTTGTTACAGGCACCGAGAATGTTGTATTCAGTG
SEQ ID




AGGGTCTTCTTACATGC
NO:





2534





FASN
NM_004104.4
GCCTCTTCCTGTTCGACGGCTCGCCCACCTACGTACTGGCCTACACCCAGAGCTACCGGGCA
SEQ ID




AAGC
NO:





2535





FBXO5
NM_012177.2
GGCTATTCCTCATTTTCTCTACAAAGTGGCCTCAGTGAACATGAAGAAGGTAGCCTCCTGGA
SEQ ID




GGAGAATTTCGGTGACAGTCTACAATCC
NO:





2536





FBXW7
NM_033632.1
CCCCAGTTTCAACGAGACTTCATTTCATTGCTCCCTAAAGAGTTGGCACTCTATGTGCTTTCA
SEQ ID




TTCCTGGAAC
NO:





2537





FDXR
NM_004110.2
GAGATGATTCAGTTACCGGGAGCCCGGCCCATTTTGGATCCTGTGGATTTCTTGGGTCTCCA
SEQ ID




GGACAAGAT
NO:





2538





FES
NM_002005.2
CTCTGCAGGCCTAGGTGCAGCTCCTCAGCGGCTCCAGCTCATATGCTGACAGCTCTTCACAG
SEQ ID




TCCTGG
NO:





2539





FGF18
NM_003862.1
CGGTAGTCAAGTCCGGATCAAGGGCAAGGAGACGGAATTCTACCTGTGCATGAACCGCAAA
SEQ ID




GGCAAGC
NO:





2540





FGF2
NM_002006.2
AGATGCAGGAGAGAGGAAGCCTTGCAAACCTGCAGACTGCTTTTTGCCCAATATAGATTGG
SEQ ID




GTAAGGCTGCAAAAC
NO:





2541





FGFR1
NM_023109.1
CACGGGACATTCACCACATCGACTACTATAAAAAGACAACCAACGGCCGACTGCCTGTGAA
SEQ ID




GTGGATGGCACCC
NO:





2542





FGFR2
NM_000141.2
GAGGGACTGTTGGCATGCAGTGCCCTCCCAGAGACCAACGTTCAAGCAGTTGGTAGAAGAC
SEQ ID


isoform 1

TTGGATCGAATTCTCACTC
NO:





2543





FHIT
NM_002012.1
CCAGTGGAGCGCTTCCATGACCTGCGTCCTGATGAAGTGGCCGATTTGTTTCAGACGACCCA
SEQ ID




GAGAG
NO:





2544





FIGF
NM_004469.2
GGTTCCAGCTTTCTGTAGCTGTAAGCATTGGTGGCCACACCACCTCCTTACAAAGCAACTAG
SEQ ID




AACCTGCGGC
NO:





2545





FLJ12455
NM_022078.1
CCACCAGCATGAAGTTTCGGACAGACATGGCCTTTGTGAGGGGTTCCAGTTGTGCTTCAGAC
SEQ ID




AGCC
NO:





2546





FLJ20712
AK000719.1
GCCACACAAACATGCTCCTGCTCCTGGCGGAGGCAGAGCTGCTGGGAAAGACATTTCGGAA
SEQ ID




GTTTCCTGTGGC
NO:





2547





FLT1
NM_002019.1
GGCTCCCGAATCTATCTTTGACAAAATCTACAGCACCAAGAGCGACGTGTGGTCTTACGGAG
SEQ ID




TATTGCTGTGGGA
NO:





2548





FLT4
NM_002020.1
ACCAAGAAGCTGAGGACCTGTGGCTGAGCCCGCTGACCATGGAAGATCTTGTCTGCTACAG
SEQ ID




CTTCCAGG
NO:





2549





FOS
NM_005252.2
CGAGCCCTTTGATGACTTCCTGTTCCCAGCATCATCCAGGCCCAGTGGCTCTGAGACAGCCC
SEQ ID




GCTCC
NO:





2550





FOXO3A
NM_001455.1
TGAAGTCCAGGACGATGATGCGCCTCTCTCGCCCATGCTCTACAGCAGCTCAGCCAGCCTGT
SEQ ID




CACCTTCAGTAAGCAAGCCGT
NO:





2551





FPGS
NM_004957.3
CAGCCCTGCCAGTTTGACTATGCCGTCTTCTGCCCTAACCTGACAGAGGTGTCATCCACAGG
SEQ ID




CAAC
NO:





2552





FRP1
NM_003012.2
TTGGTACCTGTGGGTTAGCATCAAGTTCTCCCCAGGGTAGAATTCAATCAGAGCTCCAGTTT
SEQ ID




GCATTTGGATGTG
NO:





2553





FST
NM_006350.2
GTAAGTCGGATGAGCCTGTCTGTGCCAGTGACAATGCCACTTATGCCAGCGAGTGTGCCATG
SEQ ID




AAGGAAGCTG
NO:





2554





Furin
NM_002569.1
AAGTCCTCGATACGCACTATAGCACCGAGAATGACGTGGAGACCATCCGGGCCAGCGTCTG
SEQ ID




CGCCCCCTGCCACGCCTCATGTGCCACATGCCAG
NO:





2555





FUS
NM_004960.1
GGATAATTCAGACAACAACACCATCTTTGTGCAAGGCCTGGGTGAGAATGTTACAATTGAGT
SEQ ID




CTGTGGCTGATTACTTCA
NO:





2556





FUT1
NM_000148.1
CCGTGCTCATTGCTAACCACTGTCTGTCCCTGAACTCCCAGAACCACTACATCTGGCTTTGGG
SEQ ID




CAG
NO:





2557





FUT3
NM_000149.1
CAGTTCGGTCCAACAGAGAAAGCAGGCAACCACCATGTCATTTGAAAACAGTTTCATCGGG
SEQ ID




ATATAATTCGCA
NO:





2558





FUT6
NM_000150.1
CGTGTGTCTCAAGACGATCCCACTGTGTACCCTAATGGGTCCCGCTTCCCAGACAGCACAGG
SEQ ID




GACC
NO:





2559





FXYD5
NM_014164.4
AGAGCACCAAAGCAGCTCATCCCACTGATGACACCACGACGCTCTCTGAGAGACCATCCCC
SEQ ID




AAGCAC
NO:





2560





FYN
NM_002037.3
GAAGCGCAGATCATGAAGAAGCTGAAGCACGACAAGCTGGTCCAGCTCTATGCAGTGGTGT
SEQ ID




CTGAGGAG
NO:





2561





FZD1
NM_003505.1
GGTGCACCAGTTCTACCCTCTAGTGAAAGTGCAGTGTTCCGCTGAGCTCAAGTTCTTCCTGTG
SEQ ID




CTCCATGTACGC
NO:





2562





FZD2
NM_001466.2
TGGATCCTCACCTGGTCGGTGCTGTGCTGCGCTTCCACCTTCTTCACTGTCACCACGTACTTG
SEQ ID




GTAGACATGCAGCGC
NO:





2563





FZD6
NM_003506.2
AATGAGAGAGGTGAAAGCGGACGGAGCTAGCACCCCCAGGTTAAGAGAACAGGACTGTGG
SEQ ID




TGAACCT
NO:





2564





G-Catenin
NM_002230.1
TCAGCAGCAAGGGCATCATGGAGGAGGATGAGGCCTGCGGGCGCCAGTACACGCTCAAGAA
SEQ ID




AACCACC
NO:





2565





G1P2
NM_005101.1
CAACGAATTCCAGGTGTCCCTGAGCAGCTCCATGTCGGTGTCAGAGCTGAAGGCGCAGATC
SEQ ID





NO:





2566





GADD45
NM_001924.2
GTGCTGGTGACGAATCCACATTCATCTCAATGGAAGGATCCTGCCTTAAGTCAACTTATTTG
SEQ ID




TTTTTGCCGGG
NO:





2567





GADD45B
NM_015675.1
ACCCTCGACAAGACCACACTTTGGGACTTGGGAGCTGGGGCTGAAGTTGCTCTGTACCCATG
SEQ ID




AACTCCCA
NO:





2568





GADD45G
NM_006705.2
CGCGCTGCAGATCCATTTTACGCTGATCCAGGCTTTCTGCTGCGAGAACGACATCGACATAG
SEQ ID




TGCG
NO:





2569





GAGE4
NM_001474.1
GGAACAGGGTCACCCACAGACTGGGTGTGAGTGTGAAGATGGTCCTGATGGGCAGGAGATG
SEQ ID




GACCCGCCAAATC
NO:





2570





GBP1
NM_002053.1
TTGGGAAATATTTGGGCATTGGTCTGGCCAAGTCTACAATGTCCCAATATCAAGGACAACCA
SEQ ID




CCCTAGCTTCT
NO:





2571





GBP2
NM_004120.2
GCATGGGAACCATCAACCAGCAGGCCATGGACCAACTTCACTATGTGACAGAGCTGACAGA
SEQ ID




TCGAATCAAGGCAAACTCCTCA
NO:





2572





GCLC
NM_001498.1
CTGTTGCAGGAAGGCATTGATCATCTCCTGGCCCAGCATGTTGCTCATCTCTTTATTAGAGAC
SEQ ID




CCACTGAC
NO:





2573





GCLM
NM_002061.1
TGTAGAATCAAACTCTTCATCATCAACTAGAAGTGCAGTTGACATGGCCTGTTCAGTCCTTG
SEQ ID




GAGTTGCACAGCTGGATTCTGTG
NO:





2574





GCNT1
NM_001490.3
TGGTGCTTGGAGCATAGAAGACTGCCCTTCACAAAGGAAATCCCTGATTATTGTTTGAAATG
SEQ ID




CTGAGGACGTTGC
NO:





2575





GDF15
NM_004864.1
CGCTCCAGACCTATGATGACTTGTTAGCCAAAGACTGCCACTGCATATGAGCAGTCCTGGTC
SEQ ID




CTTCCACTGT
NO:





2576





GIT1
NM_014030.2
GTGTATGACGAGGTGGATCGAAGAGAAAATGATGCAGTGTGGCTGGCTACCCAAAACCACA
SEQ ID




GCACTCTGGT
NO:





2577





GJA1
NM_000165.2
GTTCACTGGGGGTGTATGGGGTAGATGGGTGGAGAGGGAGGGGATAAGAGAGGTGCATGTT
SEQ ID




GGTATTT
NO:





2578





GJB2
NM_004004.3
TGTCATGTACGACGGCTTCTCCATGCAGCGGCTGGTGAAGTGCAACGCCTGGCCTTGTCCCA
SEQ ID




ACACTGTGGACT
NO:





2579





GPX1
NM_000581.2
GCTTATGACCGACCCCAAGCTCATCACCTGGTCTCCGGTGTGTCGCAACGATGTTGCCTGGA
SEQ ID




ACTTT
NO:





2580





GPX2
NM_002083.1
CACACAGATCTCCTACTCCATCCAGTCCTGAGGAGCCTTAGGATGCAGCATGCCTTCAGGAG
SEQ ID




ACACTGCTGGACC
NO:





2581





Grb10
NM_005311.2
CTTCGCCTTTGCTGATTGCCTCTCCAAACGCCTGCCTGACGACTGCCTTGGAGCATGTGCGTT
SEQ ID




ATGG
NO:





2582





GRB14
NM_004490.1
TCCCACTGAAGCCCTTTCAGTTGCGGTTGAAGAAGGACTCGCTTGGAGGAAAAAAGGATGTT
SEQ ID




TACGCCTGGGCACT
NO:





2583





GRB2
NM_002086.2
GTCCATCAGTGCATGACGTTTAAGGCCACGTATAGTCCTAGCTGACGCCAATAATAAAAAAC
SEQ ID




AAGAAACCAAGTGGGCT
NO:





2584





GRB7
NM_005310.1
CCATCTGCATCCATCTTGTTTGGGCTCCCCACCCTTGAGAAGTGCCTCAGATAATACCCTGGT
SEQ ID




GGCC
NO:





2585





GRIK1
NM_000830.2
GTTGGGTGCATCTCTCGGGCGTCCGGCAGCGGCTGTATCTCGGCATGAATTAAGAAGCTAGG
SEQ ID




AAGATGGAGCACG
NO:





2586





GRO1
NM_001511.1
CGAAAAGATGCTGAACAGTGACAAATCCAACTGACCAGAAGGGAGGAGGAAGCTCACTGG
SEQ ID




TGGCTGTTCCTGA
NO:





2587





GRP
NM_002091.1
CTGGGTCTCATAGAAGCAAAGGAGAACAGAAACCACCAGCCACCTCAACCCAAGGCCTTGG
SEQ ID




GCAATCAGCAGCCTTCGTGG
NO:





2588





GRPR
NM_005314.1
ATGCTGCTGGCCATTCCAGAGGCCGTGTTTTCTGACCTCCATCCCTTCCATGAGGAAAGCAC
SEQ ID




CAACCAGACCT
NO:





2589





GSK3B
NM_002093.2
GACAAGGACGGCAGCAAGGTGACAACAGTGGTGGCAACTCCTGGGCAGGGTCCAGACAGG
SEQ ID




CCACAA
NO:





2590





GSTA3
NM_000847.3
TCTCCAACTTCCCTCTGCTGAAGGCCCTGAAAACCAGAATCAGCAACCTGCCCACGGTGAAG
SEQ ID




AAGT
NO:





2591





GSTM1
NM_000561.1
AAGCTATGAGGAAAAGAAGTACACGATGGGGGACGCTCCTGATTATGACAGAAGCCAGTGG
SEQ ID




CTGAATGAAAAATTCAAGCTGGGCC
NO:





2592





GSTM3
NM_000849.3
CAATGCCATCTTGCGCTACATCGCTCGCAAGCACAACATGTGTGGTGAGACTGAAGAAGAA
SEQ ID




AAGATTCGAGTGGAC
NO:





2593





GSTp
NM_000852.2
GAGACCCTGCTGTCCCAGAACCAGGGAGGCAAGACCTTCATTGTGGGAGACCAGATCTCCTT
SEQ ID




CGCTGACTACAACC
NO:





2594





GSTT1
NM_000853.1
CACCATCCCCACCCTGTCTTCCACAGCCGCCTGAAAGCCACAATGAGAATGATGCACACTGA
SEQ ID




GGCC
NO:





2595





H2AFZ
NM_002106.2
CCGGAAAGGCCAAGACAAAGGCGGTTTCCCGCTCGCAGAGAGCCGGCTTGCAGTTCCCAGT
SEQ ID




GGGCCGTATT
NO:





2596





HB-EGF
NM_001945.1
GACTCCTTCGTCCCCAGTTGCCGTCTAGGATTGGGCCTCCCATAATTGCTTTGCCAAAATACC
SEQ ID




AGAGCCTTCAAGTGCCA
NO:





2597





hCRA a
U78556.1
TGACACCCTTACCTTCCTGAGAAATACCCCCTGGGAGCGCGGAAAGCAGAGCGGACAGGTC
SEQ ID




AGTGACTTCTATTTTTGACTCGTGTTTTT
NO:





2598





HDAC1
NM_004964.2
CAAGTACCACAGCGATGACTACATTAAATTCTTGCGCTCCATCCGTCCAGATAACATGTCGG
SEQ ID




AGTACAGCAAGC
NO:





2599





HDAC2
NM_001527.1
GGTGGCTACACAATCCGTAATGTTGCTCGATGTTGGACATATGAGACTGCAGTTGCCCTTGA
SEQ ID




TTGTGAGATTCCCA
NO:





2600





HDGF
NM_004494.1
TCCTAGGCATTCTGGACCTCTGGGTTGGGATCAGGGGTAGGAATGGAAGGATGGAGCATCA
SEQ ID




ACAGC
NO:





2601





hENT1
NM_004955.1
AGCCGTGACTGTTGAGGTCAAGTCCAGCATCGCAGGCAGCAGCACCTGGGAACGTTACTT
SEQ ID





NO:





2602





Hepsin
NM_002151.1
AGGCTGCTGGAGGTCATCTCCGTGTGTGATTGCCCCAGAGGCCGTTTCTTGGCCGCCATCTG
SEQ ID




CCAAGACTGTGGCCGCAGGAAG
NO:





2603





HER2
NM_004448.1
CGGTGTGAGAAGTGCAGCAAGCCCTGTGCCCGAGTGTGCTATGGTCTGGGCATGGAGCACTT
SEQ ID




GCGAGAGG
NO:





2604





Herstatin
AF177761.2
CACCCTGTCCTATCCTTCCTCAGACCCTCTTGGGACCTAGTCTCTGCCTTCTACTCTCTACCCC
SEQ ID




TGGCC
NO:





2605





HES6
NM_018645.3
TTAGGGACCCTGCAGCTCTGGAGTGGGTGGAGGGAGGGAGCTACGGGCAGGAGGAAGAATT
SEQ ID




TTGTAG
NO:





2606





HGF
M29145.1
CCGAAATCCAGATGATGATGCTCATGGACCCTGGTGCTACACGGGAAATCCACTCATTCCTT
SEQ ID




GGG
NO:





2607





HIF1A
NM_001530.1
TGAACATAAAGTCTGCAACATGGAAGGTATTGCACTGCACAGGCCACATTCACGTATATGAT
SEQ ID




ACCAACAGTAACCAACCTCA
NO:





2608





HK1
NM_000188.1
TACGCACAGAGGCAAGCAGCTAAGAGTCCGGGATCCCCAGCCTACTGCCTCTCCAGCACTTC
SEQ ID




TCTC
NO:





2609





HLA-DPB1
NM_002121.4
TCCATGATGGTTCTGCAGGTTTCTGCGGCCCCCCGGACAGTGGCTCTGACGGCGTTACTGAT
SEQ ID




GGTGCTGCTCA
NO:





2610





HLA-DRA
NM_019111.3
GACGATTTGCCAGCTTTGAGGCTCAAGGTGCATTGGCCAACATAGCTGTGGACAAAGCCAA
SEQ ID




CCTGGA
NO:





2611





HLA-DRB1
NM_002124.1
GCTTTCTCAGGACCTGGTTGCTACTGGTTCGGCAACTGCAGAAAATGTCCTCCCTTGTGGCTT
SEQ ID




CCT
NO:





2612





HLA-G
NM_002127.2
CCTGCGCGGCTACTACAACCAGAGCGAGGCCAGTTCTCACACCCTCCAGTGGATGATTGGCT
SEQ ID




GCGACCTG
NO:





2613





HMGB1
NM_002128.3
TGGCCTGTCCATTGGTGATGTTGCGAAGAAACTGGGAGAGATGTGGAATAACACTGCTGCA
SEQ ID




GATGACAAGC
NO:





2614





hMLH
NM_000249.2
CTACTTCCAGCAACCCCAGAAAGAGACATCGGGAAGATTCTGATGTGGAAATGGTGGAAGA
SEQ ID




TGATTCCCGAAAG
NO:





2615





HNRPAB
NM_004499.2
CAAGGGAGCGACCAACTGATCGCACACATGCTTTGTTTGGATATGGAGTGAACACAATTATG
SEQ ID




TACCAAATTTAACTTGGCAAAC
NO:





2616





HNRPD
NM_031370.2
GCCAGTAAGAACGAGGAGGATGAAGGCCATTCAAACTCCTCCCCACGACACTCTGAAGCAG
SEQ ID




CGACG
NO:





2617





HoxA1
NM_005522.3
AGTGACAGATGGACAATGCAAGAATGAACTCCTTCCTGGAATACCCCATACTTAGCAGTGG
SEQ ID




CGACTCGG
NO:





2618





HoxA5
NM_019102.2
TCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGA
SEQ ID




GCCTGTTTATTGCC
NO:





2619





HOXB13
NM_006361.2
CGTGCCTTATGGTTACTTTGGAGGCGGGTACTACTCCTGCCGAGTGTCCCGGAGCTCGCTGA
SEQ ID




AACCCTGTG
NO:





2620





HOXB7
NM_004502.2
CAGCCTCAAGTTCGGTTTTCGCTACCGGAGCCTTCCCAGAACAAACTTCTTGTGCGTTTGCTT
SEQ ID




CCAAC
NO:





2621





HRAS
NM_005343.2
GGACGAATACGACCCCACTATAGAGGATTCCTACCGGAAGCAGGTGGTCATTGATGGGGAG
SEQ ID




ACGTGC
NO:





2622





HSBP1
NM_001537.1
GGAGATGGCCGAGACTGACCCCAAGACCGTGCAGGACCTCACCTCGGTGGTGCAGACACTC
SEQ ID




CTGCAG
NO:





2623





HSD17B1
NM_000413.1
CTGGACCGCACGGACATCCACACCTTCCACCGCTTCTACCAATACCTCGCCCACAGCAAGCA
SEQ ID




AGTCTTTCGCGAGGCG
NO:





2624





HSD17B2
NM_002153.1
GCTTTCCAAGTGGGGAATTAAAGTTGCTTCCATCCAACCTGGAGGCTTCCTAACAAATATCG
SEQ ID




CAGGCA
NO:





2625





HSPA1A
NM_005345.4
CTGCTGCGACAGTCCACTACCTTTTTCGAGAGTGACTCCCGTTGTCCCAAGGCTTCCCAGAG
SEQ ID




CGAACCTG
NO:





2626





HSPA1B
NM_005346.3
GGTCCGCTTCGTCTTTCGAGAGTGACTCCCGCGGTCCCAAGGCTTTCCAGAGCGAACCTGTGC
SEQ ID





NO:





2627





HSPA4
NM_002154.3
TTCAGTGTGTCCAGTGCATCTTTAGTGGAGGTTCACAAGTCTGAGGAAAATGAGGAGCCAAT
SEQ ID




GGAAACAGAT
NO:





2628





HSPA5
NM_005347.2
GGCTAGTAGAACTGGATCCCAACACCAAACTCTTAATTAGACCTAGGCCTCAGCTGCACTGC
SEQ ID




CCGAAAAGCATTTGGGCAGACC
NO:





2629





HSPA8
NM_006597.3
CCTCCCTCTGGTGGTGCTTCCTCAGGGCCCACCATTGAAGAGGTTGATTAAGCCAACCAAGT
SEQ ID




GTAGATGTAGC
NO:





2630





HSPB1
NM_001540.2
CCGACTGGAGGAGCATAAAAGCGCAGCCGAGCCCAGCGCCCCGCACTTTTCTGAGCAGACG
SEQ ID




TCCAGAGCAGAGTCAGCCAGCAT
NO:





2631





HSPCA
NM_005348.2
CAAAAGGCAGAGGCTGATAAGAACGACAAGTCTGTGAAGGATCTGGTCATCTTGCTTTATG
SEQ ID




AAACTGCGCT
NO:





2632





HSPE1
NM_002157.1
GCAAGCAACAGTAGTCGCTGTTGGATCGGGTTCTAAAGGAAAGGGTGGAGAGATTCAACCA
SEQ ID




GTTAGCGTGAAAGTTGG
NO:





2633





HSPG2
NM_005529.2
GAGTACGTGTGCCGAGTGTTGGGCAGCTCCGTGCCTCTAGAGGCCTCTGTCCTGGTCACCAT
SEQ ID




TGAG
NO:





2634





ICAM1
NM_000201.1
GCAGACAGTGACCATCTACAGCTTTCCGGCGCCCAACGTGATTCTGACGAAGCCAGAGGTCT
SEQ ID




CAGAAG
NO:





2635





ICAM2
NM_000873.2
GGTCATCCTGACACTGCAACCCACTTTGGTGGCTGTGGGCAAGTCCTTCACCATTGAGTGCA
SEQ ID





NO:





2636





ID1
NM_002165.1
AGAACCGCAAGGTGAGCAAGGTGGAGATTCTCCAGCACGTCATCGACTACATCAGGGACCT
SEQ ID




TCAGTTGGA
NO:





2637





ID2
NM_002166.1
AACGACTGCTACTCCAAGCTCAAGGAGCTGGTGCCCAGCATCCCCCAGAACAAGAAGGTGA
SEQ ID




GCAAGATGGAAATCC
NO:





2638





ID3
NM_002167.2
CTTCACCAAATCCCTTCCTGGAGACTAAACCTGGTGCTCAGGAGCGAAGGACTGTGAACTTG
SEQ ID




TAGCCTGAAGAGCCAGAG
NO:





2639





ID4
NM_001546.2
TGGCCTGGCTCTTAATTTGCTTTTGTTTTGCCCAGTATAGACTCGGAAGTAAGAGTTATAGCT
SEQ ID




AGTGGTCTTGCATGATTGCA
NO:





2640





IFIT1
NM_001548.1
TGACAACCAAGCAAATGTGAGGAGTCTGGTGACCTGGGGCAACTTTGCCTGGATGTATTACC
SEQ ID




ACATGGGCAGACTG
NO:





2641





IGF1
NM_000618.1
TCCGGAGCTGTGATCTAAGGAGGCTGGAGATGTATTGCGCACCCCTCAAGCCTGCCAAGTCA
SEQ ID




GCTCGCTCTGTCCG
NO:





2642





IGF1R
NM_000875.2
GCATGGTAGCCGAAGATTTCACAGTCAAAATCGGAGATTTTGGTATGACGCGAGATATCTAT
SEQ ID




GAGACAGACTATTACCGGAAA
NO:





2643





IGF2
NM_000612.2
CCGTGCTTCCGGACAACTTCCCCAGATACCCCGTGGGCAAGTTCTTCCAATATGACACCTGG
SEQ ID




AAGCAGTCCA
NO:





2644





IGFBP2
NM_000597.1
GTGGACAGCACCATGAACATGTTGGGCGGGGGAGGCAGTGCTGGCCGGAAGCCCCTCAAGT
SEQ ID




CGGGTATGAAGG
NO:





2645





IGFBP3
NM_000598.1
ACGCACCGGGTGTCTGATCCCAAGTTCCACCCCCTCCATTCAAAGATAATCATCATCAAGAA
SEQ ID




AGGGCA
NO:





2646





IGFBP5
NM_000599.1
TGGACAAGTACGGGATGAAGCTGCCAGGCATGGAGTACGTTGACGGGGACTTTCAGTGCCA
SEQ ID




CACCTTCG
NO:





2647


IGFBP6
NM_002178.1
TGAACCGCAGAGACCAACAGAGGAATCCAGGCACCTCTACCACGCCCTCCCAGCCCAATTC
SEQ ID




TGCGGGTGTCCAAGAC
NO:





2648





IGFBP7
NM_001553
GGGTCACTATGGAGTTCAAAGGACAGAACTCCTGCCTGGTGACCGGGACAACCTGGCCATT
SEQ ID




CAGACCC
NO:





2649





IHH
NM_002181.1
AAGGACGAGGAGAACACAGGCGCCGACCGCCTCATGACCCAGCGCTGCAAGGACCGCCTGA
SEQ ID




ACTCGCTGGCTATCT
NO:





2650





IL-8
NM_000584.2
AAGGAACCATCTCACTGTGTGTAAACATGACTTCCAAGCTGGCCGTGGCTCTCTTGGCAGCC
SEQ ID




TTCCTGAT
NO:





2651





IL10
NM_000572.1
GGCGCTGTCATCGATTTCTTCCCTGTGAAAACAAGAGCAAGGCCGTGGAGCAGGTGAAGAA
SEQ ID




TGCCTTTAATAAGCTCCA
NO:





2652





IL1B
NM_000576.2
AGCTGAGGAAGATGCTGGTTCCCTGCCCACAGACCTTCCAGGAGAATGACCTGAGCACCTTC
SEQ ID




TTTCC
NO:





2653





IL6
NM_000600.1
CCTGAACCTTCCAAAGATGGCTGAAAAAGATGGATGCTTCCAATCTGGATTCAATGAGGAG
SEQ ID




ACTTGCCTGGT
NO:





2654





IL6ST
NM_002184.2
GGCCTAATGTTCCAGATCCTTCAAAGAGTCATATTGCCCAGTGGTCACCTCACACTCCTCCA
SEQ ID




AGGCACAATTTT
NO:





2655





ILT-2
NM_006669.1
AGCCATCACTCTCAGTGCAGCCAGGTCCTATCGTGGCCCCTGAGGAGACCCTGACTCTGCAGT
SEQ ID





NO:





2656





IMP-1
NM_006546.2
GAAAGTGTTTGCGGAGCACAAGATCTCCTACAGCGGCCAGTTCTTGGTCAAATCCGGCTACG
SEQ ID




CCTTC
NO:





2657





IMP2
NM_006548.3
CAATCTGATCCCAGGGTTGAACCTCAGCGCACTTGGCATCTTTTCAACAGGACTGTCCGTGC
SEQ ID




TATCTCCACCAGCAGGGCC
NO:





2658





ING1L
NM_001564.1
TGTTTCCAAGATCCTGCTGAAAGTGAACGAGCCTCAGATAAAGCAAAGATGGATTCCAGCC
SEQ ID




AACCAGAAAGA
NO:





2659





ING5
NM_032329.4
CCTACAGCAAGTGCAAGGAATACAGTGACGACAAAGTGCAGCTGGCCATGCAGACCTACGA
SEQ ID




GATG
NO:





2660





INHA
NM_002191.2
CCTCCCAGTTTCATCTTCCACTACTGTCATGGTGGTTGTGGGCTGCAGATCCCACCAAACCTG
SEQ ID




TCCCTTCCAGTCCCT
NO:





2661





INHBA
NM_002192.1
GTGCCCGAGCCATATAGCAGGCACGTCCGGGTCCTCACTGTCCTTCCACTCAACAGTCATCA
SEQ ID




ACCACTACCG
NO:





2662





INHBB
NM_002193.1
AGCCTCCAGGATACCAGCAAATGGATGCGGTGACAAATGGCAGCTTAGCTACAAATGCCTG
SEQ ID




TCAGTCGGAGA
NO:





2663





IRS1
NM_005544.1
CCACAGCTCACCTTCTGTCAGGTGTCCATCCCAGCTCCAGCCAGCTCCCAGAGAGGAAGAGA
SEQ ID




CTGGCACTGAGG
NO:





2664





ITGA3
NM_002204.1
CCATGATCCTCACTCTGCTGGTGGACTATACACTCCAGACCTCGCTTAGCATGGTAAATCAC
SEQ ID




CGGCTACAAAGCTTC
NO:





2665





ITGA4
NM_000885.2
CAACGCTTCAGTGATCAATCCCGGGGCGATTTACAGATGCAGGATCGGAAAGAATCCCGGC
SEQ ID




CAGAC
NO:





2666





ITGA5
NM_002205.1
AGGCCAGCCCTACATTATCAGAGCAAGAGCCGGATAGAGGACAAGGCTCAGATCTTGCTGG
SEQ ID




ACTGTGGAGAAGAC
NO:





2667





ITGA6
NM_000210.1
CAGTGACAAACAGCCCTTCCAACCCAAGGAATCCCACAAAAGATGGCGATGACGCCCATGA
SEQ ID




GGCTAAAC
NO:





2668





ITGA7
NM_002206.1
GATATGATTGGTCGCTGCTTTGTGCTCAGCCAGGACCTGGCCATCCGGGATGAGTTGGATGG
SEQ ID




TGGGGAATGGAAGTTCT
NO:





2669





ITGAV
NM_002210.2
ACTCGGACTGCACAAGCTATTTTTGATGACAGCTATTTGGGTTATTCTGTGGCTGTCGGAGAT
SEQ ID




TTCAATGGTGATGGCA
NO:





2670





ITGB1
NM_002211.2
TCAGAATTGGATTTGGCTCATTTGTGGAAAAGACTGTGATGCCTTACATTAGCACAACACCA
SEQ ID




GCTAAGCTCAGG
NO:





2671





ITGB3
NM_000212.1
ACCGGGAGCCCTACATGACCGAAAATACCTGCAACCGTTACTGCCGTGACGAGATTGAGTC
SEQ ID




AGTGAAAGAGCTTAAGG
NO:





2672





ITGB4
NM_000213.2
CAAGGTGCCCTCAGTGGAGCTCACCAACCTGTACCCGTATTGCGACTATGAGATGAAGGTGT
SEQ ID




GCGC
NO:





2673





ITGB5
NM_002213.3
TCGTGAAAGATGACCAGGAGGCTGTGCTATGTTTCTACAAAACCGCCAAGGACTGCGTCATG
SEQ ID




ATGTTCACC
NO:





2674





K-ras
NM_033360.2
GTCAAAATGGGGAGGGACTAGGGCAGTTTGGATAGCTCAACAAGATACAATCTCACTCTGT
SEQ ID




GGTGGTCCTG
NO:





2675





KCNH2 iso
NM_000238.2
GAGCGCAAAGTGGAAATCGCCTTCTACCGGAAAGATGGGAGCTGCTTCCTATGTCTGGTGG
SEQ ID


a/b

ATGTGGTGCCCGTGAAGA
NO:





2676





KCNH2 iso
NM_172057.1
TCCTGCTGCTGGTCATCTACACGGCTGTCTTCACACCCTACTCGGCTGCCTTCCTGCTGAAGG
SEQ ID


a/c

AGACGGAAGAAGG
NO:





2677





KCNK4
NM_016611.2
CCTATCAGCCGCTGGTGTGGTTCTGGATCCTGCTCGGCCTGGCTTACTTCGCCTCAGTGCTCA
SEQ ID




CCACCA
NO:





2678





KDR
NM_002253.1
GAGGACGAAGGCCTCTACACCTGCCAGGCATGCAGTGTTCTTGGCTGTGCAAAAGTGGAGG
SEQ ID




CATTTTT
NO:





2679





Ki-67
NM_002417.1
CGGACTTTGGGTGCGACTTGACGAGCGGTGGTTCGACAAGTGGCCTTGCGGGCCGGATCGTC
SEQ ID




CCAGTGGAAGAGTTGTAA
NO:





2680





KIAA0125
NM_014792.2
GTGTCCTGGTCCATGTGGTGCACGTGTCTCCACCTCCAAGGAGAGGCTCCTCAGTGTGCACC
SEQ ID




TCCC
NO:





2681





KIF22
NM_007317.1
CTAAGGCACTTGCTGGAAGGGCAGAATGCCAGTGTGCTTGCCTATGGACCCACAGGAGCTG
SEQ ID




GGAAGA
NO:





2682





KIF2C
NM_006845.2
AATTCCTGCTCCAAAAGAAAGTCTTCGAAGCCGCTCCACTCGCATGTCCACTGTCTCAGAGC
SEQ ID




TTCGCATCACG
NO:





2683





KIFC1
XM_371813.1
CCACAGGGTTGAAGAACCAGAAGCCAGTTCCTGCTGTTCCTGTCCAGAAGTCTGGCACATCA
SEQ ID




GGTG
NO:





2684





Kitlng
NM_000899.1
GTCCCCGGGATGGATGTTTTGCCAAGTCATTGTTGGATAAGCGAGATGGTAGTACAATTGTC
SEQ ID




AGACAGCTTGACTGATC
NO:





2685





KLF5
NM_001730.3
GTGCAACCGCAGCTTCTCGCGCTCTGACCACCTGGCCCTGCATATGAAGAGGCACCAGAACT
SEQ ID




GAGCACTGCCCG
NO:





2686





KLF6
NM_001300.4
CACGAGACCGGCTACTTCTCGGCGCTGCCGTCTCTGGAGGAGTACTGGCAACAGACCTGCCT
SEQ ID




AGAGC
NO:





2687





KLK10
NM_002776.1
GCCCAGAGGCTCCATCGTCCATCCTCTTCCTCCCCAGTCGGCTGAACTCTCCCCTTGTCTGCA
SEQ ID




CTGTTCAAACCTCTG
NO:





2688





KLK6
NM_002774.2
GACGTGAGGGTCCTGATTCTCCCTGGTTTTACCCCAGCTCCATCCTTGCATCACTGGGGAGG
SEQ ID




ACGTGATGAGTGAGGA
NO:





2689





KLRK1
NM_007360.1
TGAGAGCCAGGCTTCTTGTATGTCTCAAAATGCCAGCCTTCTGAAAGTATACAGCAAAGAGG
SEQ ID




ACCAGGAT
NO:





2690





KNTC2
NM_006101.1
ATGTGCCAGTGAGCTTGAGTCCTTGGAGAAACACAAGCACCTGCTAGAAAGTACTGTTAACC
SEQ ID




AGGGGCTCA
NO:





2691





KRAS2
NM_004985.3
GAGACCAAGGTTGCAAGGCCAGGCCCTGTGTGAACCTTTGAGCTTTCATAGAGAGTTTCACA
SEQ ID




GCATGGACTG
NO:





2692





KRT19
NM_002276.1
TGAGCGGCAGAATCAGGAGTACCAGCGGCTCATGGACATCAAGTCGCGGCTGGAGCAGGAG
SEQ ID




ATTGCCACCTACCGCA
NO:





2693





KRT8
NM_002273.1
GGATGAAGCTTACATGAACAAGGTAGAGCTGGAGTCTCGCCTGGAAGGGCTGACCGACGAG
SEQ ID




ATCAACTTCCTCAGGCAGCTATATG
NO:





2694





LAMA3
NM_000227.2
CAGATGAGGCACATGGAGACCCAGGCCAAGGACCTGAGGAATCAGTTGCTCAACTACCGTT
SEQ ID




CTGCCATTTCAA
NO:





2695





LAMB3
NM_000228.1
ACTGACCAAGCCTGAGACCTACTGCACCCAGTATGGCGAGTGGCAGATGAAATGCTGCAAG
SEQ ID




TGTGAC
NO:





2696





LAMC2
NM_005562.1
ACTCAAGCGGAAATTGAAGCAGATAGGTCTTATCAGCACAGTCTCCGCCTCCTGGATTCAGT
SEQ ID




GTCTCGGCTTCAGGGAGT
NO:





2697





LAT
NM_014387.2
GTGAACGTTCCGGAGAGCGGGGAGAGCGCAGAAGCGTCTCTGGATGGCAGCCGGGAGTATG
SEQ ID




TGAATGT
NO:





2698





LCN2
NM_005564.2
CGCTGGGCAACATTAAGAGTTACCCTGGATTAACGAGTTACCTCGTCCGAGTGGTGAGCACC
SEQ ID




AACTACAACCAGCATGCT
NO:





2699





LDLRAP1
NM_015627.1
CAGTGCCTCTCGCCTGTCGACTGGGACAAGCCTGACAGCAGCGGCACAGAGCAGGATGACC
SEQ ID




TCTTCA
NO:





2700





LEF
NM_016269.2
GATGACGGAAAGCATCCAGATGGAGGCCTCTACAACAAGGGACCCTCCTACTCGAGTTATT
SEQ ID




CCGGG
NO:





2701





LGALS3
NM_002306.1
AGCGGAAAATGGCAGACAATTTTTCGCTCCATGATGCGTTATCTGGGTCTGGAAACCCAAAC
SEQ ID




CCTCAAG
NO:





2702





LGMN
NM_001008530.1
TTGGTGCCGTTCCTATAGATGATCCTGAAGATGGAGGCAAGCACTGGGTGGTGATCGTGGCA
SEQ ID




GGTTC
NO:





2703





LILRB3
NM_006864.1
CACCTGGTCTGGGAAGATACCTGGAGGTTTTGATTGGGGTCTCGGTGGCCTTCGTCCTGCTG
SEQ ID




CTCTT
NO:





2704





LMNB1
NM_005573.1
TGCAAACGCTGGTGTCACAGCCAGCCCCCCAACTGACCTCATCTGGAAGAACCAGAACTCGT
SEQ ID




GGGG
NO:





2705





LMYC
NM_012421.1
CCCATCCAGAACACTGATTGCTGTCATTCAAGTGAAAGGGATGGAGGTCAGAAAGGGTGCA
SEQ ID




TAGAAAGCAG
NO:





2706





LOX
NM_002317.3
CCAATGGGAGAACAACGGGCAGGTGTTCAGCTTGCTGAGCCTGGGCTCACAGTACCAGCCT
SEQ ID




CAGCG
NO:





2707





LOXL2
NM_002318.1
TCAGCGGGCTCTTAAACAACCAGCTGTCCCCGCAGTAAAGAAGCCTGCGTGGTCAACTCCTG
SEQ ID




TCTT
NO:





2708





LRP5
NM_002335.1
CGACTATGACCCACTGGACAAGTTCATCTACTGGGTGGATGGGCGCCAGAACATCAAGCGA
SEQ ID




GCCAAG
NO:





2709





LRP6
NM_002336.1
GGATGTAGCCATCTCTGCCTCTATAGACCTCAGGGCCTTCGCTGTGCTTGCCCTATTGGCTTT
SEQ ID




GAACT
NO:





2710





LY6D
NM_003695.2
AATGCTGATGACTTGGAGCAGGCCCCACAGACCCCACAGAGGATGAAGCCACCCCACAGAG
SEQ ID




GATGCAG
NO:





2711





MAD
NM_002357.1
TGGTTCTGATTAGGTAACGTATTGGACCTGCCCACAACTCCCTTGCACGTAAACTTCAGTGTC
SEQ ID




CCACCTTGACC
NO:





2712





MAD1L1
NM_003550.1
AGAAGCTGTCCCTGCAAGAGCAGGATGCAGCGATTGTGAAGAACATGAAGTCTGAGCTGGT
SEQ ID




ACGGCT
NO:





2713





MAD2L1
NM_002358.2
CCGGGAGCAGGGAATCACCCTGCGCGGGAGCGCCGAAATCGTGGCCGAGTTCTTCTCATTC
SEQ ID




GGCATCAACAGCAT
NO:





2714





MADH2
NM_005901.2
GCTGCCTTTGGTAAGAACATGTCGTCCATCTTGCCATTCACGCCGCCAGTTGTGAAGAGACT
SEQ ID




GCTGGGAT
NO:





2715





MADH4
NM_005359.3
GGACATTACTGGCCTGTTCACAATGAGCTTGCATTCCAGCCTCCCATTTCCAATCATCCTGCT
SEQ ID




CCTGAGTATTGGT
NO:





2716





MADH7
NM_005904.1
TCCATCAAGGCTTTCGACTACGAGAAGGCGTACAGCCTGCAGCGGCCCAATGACCACGAGT
SEQ ID




TTATGCAGCAG
NO:





2717





MAP2
NM_031846.1
CGGACCACCAGGTCAGAGCCAATTCGCAGAGCAGGGAAGAGTGGTACCTCAACACCCACTA
SEQ ID




CCCCTG
NO:





2718





MAP2K1
NM_002755.2
GCCTTTCTTACCCAGAAGCAGAAGGTGGGAGAACTGAAGGATGACGACTTTGAGAAGATCA
SEQ ID




GTGAGCTGGGGGCTG
NO:





2719





MAP3K1
XM_042066.8
GGTTGGCATCAAAAGGAACTGGTGCAGGAGAGTTTCAGGGACAATTACTGGGGACAATTGC
SEQ ID




ATTTATGGCA
NO:





2720





MAPK14
NM_139012.1
TGAGTGGAAAAGCCTGACCTATGATGAAGTCATCAGCTTTGTGCCACCACCCCTTGACCAAG
SEQ ID




AAGAGATGGAGTCC
NO:





2721





Maspin
NM_002639.1
CAGATGGCCACTTTGAGAACATTTTAGCTGACAACAGTGTGAACGACCAGACCAAAATCCTT
SEQ ID




GTGGTTAATGCTGCC
NO:





2722





MAX
NM_002382.3
CAAACGGGCTCATCATAATGCACTGGAACGAAAACGTAGGGACCACATCAAAGACAGCTTT
SEQ ID




CACAGTTTGCGGGA
NO:





2723





MCM2
NM_004526.1
GACTTTTGCCCGCTACCTTTCATTCCGGCGTGACAACAATGAGCTGTTGCTCTTCATACTGAA
SEQ ID




GCAGTTAGTGGC
NO:





2724





MCM3
NM_002388.2
GGAGAACAATCCCCTTGAGACAGAATATGGCCTTTCTGTCTACAAGGATCACCAGACCATCA
SEQ ID




CCATCCAGGAGAT
NO:





2725





MCM6
NM_005915.2
TGATGGTCCTATGTGTCACATTCATCACAGGTTTCATACCAACACAGGCTTCAGCACTTCCTT
SEQ ID




TGGTGTGTTTCCTGTCCCA
NO:





2726





MCP1
NM_002982.1
CGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAATAGGAAGA
SEQ ID




TCTCAGTGC
NO:





2727





MDK
NM_002391.2
GGAGCCGACTGCAAGTACAAGTTTGAGAACTGGGGTGCGTGTGATGGGGGCACAGGCACCA
SEQ ID




AAGTC
NO:





2728





MDM2
NM_002392.1
CTACAGGGACGCCATCGAATCCGGATCTTGATGCTGGTGTAAGTGAACATTCAGGTGATTGG
SEQ ID




TTGGAT
NO:





2729





MGAT5
NM_002410.2
GGAGTCGAAGGTGGACAATCTTGTTGTCAATGGCACCGGAACAAACTCAACCAACTCCACT
SEQ ID




ACAGCTGTTCCCA
NO:





2730





MGMT
NM_002412.1
GTGAAATGAAACGCACCACACTGGACAGCCCTTTGGGGAAGCTGGAGCTGTCTGGTTGTGA
SEQ ID




GCAGGGTC
NO:





2731





mGST1
NM_020300.2
ACGGATCTACCACACCATTGCATATTTGACACCCCTTCCCCAGCCAAATAGAGCTTTGAGTT
SEQ ID




TTTTTGTTGGATATGGA
NO:





2732





MMP1
NM_002421.2
GGGAGATCATCGGGACAACTCTCCTTTTGATGGACCTGGAGGAAATCTTGCTCATGCTTTTC
SEQ ID




AACCAGGCCC
NO:





2733





MMP12
NM_002426.1
CCAACGCTTGCCAAATCCTGACAATTCAGAACCAGCTCTCTGTGACCCCAATTTGAGTTTTG
SEQ ID




ATGCTGTCACTACCGT
NO:





2734





MMP2
NM_004530.1
CCATGATGGAGAGGCAGACATCATGATCAACTTTGGCCGCTGGGAGCATGGCGATGGATAC
SEQ ID




CCCTTTGACGGTAAGGACGGACTCC
NO:





2735





MMP7
NM_002423.2
GGATGGTAGCAGTCTAGGGATTAACTTCCTGTATGCTGCAACTCATGAACTTGGCCATTCTTT
SEQ ID




GGGTATGGGACATTCC
NO:





2736





MMP9
NM_004994.1
GAGAACCAATCTCACCGACAGGCAGCTGGCAGAGGAATACCTGTACCGCTATGGTTACACT
SEQ ID




CGGGTG
NO:





2737





MRP1
NM_004996.2
TCATGGTGCCCGTCAATGCTGTGATGGCGATGAAGACCAAGACGTATCAGGTGGCCCACAT
SEQ ID




GAAGAGCAAAGACAATCG
NO:





2738





MRP2
NM_000392.1
AGGGGATGACTTGGACACATCTGCCATTCGACATGACTGCAATTTTGACAAAGCCATGCAGT
SEQ ID




TTT
NO:





2739





MRP3
NM_003786.2
TCATCCTGGCGATCTACTTCCTCTGGCAGAACCTAGGTCCCTCTGTCCTGGCTGGAGTCGCTT
SEQ ID




TCATGGTCTTGCTGATTCCACTCAACGG
NO:





2740





MRP4
NM_005845.1
AGCGCCTGGAATCTACAACTCGGAGTCCAGTGTTTTCCCACTTGTCATCTTCTCTCCAGGGGC
SEQ ID




TCT
NO:





2741





MRPL40
NM_003776.2
ACTTGCAGGCTGCTATCCTTAACATGCTGCCCCTGAGAGTAGGAATGACCAGGGTTCAAGTC
SEQ ID




TGCT
NO:





2742





MSH2
NM_000251.1
GATGCAGAATTGAGGCAGACTTTACAAGAAGATTTACTTCGTCGATTCCCAGATCTTAACCG
SEQ ID




ACTTGCCAAGA
NO:





2743





MSH3
NM_002439.1
TGATTACCATCATGGCTCAGATTGGCTCCTATGTTCCTGCAGAAGAAGCGACAATTGGGATT
SEQ ID




GTGGATGGCATTTTCACAAG
NO:





2744





MSH6
NM_000179.1
TCTATTGGGGGATTGGTAGGAACCGTTACCAGCTGGAAATTCCTGAGAATTTCACCACTCGC
SEQ ID




AATTTG
NO:





2745





MT3
NM_005954.1
GTGTGAGAAGTGTGCCAAGGACTGTGTGTGCAAAGGCGGAGAGGCAGCTGAGGCAGAAGC
SEQ ID




AGAGAAGTGCAG
NO:





2746





MTA1
NM_004689.2
CCGCCCTCACCTGAAGAGAAACGCGCTCCTTGGCGGACACTGGGGGAGGAGAGGAAGAAGC
SEQ ID




GCGGCTAACTTATTCC
NO:





2747





MUC1
NM_002456.1
GGCCAGGATCTGTGGTGGTACAATTGACTCTGGCCTTCCGAGAAGGTACCATCAATGTCCAC
SEQ ID




GACGTGGAG
NO:





2748





MUC2
NM_002457.1
CTATGAGCCATGTGGGAACCGGAGCTTCGAGACCTGCAGGACCATCAACGGCATCCACTCC
SEQ ID




AACAT
NO:





2749





MUC5B
XM_039877.11
TGCCCTTGCACTGTCCTAACGGCTCAGCCATCCTGCACACCTACACCCACGTGGATGAGTGT
SEQ ID




GGCTG
NO:





2750





MUTYH
NM_012222.1
GTACGACCAAGAGAAACGGGACCTACCATGGAGAAGACGGGCAGAAGATGAGATGGACCT
SEQ ID




GGACAGG
NO:





2751





MVP
NM_017458.1
ACGAGAACGAGGGCATCTATGTGCAGGATGTCAAGACCGGAAAGGTGCGCGCTGTGATTGG
SEQ ID




AAGCACCTACATGC
NO:





2752





MX1
NM_002462.2
GAAGGAATGGGAATCAGTCATGAGCTAATCACCCTGGAGATCAGCTCCCGAGATGTCCCGG
SEQ ID




ATCTGACTCTAATAGAC
NO:





2753





MXD4
NM_006454.2
AGAAACTGGAGGAGCAGGACCGCCGGGCACTGAGCATCAAGGAGCAGCTGCAGCAGGAGC
SEQ ID




ATCGTTTCCTGAAG
NO:





2754





MYBL2
NM_002466.1
GCCGAGATCGCCAAGATGTTGCCAGGGAGGACAGACAATGCTGTGAAGAATCACTGGAACT
SEQ ID




CTACCATCAAAAG
NO:





2755





MYH11
NM_002474.1
CGGTACTTCTCAGGGCTAATATATACGTACTCTGGCCTCTTCTGCGTGGTGGTCAACCCCTAT
SEQ ID




AAACACCTGCCCATCTACTCGG
NO:





2756





MYLK
NM_053025.1
TGACGGAGCGTGAGTGCATCAAGTACATGCGGCAGATCTCGGAGGGAGTGGAGTACATCCA
SEQ ID




CAAGCAGGGCAT
NO:





2757





NAT2
NM_000015.1
TAACTGACATTCTTGAGCACCAGATCCGGGCTGTTCCCTTTGAGAACCTTAACATGCATTGT
SEQ ID




GGGCAAGCCAT
NO:





2758





NAV2
NM_182964.3
CTCTCCCAGCACAGCTTGAACCTCACTGAGTCAACCAGCCTGGACATGTTGCTGGATGACAC
SEQ ID




TGGTG
NO:





2759





NCAM1
NM_000615.1
TAGTTCCCAGCTGACCATCAAAAAGGTGGATAAGAACGACGAGGCTGAGTACATCTGCATT
SEQ ID




GCTGAGAACAAGGCTG
NO:





2760





NDE1
NM_017668.1
CTACTGCGGAAAGTCGGGGCACTGGAGTCCAAACTCGCTTCCTGCCGGAACCTCGTGTACGA
SEQ ID




TCAGTCC
NO:





2761





NDRG1
NM_006096.2
AGGGCAACATTCCACAGCTGCCCTGGCTGTGATGAGTGTCCTTGCAGGGGCCGGAGTAGGA
SEQ ID




GCACTG
NO:





2762





NDUFS3
NM_004551.1
TATCCATCCTGATGGCGTCATCCCAGTGCTGACTTTCCTCAGGGATCACACCAATGCACAGT
SEQ ID




TCAA
NO:





2763





NEDD8
NM_006156.1
TGCTGGCTACTGGGTGTTAGTTTGCAGTCCTGTGTGCTTCCCTCTCTTATGACTGTGTCCCTG
SEQ ID




GTTGTC
NO:





2764





NEK2
NM_002497.1
GTGAGGCAGCGCGACTCTGGCGACTGGCCGGCCATGCCTTCCCGGGCTGAGGACTATGAAG
SEQ ID




TGTTGTACACCATTGGCA
NO:





2765





NF2
NM_000268.2
ACTCCAGAGCTGACCTCCACCGCCCAGCCTGGGAAGTCATTGTAGGGAGTGAGACACTGAA
SEQ ID




GCCCTGA
NO:





2766





NFKBp50
NM_003998.1
CAGACCAAGGAGATGGACCTCAGCGTGGTGCGGCTCATGTTTACAGCTTTTCTTCCGGATAG
SEQ ID




CACTGGCAGCT
NO:





2767





NFKBp65
NM_021975.1
CTGCCGGGATGGCTTCTATGAGGCTGAGCTCTGCCCGGACCGCTGCATCCACAGTTTCCAGA
SEQ ID




ACCTGG
NO:





2768





NISCH
NM_007184.1
CCAAGGAATCATGTTCGTTCAGGAGGAGGCCCTGGCCAGCAGCCTCTCGTCCACTGACAGTC
SEQ ID




TGACTCCCGAGCACCA
NO:





2769





Nkd-1
NM_033119.3
GAGAGAGTGAGCGAACCCTGCCCAGGCTCCAAGAAGCAGCTGAAGTTTGAAGAGCTCCAGT
SEQ ID




GCGACG
NO:





2770





NMB
NM_021077.1
GGCTGCTGGTACAAATACTGCAGAAATGACACCAATAATAGGGGCAGACACAACAGCGTGG
SEQ ID




CTTAGATTG
NO:





2771





NMBR
NM_002511.1
TGATCCATCTCTAGGCCACATGATTGTCACCTTAGTTGCCCGGGTTCTCAGTTTTGGCAATTC
SEQ ID




TTGTGTCAACCCATTTGCTC
NO:





2772





NME1
NM_000269.1
CCAACCCTGCAGACTCCAAGCCTGGGACCATCCGTGGAGACTTCTGCATACAAGTTGGCAGG
SEQ ID




AACATTATACAT
NO:





2773





NOS3
NM_000603.2
ATCTCCGCCTCGCTCATGGGCACGGTGATGGCGAAGCGAGTGAAGGCGACAATCCTGTATG
SEQ ID




GCTCCGA
NO:





2774





NOTCH1
NM_017617.2
CGGGTCCACCAGTTTGAATGGTCAATGCGAGTGGCTGTCCCGGCTGCAGAGCGGCATGGTGC
SEQ ID




CGAACCAATACAAC
NO:





2775





NOTCH2
NM_024408.2
CACTTCCCTGCTGGGATTATATCAACAACCAGTGTGATGAGCTGTGCAACACGGTCGAGTGC
SEQ ID




CTGTTTGACAACT
NO:





2776





NPM1
NM_002520.2
AATGTTGTCCAGGTTCTATTGCCAAGAATGTGTTGTCCAAAATGCCTGTTTAGTTTTTAAAGA
SEQ ID




TGGAACTCCACCCTTTGCTTG
NO:





2777





NR4A1
NM_002135.2
CACAGCTTGCTTGTCGATGTCCCTGCCTTCGCCTGCCTCTCTGCCCTTGTCCTCATCACCGAC
SEQ ID




CGGCAT
NO:





2778





NRG1
NM_013957.1
CGAGACTCTCCTCATAGTGAAAGGTATGTGTCAGCCATGACCACCCCGGCTCGTATGTCACC
SEQ ID




TGTAGATTTCCACACGCCAAG
NO:





2779





NRP1
NM_003873.1
CAGCTCTCTCCACGCGATTCATCAGGATCTACCCCGAGAGAGCCACTCATGGCGGACTGGGG
SEQ ID




CTCAGAATGGAGCTGCTGGG
NO:





2780





NRP2
NM_003872.1
CTACAGCCTAAACGGCAAGGACTGGGAATACATTCAGGACCCCAGGACCCAGCAGCCAAAG
SEQ ID




CTGTTCGAAGGGAAC
NO:





2781





NTN1
NM_004822.1
AGAAGGACTATGCCGTCCAGATCCACATCCTGAAGGCGGACAAGGCGGGGGACTGGTGGAA
SEQ ID




GTTCACGG
NO:





2782





NUFIP1
NM_012345.1
GCTTCCACATCGTGGTATTGGAGACAGTCTTCTGATAGGTTTCCTCGGCATCAGAAGTCCTTC
SEQ ID




AACCCTGCAGTT
NO:





2783





ODC1
NM_002539.1
AGAGATCACCGGCGTAATCAACCCAGCGTTGGACAAATACTTTCCGTCAGACTCTGGAGTGA
SEQ ID




GAATCATAGCTGAGCCCG
NO:





2784





OPN,
NM_000582.1
CAACCGAAGTTTTCACTCCAGTTGTCCCCACAGTAGACACATATGATGGCCGAGGTGATAGT
SEQ ID


osteopontin

GTGGTTTATGGACTGAGG
NO:





2785





ORC1L
NM_004153.2
TCCTTGACCATACCGGAGGGTGCATGTACATCTCCGGTGTCCCTGGGACAGGGAAGACTGCC
SEQ ID




ACTG
NO:





2786





OSM
NM_020530.3
GTTTCTGAAGGGGAGGTCACAGCCTGAGCTGGCCTCCTATGCCTCATCATGTCCCAAACCAG
SEQ ID




ACACCT
NO:





2787





OSMR
NM_003999.1
GCTCATCATGGTCATGTGCTACTTGAAAAGTCAGTGGATCAAGGAGACCTGTTATCCTGACA
SEQ ID




TCCCTGACCCTTACA
NO:





2788





P14ARF
S78535.1
CCCTCGTGCTGATGCTACTGAGGAGCCAGCGTCTAGGGCAGCAGCCGCTTCCTAGAAGACCA
SEQ ID




GGTCATGATG
NO:





2789





p16-INK4
L27211.1
GCGGAAGGTCCCTCAGACATCCCCGATTGAAAGAACCAGAGAGGCTCTGAGAAACCTCGGG
SEQ ID




AAACTTAGATCATCA
NO:





2790





p21
NM_000389.1
TGGAGACTCTCAGGGTCGAAAACGGCGGCAGACCAGCATGACAGATTTCTACCACTCCAAA
SEQ ID




CGCC
NO:





2791





p27
NM_004064.1
CGGTGGACCACGAAGAGTTAACCCGGGACTTGGAGAAGCACTGCAGAGACATGGAAGAGG
SEQ ID




CGAGCC
NO:





2792





P53
NM_000546.2
CTTTGAACCCTTGCTTGCAATAGGTGTGCGTCAGAAGCACCCAGGACTTCCATTTGCTTTGTC
SEQ ID




CCGGG
NO:





2793





p53R2
AB036063.1
CCCAGCTAGTGTTCCTCAGAACAAAGATTGGAAAAAGCTGGCCGAGAACCATTTATACATA
SEQ ID




GAGGAAGGGCTTACGG
NO:





2794





PADI4
NM_012387.1
AGCAGTGGCTTGCTTTCTTCTCCTGTGATGTCCCAGTTTCCCACTCTGAAGATCCCAACATGG
SEQ ID




TCCTAGCA
NO:





2795





PAI1
NM_000602.1
CCGCAACGTGGTTTTCTCACCCTATGGGGTGGCCTCGGTGTTGGCCATGCTCCAGCTGACAA
SEQ ID




CAGGAGGAGAAACCCAGCA
NO:





2796





Pak1
NM_002576.3
GAGCTGTGGGTTGTTATGGAATACTTGGCTGGAGGCTCCTTGACAGATGTGGTGACAGAAAC
SEQ ID




TTGCATGG
NO:





2797





PARC
NM_015089.1
GGAGCTGACCTGCTTCCTACATCGCCTGGCCTCGATGCATAAGGACTATGCTGTGGTGCTCT
SEQ ID




GCT
NO:





2798





PCAF
NM_003884.3
AGGTGGCTGTGTTACTGCAACGTGCCACAGTTCTGCGACAGTCTACCTCGGTACGAAACCAC
SEQ ID




ACAGGTG
NO:





2799





PCNA
NM_002592.1
GAAGGTGTTGGAGGCACTCAAGGACCTCATCAACGAGGCCTGCTGGGATATTAGCTCCAGC
SEQ ID




GGTGTAAACC
NO:





2800





PDGFA
NM_002607.2
TTGTTGGTGTGCCCTGGTGCCGTGGTGGCGGTCACTCCCTCTGCTGCCAGTGTTTGGACAGA
SEQ ID




ACCCA
NO:





2801





PDGFB
NM_002608.1
ACTGAAGGAGACCCTTGGAGCCTAGGGGCATCGGCAGGAGAGTGTGTGGGCAGGGTTATTTA
SEQ ID





NO:





2802





PDGFC
NM_016205.1
AGTTACTAAAAAATACCACGAGGTCCTTCAGTTGAGACCAAAGACCGGTGTCAGGGGATTG
SEQ ID




CACAAATCACTCACCGAC
NO:





2803





PDGFD
NM_025208.2
TATCGAGGCAGGTCATACCATGACCGGAAGTCAAAAGTTGACCTGGATAGGCTCAATGATG
SEQ ID




ATGCCAAGCGTTA
NO:





2804





PDGFRa
NM_006206.2
GGGAGTTTCCAAGAGATGGACTAGTGCTTGGTCGGGTCTTGGGGTCTGGAGCGTTTGGGAAG
SEQ ID




GTGGTTGAAG
NO:





2805





PDGFRb
NM_002609.2
CCAGCTCTCCTTCCAGCTACAGATCAATGTCCCTGTCCGAGTGCTGGAGCTAAGTGAGAGCC
SEQ ID




ACCC
NO:





2806





PFN1
NM_005022.2
GGAAAACGTTCGTCAACATCACGCCAGCTGAGGTGGGTGTCCTGGTTGGCAAAGACCGGTC
SEQ ID




AAGTTTT
NO:





2807





PFN2
NM_053024.1
TCTATACGTCGATGGTGACTGCACAATGGACATCCGGACAAAGAGTCAAGGTGGGGAGCCA
SEQ ID




ACATACAATGTGGCTGTCGGC
NO:





2808





PGK1
NM_000291.1
AGAGCCAGTTGCTGTAGAACTCAAATCTCTGCTGGGCAAGGATGTTCTGTTCTTGAAGGACT
SEQ ID




GTGTAGGCCCAG
NO:





2809





PI3K
NM_002646.2
TGCTACCTGGACAGCCCGTTGGTGCGCTTCCTCCTGAAACGAGCTGTGTCTGACTTGAGAGT
SEQ ID




GACTCACTACTTCTTCTGGTTACTGAAGGACGGCCT
NO:





2810





PI3KC2A
NM_002645.1
ATACCAATCACCGCACAAACCCAGGCTATTTGTTAAGTCCAGTCACAGCGCAAAGAAACAT
SEQ ID




ATGCGGAGAAAATGCTAGTGTG
NO:





2811





PIK3CA
NM_006218.1
GTGATTGAAGAGCATGCCAATTGGTCTGTATCCCGAGAAGCAGGATTTAGCTATTCCCACGC
SEQ ID




AGGAC
NO:





2812





PIM1
NM_002648.2
CTGCTCAAGGACACCGTCTACACGGACTTCGATGGGACCCGAGTGTATAGCCCTCCAGAGTG
SEQ ID




GATCC
NO:





2813





Pin1
NM_006221.1
GATCAACGGCTACATCCAGAAGATCAAGTCGGGAGAGGAGGACTTTGAGTCTCTGGCCTCA
SEQ ID




CAGTTCA
NO:





2814





PKD1
NM_000296.2
CAGCACCAGCGATTACGACGTTGGCTGGGAGAGTCCTCACAATGGCTCGGGGACGTGGGCC
SEQ ID




TATTCAG
NO:





2815





PKR2
NM_002654.3
CCGCCTGGACATTGATTCACCACCCATCACAGCCCGGAACACTGGCATCATCTGTACCATTG
SEQ ID




GCCCAG
NO:





2816





PLA2G2A
NM_000300.2
GCATCCCTCACCCATCCTAGAGGCCAGGCAGGAGCCCTTCTATACCCACCCAGAATGAGACA
SEQ ID




TCCAGCAGATTTCCAGC
NO:





2817





PLAUR
NM_002659.1
CCCATGGATGCTCCTCTGAAGAGACTTTCCTCATTGACTGCCGAGGCCCCATGAATCAATGT
SEQ ID




CTGGTAGCCACCGG
NO:





2818





PLK
NM_005030.2
AATGAATACAGTATTCCCAAGCACATCAACCCCGTGGCCGCCTCCCTCATCCAGAAGATGCT
SEQ ID




TCAGACA
NO:





2819





PLK3
NM_004073.2
TGAAGGAGACGTACCGCTGCATCAAGCAGGTTCACTACACGCTGCCTGCCAGCCTCTCACTG
SEQ ID




CCTG
NO:





2820





PLOD2
NM_000935.2
CAGGGAGGTGGTTGCAAATTTCTAAGGTACAATTGCTCTATTGAGTCACCACGAAAAGGCTG
SEQ ID




GAGCTTCATGCATCCTGGGAGA
NO:





2821





PMS1
NM_000534.2
CTTACGGTTTTCGTGGAGAAGCCTTGGGGTCAATTTGTTGTATAGCTGAGGTTTTAATTACAA
SEQ ID




CAAGAACGGCTGCT
NO:





2822





PMS2
NM_000535.2
GATGTGGACTGCCATTCAAACCAGGAAGATACCGGATGTAAATTTCGAGTTTTGCCTCAGCC
SEQ ID




AACTAATCTCGCA
NO:





2823





PPARG
NM_005037.3
TGACTTTATGGAGCCCAAGTTTGAGTTTGCTGTGAAGTTCAATGCACTGGAATTAGATGACA
SEQ ID




GCGACTTGGC
NO:





2824





PPID
NM_005038.1
TCCTCATTTGGATGGGAAACATGTGGTGTTTGGCCAAGTAATTAAAGGAATAGGAGTGGCA
SEQ ID




AGGATATTGG
NO:





2825





PPM1D
NM_003620.1
GCCATCCGCAAAGGCTTTCTCGCTTGTCACCTTGCCATGTGGAAGAAACTGGCGGAATGGCC
SEQ ID





NO:





2826





PPP2R4
NM_178001.1
GGCTCAGAGCATAAGGCTTCAGGGCCCAAGTTGGGAGAAGTGACCAAAGTGTAGCCAGTTT
SEQ ID




TCTGAGTTCCCGT
NO:





2827





PR
NM_000926.2
GCATCAGGCTGTCATTATGGTGTCCTTACCTGTGGGAGCTGTAAGGTCTTCTTTAAGAGGGC
SEQ ID




AATGGAAGGGCAGCACAACTACT
NO:





2828





PRDX2
NM_005809.4
GGTGTCCTTCGCCAGATCACTGTTAATGATTTGCCTGTGGGACGCTCCGTGGATGAGGCTCT
SEQ ID




GCGGCTG
NO:





2829





PRDX3
NM_006793.2
TGACCCCAATGGAGTCATCAAGCATTTGAGCGTCAACGATCTCCCAGTGGGCCGAAGCGTG
SEQ ID




GAAGAAACCCTCCGCTTGG
NO:





2830





PRDX4
NM_006406.1
TTACCCATTTGGCCTGGATTAATACCCCTCGAAGACAAGGAGGACTTGGGCCAATAAGGATT
SEQ ID




CCACTTCTTTCAG
NO:





2831





PRDX6
NM_004905.2
CTGTGAGCCAGAGGATGTCAGCTGCCAATTGTGTTTTCCTGCAGCAATTCCATAAACACATC
SEQ ID




CTGGTGTCATCACA
NO:





2832





PRKCA
NM_002737.1
CAAGCAATGCGTCATCAATGTCCCCAGCCTCTGCGGAATGGATCACACTGAGAAGAGGGGG
SEQ ID




CGGATTTAC
NO:





2833





PRKCB1
NM_002738.5
GACCCAGCTCCACTCCTGCTTCCAGACCATGGACCGCCTGTACTTTGTGATGGAGTACGTGA
SEQ ID




ATGGG
NO:





2834





PRKCD
NM_006254.1
CTGACACTTGCCGCAGAGAATCCCTTTCTCACCCACCTCATCTGCACCTTCCAGACCAAGGA
SEQ ID




CCACCT
NO:





2835





PRKR
NM_002759.1
GCGATACATGAGCCCAGAACAGATTTCTTCGCAAGACTATGGAAAGGAAGTGGACCTCTAC
SEQ ID




GCTTTGGGGCTAATTCTTGCTGA
NO:





2836





pS2
NM_003225.1
GCCCTCCCAGTGTGCAAATAAGGGCTGCTGTTTCGACGACACCGTTCGTGGGGTCCCCTGGT
SEQ ID




GCTTCTATCCTAATACCATCGACG
NO:





2837





PTCH
NM_000264.2
CCACGACAAAGCCGACTACATGCCTGAAACAAGGCTGAGAATCCCGGCAGCAGAGCCCATC
SEQ ID




GAGTA
NO:





2838





PTEN
NM_000314.1
TGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAA
SEQ ID




CTGGTGTAATGATATGTGCA
NO:





2839





PTGER3
NM_000957.2
TAACTGGGGCAACCTTTTCTTCGCCTCTGCCTTTGCCTTCCTGGGGCTCTTGGCGCTGACAGT
SEQ ID




CACCTTTTCCTGCAA
NO:





2840





PTHLH
NM_002820.1
AGTGACTGGGAGTGGGCTAGAAGGGGACCACCTGTCTGACACCTCCACAACGTCGCTGGAG
SEQ ID




CTCGATTCACGGTAACAGGCTT
NO:





2841





PTHR1
NM_000316.1
CGAGGTACAAGCTGAGATCAAGAAATCTTGGAGCCGCTGGACACTGGCACTGGACTTCAAG
SEQ ID




CGAAAGGCACGC
NO:





2842





PTK2
NM_005607.3
GACCGGTCGAATGATAAGGTGTACGAGAATGTGACGGGCCTGGTGAAAGCTGTCATCGAGA
SEQ ID




TGTCCAG
NO:





2843





PTK2B
NM_004103.3
CAAGCCCAGCCGACCTAAGTACAGACCCCCTCCGCAAACCAACCTCCTGGCTCCAAAGCTG
SEQ ID




CAGTTCCAGGTTC
NO:





2844





PTP4A3
NM_007079.2
AATATTTGTGCGGGGTATGGGGGTGGGTTTTTAAATCTCGTTTCTCTTGGACAAGCACAGGG
SEQ ID




ATCTCGTT
NO:





2845





PTP4A3 v2
NM_032611.1
CCTGTTCTCGGCACCTTAAATTATTAGACCCCGGGGCAGTCAGGTGCTCCGGACACCCGAAG
SEQ ID




GCAATA
NO:





2846





PTPD1
NM_007039.2
CGCTTGCCTAACTCATACTTTCCCGTTGACACTTGATCCACGCAGCGTGGCACTGGGACGTA
SEQ ID




AGTGGCGCAGTCTGAATGG
NO:





2847





PTPN1
NM_002827.2
AATGAGGAAGTTTCGGATGGGGCTGATCCAGACAGCCGACCAGCTGCGCTTCTCCTACCTGG
SEQ ID




CTGTGATCGAAG
NO:





2848





PTPRF
NM_002840.2
TGTTTTAGCTGAGGGACGTGGTGCCGACGTCCCCAAACCTAGCTAGGCTAAGTCAAGATCAA
SEQ ID




CATTCCAGGGTTGGTA
NO:





2849





PTPRJ
NM_002843.2
AACTTCCGGTACCTCGTTCGTGACTACATGAAGCAGAGTCCTCCCGAATCGCCGATTCTGGT
SEQ ID




GCATTGCAGTGCT
NO:





2850





PTPRO
NM_030667.1
CATGGCCTGATCATGGTGTGCCCACAGCAAATGCTGCAGAAAGTATCCTGCAGTTTGTACAC
SEQ ID




ATGG
NO:





2851





PTTG1
NM_004219.2
GGCTACTCTGATCTATGTTGATAAGGAAAATGGAGAACCAGGCACCCGTGTGGTTGCTAAG
SEQ ID




GATGGGCTGAAGC
NO:





2852





RAB32
NM_006834.2
CCTGCAGCTGTGGGACATCGCGGGGCAGGAGCGATTTGGCAACATGACCCGAGTATACTAC
SEQ ID




AAGGAAGCTGTTGGTGCT
NO:





2853





RAB6C
NM_032144.1
GCGACAGCTCCTCTAGTTCCACCATGTCCGCGGGCGGAGACTTCGGGAATCCGCTGAGGAA
SEQ ID




ATTCAAGCTGGTGTTCC
NO:





2854





RAC1
NM_006908.3
TGTTGTAAATGTCTCAGCCCCTCGTTCTTGGTCCTGTCCCTTGGAACCTTTGTACGCTTTGCTC
SEQ ID




AA
NO:





2855





RAD51C
NM_058216.1
GAACTTCTTGAGCAGGAGCATACCCAGGGCTTCATAATCACCTTCTGTTCAGCACTAGATGA
SEQ ID




TATTCTTGGGGGTGGA
NO:





2856





RAD54L
NM_003579.2
AGCTAGCCTCAGTGACACACATGACAGGTTGCACTGCCGACGTTGTGTCAACAGCCGTCAGA
SEQ ID




TCCGG
NO:





2857





RAF1
NM_002880.1
CGTCGTATGCGAGAGTCTGTTTCCAGGATGCCTGTTAGTTCTCAGCACAGATATTCTACACCT
SEQ ID




CACGCCTTCA
NO:





2858





RALBP1
NM_006788.2
GGTGTCAGATATAAATGTGCAAATGCCTTCTTGCTGTCCTGTCGGTCTCAGTACGTTCACTTT
SEQ ID




ATAGCTGCTGGCAATATCGAA
NO:





2859





RANBP2
NM_006267.3
TCCTTCAGCTTTCACACTGGGCTCAGAAATGAAGTTGCATGACTCTTCTGGAAGTCAGGTGG
SEQ ID




GAACAGGATTT
NO:





2860





ranBP7
NM_006391.1
AACATGATTATCCAAGCCGCTGGACTGCCATTGTGGACAAAATTGGCTTTTATCTTCAGTCC
SEQ ID




GATAACAGTGCTTGTTGGC
NO:





2861





RANBP9
NM_005493.2
CAAGTCAGTTGAGACGCCAGTTGTGTGGAGGAAGTCAGGCCGCCATAGAAAGAATGATCCA
SEQ ID




CTTTGGACGAGAGCTGCA
NO:





2862





RAP1GDS1
NM_021159.3
TGTGGATGCTGGATTGATTTCACCACTGGTGCAGCTGCTAAATAGCAAAGACCAGGAAGTGC
SEQ ID




TGCTT
NO:





2863





RARA
NM_000964.1
AGTCTGTGAGAAACGACCGAAACAAGAAGAAGAAGGAGGTGCCCAAGCCCGAGTGCTCTG
SEQ ID




AGAGCTACACGCTGACGCCG
NO:





2864





RARB
NM_016152.2
TGCCTGGACATCCTGATTCTTAGAATTTGCACCAGGTATACCCCAGAACAAGACACCATGAC
SEQ ID




TTTCTCAGACGGCCTT
NO:





2865





RASSF1
NM_007182.3
AGTGGGAGACACCTGACCTTTCTCAAGCTGAGATTGAGCAGAAGATCAAGGAGTACAATGC
SEQ ID




CCAGATCA
NO:





2866





RBM5
NM_005778.1
CGAGAGGGAGAGCAAGACCATCATGCTGCGCGGCCTTCCCATCACCATCACAGAGAGCGAT
SEQ ID




ATTCGAGA
NO:





2867





RBX1
NM_014248.2
GGAACCACATTATGGATCTTTGCATAGAATGTCAAGCTAACCAGGCGTCCGCTACTTCAGAA
SEQ ID




GAGTGTACTGTCGCATG
NO:





2868





RCC1
NM_001269.2
GGGCTGGGTGAGAATGTGATGGAGAGGAAGAAGCCGGCCCTGGTATCCATTCCGGAGGATG
SEQ ID




TTGTG
NO:





2869





REG4
NM_032044.2
TGCTAACTCCTGCACAGCCCCGTCCTCTTCCTTTCTGCTAGCCTGGCTAAATCTGCTCATTAT
SEQ ID




TTCAGAGGGGAAACCTAGCA
NO:





2870





RFC
NM_003056.1
TCAAGACCATCATCACTTTCATTGTCTCGGACGTGCGGGGCCTGGGCCTCCCGGTCCGCAAG
SEQ ID




CAGTTCCAGTTATACTCCGTGTACTTCCTGATCC
NO:





2871





RhoB
NM_004040.2
AAGCATGAACAGGACTTGACCATCTTTCCAACCCCTGGGGAAGACATTTGCAACTGACTTGG
SEQ ID




GGAGG
NO:





2872





rhoC
NM_175744.1
CCCGTTCGGTCTGAGGAAGGCCGGGACATGGCGAACCGGATCAGTGCCTTTGGCTACCTTGA
SEQ ID




GTGCTC
NO:





2873





RIZ1
NM_012231.1
CCAGACGAGCGATTAGAAGCGGCAGCTTGTGAGGTGAATGATTTGGGGGAAGAGGAGGAG
SEQ ID




GAGGAAGAGGAGGA
NO:





2874





RNF11
NM_014372.3
ACCCTGGAAGAGATGGATCAGAAAAAAAGATCCGGGAGTGTGTGATCTGTATGATGGACTT
SEQ ID




TGTTTATGGGGACCCAAT
NO:





2875





ROCK1
NM_005406.1
TGTGCACATAGGAATGAGCTTCAGATGCAGTTGGCCAGCAAAGAGAGTGATATTGAGCAAT
SEQ ID




TGCGTGCTAAAC
NO:





2876





ROCK2
NM_004850.3
GATCCGAGACCCTCGCTCCCCCATCAACGTGGAGAGCTTGCTGGATGGCTTAAATTCCTTGG
SEQ ID




TCCT
NO:





2877





RPLPO
NM_001002.2
CCATTCTATCATCAACGGGTACAAACGAGTCCTGGCCTTGTCTGTGGAGACGGATTACACCT
SEQ ID




TCCCACTTGCTGA
NO:





2878





RPS13
NM_001017.2
CAGTCGGCTTTACCCTATCGACGCAGCGTCCCCACTTGGTTGAAGTTGACATCTGACGACGT
SEQ ID




GAAGGAGCAGA
NO:





2879





RRM1
NM_001033.1
GGGCTACTGGCAGCTACATTGCTGGGACTAATGGCAATTCCAATGGCCTTGTACCGATGCTG
SEQ ID




AGAG
NO:





2880





RRM2
NM_001034.1
CAGCGGGATTAAACAGTCCTTTAACCAGCACAGCCAGTTAAAAGATGCAGCCTCACTGCTTC
SEQ ID




AACGCAGAT
NO:





2881





RTN4
NM_007008.1
GACTGGAGTGGTGTTTGGTGCCAGCCTATTCCTGCTGCTTTCATTGACAGTATTCAGCATTGT
SEQ ID




GAGCGTAACAG
NO:





2882





RUNX1
NM_001754.2
AACAGAGACATTGCCAACCATATTGGATCTGCTTGCTGTCCAAACCAGCAAACTTCCTGGGC
SEQ ID




AAATCAC
NO:





2883





RXRA
NM_002957.3
GCTCTGTTGTGTCCTGTTGCCGGCTCTGGCCTTCCTGTGACTGACTGTGAAGTGGCTTCTCCG
SEQ ID




TAC
NO:





2884





S100A1
NM_006271.1
TGGACAAGGTGATGAAGGAGCTAGACGAGAATGGAGACGGGGAGGTGGACTTCCAGGAGT
SEQ ID




ATGTGGTGCT
NO:





2885





S100A2
NM_005978.2
TGGCTGTGCTGGTCACTACCTTCCACAAGTACTCCTGCCAAGAGGGCGACAAGTTCAAGCTG
SEQ ID




AGTAAGGGGGA
NO:





2886





S100A4
NM_002961.2
GACTGCTGTCATGGCGTGCCCTCTGGAGAAGGCCCTGGATGTGATGGTGTCCACCTTCCACA
SEQ ID




AGTACTCG
NO:





2887





S100A8
NM_002964.3
ACTCCCTGATAAAGGGGAATTTCCATGCCGTCTACAGGGATGACCTGAAGAAATTGCTAGA
SEQ ID




GACCGAGTGTCCTCA
NO:





2888





S100A9
NM_002965.2
CTTTGGGACAGAGTGCAAGACGATGACTTGCAAAATGTCGCAGCTGGAACGCAACATAGAG
SEQ ID




ACCA
NO:





2889





S100P
NM_005980.2
AGACAAGGATGCCGTGGATAAATTGCTCAAGGACCTGGACGCCAATGGAGATGCCCAGGTG
SEQ ID




GACTTC
NO:





2890





SAT
NM_002970.1
CCTTTTACCACTGCCTGGTTGCAGAAGTGCCGAAAGAGCACTGGACTCCGGAAGGACACAG
SEQ ID




CATTGT
NO:





2891





SBA2
NM_018639.3
GGACTCAACGATGGGCAGATCAAGATCTGGGAGGTGCAGACAGGGCTCCTGCTTTTGAATC
SEQ ID




TTTCCG
NO:





2892





SDC1
NM_002997.1
GAAATTGACGAGGGGTGTCTTGGGCAGAGCTGGCTCTGAGCGCCTCCATCCAAGGCCAGGT
SEQ ID




TCTCCGTTAGCTCCT
NO:





2893





SEMA3B
NM_004636.1
GCTCCAGGATGTGTTTCTGTTGTCCTCGCGGGACCACCGGACCCCGCTGCTCTATGCCGTCTT
SEQ ID




CTCCACGT
NO:





2894





SEMA3F
NM_004186.1
CGCGAGCCCCTCATTATACACTGGGCAGCCTCCCCACAGCGCATCGAGGAATGCGTGCTCTC
SEQ ID




AGGCAAGGATGTCAACGGCGAGTG
NO:





2895





SEMA4B
NM_020210.1
TTCCAGCCCAACACAGTGAACACTTTGGCCTGCCCGCTCCTCTCCAACCTGGCGACCCGACTC
SEQ ID





NO:





2896





SFRP2
NM_003013.2
CAAGCTGAACGGTGTGTCCGAAAGGGACCTGAAGAAATCGGTGCTGTGGCTCAAAGACAGC
SEQ ID




TTGCA
NO:





2897





SFRP4
NM_003014.2
TACAGGATGAGGCTGGGCATTGCCTGGGACAGCCTATGTAAGGCCATGTGCCCCTTGCCCTA
SEQ ID




ACAAC
NO:





2898





SGCB
NM_000232.1
CAGTGGAGACCAGTTGGGTAGTGGTGACTGGGTACGCTACAAGCTCTGCATGTGTGCTGATG
SEQ ID




GGACGCTCTTCAAGG
NO:





2899





SHC1
NM_003029.3
CCAACACCTTCTTGGCTTCTGGGACCTGTGTTCTTGCTGAGCACCCTCTCCGGTTTGGGTTGG
SEQ ID




GATAACAG
NO:





2900





SHH
NM_000193.2
GTCCAAGGCACATATCCACTGCTCGGTGAAAGCAGAGAACTCGGTGGCGGCCAAATCGGGA
SEQ ID




GGCTGCTTC
NO:





2901





SI
NM_001041.1
AACGGACTCCCTCAATTTGTGCAAGATTTGCATGACCATGGACAGAAATATGTCATCATCTT
SEQ ID




GGACCCTGCAATTTC
NO:





2902





Siah-1
NM_003031.2
TTGGCATTGGAACTACATTCAATCCGCGGTATCCTCGGATTAGTTCTAGGACCCCCTTCTCCA
SEQ ID




TACC
NO:





2903





SIAT4A
NM_003033.2
AACCACAGTTGGAGGAGGACGGCAGAGACAGTTTCCCTCCCCGCTATACCAACACCCTTCCT
SEQ ID




TCG
NO:





2904





SIAT7B
NM_006456.1
TCCAGCCCAAATCCTCCTGGTGGCACATCCTACCCCAGATGCTAAAGTGATTCAAGGACTCC
SEQ ID




AGGACACC
NO:





2905





SIM2
NM_005069.2
GATGGTAGGAAGGGATGTGCCCGCCTCTCCACGCACTCAGCTATACCTCATTCACAGCTCCT
SEQ ID




TGTG
NO:





2906





SIN3A
NM_015477.1
CCAGAGTCATGCTCATCCAGCCCCACCAGTTGCACCAGTGCAGGGACAGCAGCAATTTCAG
SEQ ID




AGGCTGAAGGTGG
NO:





2907





SIR2
NM_012238.3
AGCTGGGGTGTCTGTTTCATGTGGAATACCTGACTTCAGGTCAAGGGATGGTATTTATGCTC
SEQ ID




GCCTTGCTGT
NO:





2908





SKP1A
NM_006930.2
CCATTGCCTTTGCTTTGTTCATAATTTCAGCAGGGCAGAATAAAAACCATGGGAGGCAAAGA
SEQ ID




AAGGAAATCCGGAA
NO:





2909





SKP2
NM_005983.2
AGTTGCAGAATCTAAGCCTGGAAGGCCTGCGGCTTTCGGATCCCATTGTCAATACTCTCGCA
SEQ ID




AAAAACTCA
NO:





2910





SLC25A3
NM_213611.1
TCTGCCAGTGCTGAATTCTTTGCTGACATTGCCCTGGCTCCTATGGAAGCTGCTAAGGTTCGAA
SEQ ID





NO:





2911





SLC2A1
NM_006516.1
GCCTGAGTCTCCTGTGCCCACATCCCAGGCTTCACCCTGAATGGTTCCATGCCTGAGGGTGG
SEQ ID




AGACT
NO:





2912





SLC31A1
NM_001859.2
CCGTTCGAAGAGTCGTGAGGGGGTGACGGGTTAAGATTCGGAGAGAGAGGTGCTAGTGGCT
SEQ ID




GGACT
NO:





2913





SLC5A8
NM_145913.2
CCTGCTTTCAACCACATTGAATTGAACTCAGATCAGAGTGGCAAGAGCAATGGGACTCGTTT
SEQ ID




GTGAAGCTGCTCT
NO:





2914





SLC7A5
NM_003486.4
GCGCAGAGGCCAGTTAAAGTAGATCACCTCCTCGAACCCACTCCGGTTCCCCGCAACCCACA
SEQ ID




GCTCAGCT
NO:





2915





SLPI
NM_003064.2
ATGGCCAATGTTTGATGCTTAACCCCCCCAATTTCTGTGAGATGGATGGCCAGTGCAAGCGT
SEQ ID




GACTTGAAGTGT
NO:





2916





SMARCA3
NM_003071.2
AGGGACTGTCCTGGCACATTATGCAGATGTCCTGGGTCTTTTGCTTAGACTGCGGCAAATTT
SEQ ID




GTTG
NO:





2917





SNAI1
NM_005985.2
CCCAATCGGAAGCCTAACTACAGCGAGCTGCAGGACTCTAATCCAGAGTTTACCTTCCAGCA
SEQ ID




GCCCTAC
NO:





2918





SNAI2
NM_003068.3
GGCTGGCCAAACATAAGCAGCTGCACTGCGATGCCCAGTCTAGAAAATCTTTCAGCTGTAAA
SEQ ID




TACTGTGACAAGGA
NO:





2919





SNRPF
NM_003095.1
GGCTGGTCGGCAGAGAGTAGCCTGCAACATTCGGCCGTGGTTTACATGAGTTTACCCCTCAA
SEQ ID




TCCCAAACCTTTCCTCA
NO:





2920





SOD1
NM_000454.3
TGAAGAGAGGCATGTTGGAGACTTGGGCAATGTGACTGCTGACAAAGATGGTGTGGCCGAT
SEQ ID




GTGTCTATT
NO:





2921





SOD2
NM_000636.1
GCTTGTCCAAATCAGGATCCACTGCAAGGAACAACAGGCCTTATTCCACTGCTGGGGATTGA
SEQ ID




TGTGTGGGAGCACGCT
NO:





2922





SOS1
NM_005633.2
TCTGCACCAAATTCTCCAAGAACACCGTTAACACCTCCGCCTGCTTCTGGTGCTTCCAGTACC
SEQ ID




AC
NO:





2923





SOX17
NM_022454.2
TCGTGTGCAAGCCTGAGATGGGCCTCCCCTACCAGGGGCATGACTCCGGTGTGAATCTCCCC
SEQ ID




GACAG
NO:





2924





SPARC
NM_003118.1
TCTTCCCTGTACACTGGCAGTTCGGCCAGCTGGACCAGCACCCCATTGACGGGTACCTCTCC
SEQ ID




CACACCGAGCT
NO:





2925





SPINT2
NM_021102.1
AGGAATGCAGCGGATTCCTCTGTCCCAAGTGCTCCCAGAAGGCAGGATTCTGAAGACCACTC
SEQ ID




CAGCGA
NO:





2926





SPRY1
AK026960.1
CAGACCAGTCCCTGGTCATAGGTCTGAAAGGGCAATCCGGACCCAGCCCAAGCAACTGATT
SEQ ID




GTGGATGACTTGAAGG
NO:





2927





SPRY2
NM_005842.1
TGTGGCAAGTGCAAATGTAAGGAGTGCACCTACCCAAGGCCTCTGCCATCAGACTGGATCTG
SEQ ID




CGAC
NO:





2928





SR-A1
NM_021228.1
AGATGGAAGAAGCCAACCTGGCGAGCCGAGCGAAGGCCCAGGAGCTGATCCAGGCCACCA
SEQ ID




ACCAGATCCTCAGCCACAG
NO:





2929





ST14
NM_021978.2
TGACTGCACATGGAACATTGAGGTGCCCAACAACCAGCATGTGAAGGTGCGCTTCAAATTCTT
SEQ ID





NO:





2930





STAT1
NM_007315.1
GGGCTCAGCTTTCAGAAGTGCTGAGTTGGCAGTTTTCTTCTGTCACCAAAAGAGGTCTCAAT
SEQ ID




GTGGACCAGCTGAACATGT
NO:





2931





STAT3
NM_003150.1
TCACATGCCACTTTGGTGTTTCATAATCTCCTGGGAGAGATTGACCAGCAGTATAGCCGCTT
SEQ ID




CCTGCAAG
NO:





2932





STAT5A
NM_003152.1
GAGGCGCTCAACATGAAATTCAAGGCCGAAGTGCAGAGCAACCGGGGCCTGACCAAGGAG
SEQ ID




AACCTCGTGTTCCTGGC
NO:





2933





STAT5B
NM_012448.1
CCAGTGGTGGTGATCGTTCATGGCAGCCAGGACAACAATGCGACGGCCACTGTTCTCTGGGA
SEQ ID




CAATGCTTTTGC
NO:





2934





STC1
NM_003155.1
CTCCGAGGTGAGGAGGACTCTCCCTCCCACATCAAACGCACATCCCATGAGAGTGCATAACC
SEQ ID




AGGGAGAGGT
NO:





2935





STK11
NM_000455.3
GGACTCGGAGACGCTGTGCAGGAGGGCCGTCAAGATCCTCAAGAAGAAGAAGTTGCGAAG
SEQ ID




GATCCC
NO:





2936





STK15
NM_003600.1
CATCTTCCAGGAGGACCACTCTCTGTGGCACCCTGGACTACCTGCCCCCTGAAATGATTGAA
SEQ ID




GGTCGGA
NO:





2937





STMN1
NM_005563.2
AATACCCAACGCACAAATGACCGCACGTTCTCTGCCCCGTTTCTTGCCCCAGTGTGGTTTGC
SEQ ID




ATTGTCTCC
NO:





2938





STMY3
NM_005940.2
CCTGGAGGCTGCAACATACCTCAATCCTGTCCCAGGCCGGATCCTCCTGAAGCCCTTTTCGC
SEQ ID




AGCACTGCTATCCTCCAAAGCCATTGTA
NO:





2939





STS
NM_000351.2
GAAGATCCCTTTCCTCCTACTGTTCTTTCTGTGGGAAGCCGAGAGCCACGAAGCATCAAGGC
SEQ ID




CGAACATCATCC
NO:





2940





SURV
NM_001168.1
TGTTTTGATTCCCGGGCTTACCAGGTGAGAAGTGAGGGAGGAAGAAGGCAGTGTCCCTTTTG
SEQ ID




CTAGAGCTGACAGCTTTG
NO:





2941





TAGLN
NM_003186.2
GATGGAGCAGGTGGCTCAGTTCCTGAAGGCGGCTGAGGACTCTGGGGTCATCAAGACTGAC
SEQ ID




ATGTTCCAGACT
NO:





2942





TBP
NM_003194.1
GCCCGAAACGCCGAATATAATCCCAAGCGGTTTGCTGCGGTAATCATGAGGATAAGAGAGC
SEQ ID




CACG
NO:





2943





TCF-1
NM_000545.3
GAGGTCCTGAGCACTGCCAGGAGGGACAAAGGAGCCTGTGAACCCAGGACAAGCATGGTCC
SEQ ID




CACATC
NO:





2944





TCF-7
NM_003202.2
GCAGCTGCAGTCAACAGTTCAAAGAAGTCATGGCCCAAATCCAGTGTGCACCCCTCCCCATT
SEQ ID




CACAG
NO:





2945





TCF7L1
NM_031283.1
CCGGGACACTTTCCAGAAGCCGCGGGACTATTTCGCCGAAGTGAGAAGGCCTCAGGACAGC
SEQ ID




GCGTTCT
NO:





2946





TCF7L2
NM_030756.1
CCAATCACGACAGGAGGATTCAGACACCCCTACCCCACAGCTCTGACCGTCAATGCTTCCGT
SEQ ID




GTCCA
NO:





2947





TCFL4
NM_170607.2
CTGACTGCTCTGCTTAAAGGTGAAAGTAGCAGGAACAACAACAAAAGCCAACCAAAAACAA
SEQ ID




GGTAGCCAGTGCAAGACAT
NO:





2948





TEK
NM_000459.1
ACTTCGGTGCTACTTAACAACTTACATCCCAGGGAGCAGTACGTGGTCCGAGCTAGAGTCAA
SEQ ID




CACCAAGGCCCAGG
NO:





2949





TERC
U86046.1
AAGAGGAACGGAGCGAGTCCCCGCGCGCGGCGCGATTCCCTGAGCTGTGGGACGTGCACCC
SEQ ID




AGGACTCGGCTCACACAT
NO:





2950





TERT
NM_003219.1
GACATGGAGAACAAGCTGTTTGCGGGGATTCGGCGGGACGGGCTGCTCCTGCGTTTGGTGG
SEQ ID




ATGATTTCTTGTTGGTGACACCTC
NO:





2951





TFF3
NM_003226.1
AGGCACTGTTCATCTCAGTTTTTCTGTCCCTTTGCTCCCGGCAAGCTTTCTGCTGAAAGTTCA
SEQ ID




TATCTGGAGCCTGATG
NO:





2952





TGFA
NM_003236.1
GGTGTGCCACAGACCTTCCTACTTGGCCTGTAATCACCTGTGCAGCCTTTTGTGGGCCTTCAA
SEQ ID




AACTCTGTCAAGAACTCCGT
NO:





2953





TGFB2
NM_003238.1
ACCAGTCCCCCAGAAGACTATCCTGAGCCCGAGGAAGTCCCCCCGGAGGTGATTTCCATCTA
SEQ ID




CAACAGCACCAGG
NO:





2954





TGFB3
NM_003239.1
GGATCGAGCTCTTCCAGATCCTTCGGCCAGATGAGCACATTGCCAAACAGCGCTATATCGGT
SEQ ID




GGC
NO:





2955





TGFBI
NM_000358.1
GCTACGAGTGCTGTCCTGGATATGAAAAGGTCCCTGGGGAGAAGGGCTGTCCAGCAGCCCT
SEQ ID




ACCACT
NO:





2956





TGFBR1
NM_004612.1
GTCATCACCTGGCCTTGGTCCTGTGGAACTGGCAGCTGTCATTGCTGGACCAGTGTGCTTCGT
SEQ ID




CTGC
NO:





2957





TGFBR2
NM_003242.2
AACACCAATGGGTTCCATCTTTCTGGGCTCCTGATTGCTCAAGCACAGTTTGGCCTGATGAA
SEQ ID




GAGG
NO:





2958





THBS1
NM_003246.1
CATCCGCAAAGTGACTGAAGAGAACAAAGAGTTGGCCAATGAGCTGAGGCGGCCTCCCCTA
SEQ ID




TGCTATCACAACGGAGTTCAGTAC
NO:





2959





THY1
NM_006288.2
GGACAAGACCCTCTCAGGCTGTCCCAAGCTCCCAAGAGCTTCCAGAGCTCTGACCCACAGCC
SEQ ID




TCCAA
NO:





2960





TIMP1
NM_003254.1
TCCCTGCGGTCCCAGATAGCCTGAATCCTGCCCGGAGTGGAACTGAAGCCTGCACAGTGTCC
SEQ ID




ACCCTGTTCCCAC
NO:





2961





TIMP2
NM_003255.2
TCACCCTCTGTGACTTCATCGTGCCCTGGGACACCCTGAGCACCACCCAGAAGAAGAGCCTG
SEQ ID




AACCACA
NO:





2962





TIMP3
NM_000362.2
CTACCTGCCTTGCTTTGTGACTTCCAAGAACGAGTGTCTCTGGACCGACATGCTCTCCAATTT
SEQ ID




CGGT
NO:





2963





TJP1
NM_003257.1
ACTTTGCTGGGACAAAGGTCAACTGAAGAAGTGGGCAGGCCCGAGGCAGGAGAGATGCTGA
SEQ ID




GGAGTCCATGTG
NO:





2964





TK1
NM_003258.1
GCCGGGAAGACCGTAATTGTGGCTGCACTGGATGGGACCTTCCAGAGGAAGCCATTTGGGG
SEQ ID




CCATCCTGAACCTGGTGCCGCTG
NO:





2965





TLN1
NM_006289.2
AAGCAGAAGGGAGAGCGTAAGATCTTCCAGGCACACAAGAATTGTGGGCAGATGAGTGAG
SEQ ID




ATTGAGGCCAAGG
NO:





2966





TMEPAI
NM_020182.3
CAGAAGGATGCCTGTGGCCCTCGGAGAGCACAGTGTCAGGCAACGGAATCCCAGAGCCGCA
SEQ ID




GGTCTAC
NO:





2967





TMSB10
NM_021103.2
GAAATCGCCAGCTTCGATAAGGCCAAGCTGAAGAAAACGGAGACGCAGGAAAAGAACACC
SEQ ID




CTGCCGAC
NO:





2968





TMSB4X
NM_021109.2
CACATCAAAGAACTACTGACAACGAAGGCCGCGCCTGCCTTTCCCATCTGTCTATCTATCTG
SEQ ID




GCTGGCAGG
NO:





2969





TNC
NM_002160.1
AGCTCGGAACCTCACCGTGCCTGGCAGCCTTCGGGCTGTGGACATACCGGGCCTCAAGGCTG
SEQ ID




CTAC
NO:





2970





TNF
NM_000594.1
GGAGAAGGGTGACCGACTCAGCGCTGAGATCAATCGGCCCGACTATCTCGACTTTGCCGAG
SEQ ID




TCTGGGCA
NO:





2971





TNFRSF5
NM_001250.3
TCTCACCTCGCTATGGTTCGTCTGCCTCTGCAGTGCGTCCTCTGGGGCTGCTTGCTGACCGCT
SEQ ID




GTCCATC
NO:





2972





TNFRSF6B
NM_003823.2
CCTCAGCACCAGGGTACCAGGAGCTGAGGAGTGTGAGCGTGCCGTCATCGACTTTGTGGCTT
SEQ ID




TCCAGGACA
NO:





2973





TNFSF4
NM_003326.2
CTTCATCTTCCCTCTACCCAGATTGTGAAGATGGAAAGGGTCCAACCCCTGGAAGAGAATGT
SEQ ID




GGGAAATGCAGC
NO:





2974





TOP2A
NM_001067.1
AATCCAAGGGGGAGAGTGATGACTTCCATATGGACTTTGACTCAGCTGTGGCTCCTCGGGCA
SEQ ID




AAATCTGTAC
NO:





2975





TOP2B
NM_001068.1
TGTGGACATCTTCCCCTCAGACTTCCCTACTGAGCCACCTTCTCTGCCACGAACCGGTCGGGC
SEQ ID




TAG
NO:





2976





TP
NM_001953.2
CTATATGCAGCCAGAGATGTGACAGCCACCGTGGACAGCCTGCCACTCATCACAGCCTCCAT
SEQ ID




TCTCAGTAAGAAACTCGTGG
NO:





2977





TP53BP1
NM_005657.1
TGCTGTTGCTGAGTCTGTTGCCAGTCCCCAGAAGACCATGTCTGTGTTGAGCTGTATCTGTGA
SEQ ID




AGCCAGGCAAG
NO:





2978





TP53BP2
NM_005426.1
GGGCCAAATATTCAGAAGCTTTTATATCAGAGGACCACCATAGCGGCCATGGAGACCATCTC
SEQ ID




TGTCCCATCATACCCATCC
NO:





2979





TP53I3
NM_004881.2
GCGGACTTAATGCAGAGACAAGGCCAGTATGACCCACCTCCAGGAGCCAGCAACATTTTGG
SEQ ID




GACTTGA
NO:





2980





TRAG3
NM_004909.1
GACGCTGGTCTGGTGAAGATGTCCAGGAAACCACGAGCCTCCAGCCCATTGTCCAACAACC
SEQ ID




ACCCA
NO:





2981





TRAIL
NM_003810.1
CTTCACAGTGCTCCTGCAGTCTCTCTGTGTGGCTGTAACTTACGTGTACTTTACCAACGAGCT
SEQ ID




GAAGCAGATG
NO:





2982





TS
NM_001071.1
GCCTCGGTGTGCCTTTCAACATCGCCAGCTACGCCCTGCTCACGTACATGATTGCGCACATC
SEQ ID




ACG
NO:





2983





TST
NM_003312.4
GGAGCCGGATGCAGTAGGACTGGACTCGGGCCATATCCGTGGTGCCGTCAACATGCCTTTCA
SEQ ID




TGGACTT
NO:





2984





TUBA1
NM_006000.1
TGTCACCCCGACTCAACGTGAGACGCACCGCCCGGACTCACCATGCGTGAATGCATCTCAGT
SEQ ID




CCACGT
NO:





2985





TUBB
NM_001069.1
CGAGGACGAGGCTTAAAAACTTCTCAGATCAATCGTGCATCCTTAGTGAACTTCTGTTGTCC
SEQ ID




TCAAGCATGGT
NO:





2986





TUFM
NM_003321.3
GTATCACCATCAATGCGGCTCATGTGGAGTATAGCACTGCCGCCCGCCACTACGCCCACACA
SEQ ID




GACTG
NO:





2987





TULP3
NM_003324.2
TGTGTATAGTCCTGCCCCTCAAGGTGTCACAGTAAGATGTCGGATAATCCGGGATAAAAGGG
SEQ ID




GAATGGATCGGG
NO:





2988





tusc4
NM_006545.4
GGAGGAGCTAAATGCCTCAGGCCGGTGCACTCTGCCCATTGATGAGTCCAACACCATCCACT
SEQ ID




TGAAGG
NO:





2989





UBB
NM_018955.1
GAGTCGACCCTGCACCTGGTCCTGCGTCTGAGAGGTGGTATGCAGATCTTCGTGAAGACCCT
SEQ ID




GACCGGCAAGACCATCACCCTGGAAGTGGAGCCCAGTGACACCATCGAAAATGTGAAGGCC
NO:




AAGATCCAGGATAAAGAAGGCATCCCTCCCGACCAGCAGAGGCTCATCTTTGCAGGCAAGC
2990




AGCTGGAAGATGGCCGCACTCTTTCTGACTACAACATCCAGAAGGAGTCGACCCTGCACCTG




GTCCTGCGTCTGAGAGGTGGTATGCAGATCTTCGTGAAGACCCTGACCGGCAAGACCATCAC




TCTGGAAGTGGAGCCCAGTGACACCATCGAAAATGTGAAGGCCAAGATCCAAGATAAAGAA




GGCATCCCTCCCGACCAGCAGAGGCTCATCTTTGCAGGCAAGCAGCTGGAAGATGGCCGCA




CTCTTTCTGACTACAACATCCAGAAGGAGTCGACCCTGCACCTGGTCCTGCGCCTGAGGGGT




GGCTGTTAATTCTTCAGTCATGGCATTCGC





UBC
NM_021009.2
ACGCACCCTGTCTGACTACAACATCCAGAAAGAGTCCACCCTGCACCTGGTGCTCCGTCTTA
SEQ ID




GAGGT
NO:





2991





UBE2C
NM_007019.2
TGTCTGGCGATAAAGGGATTTCTGCCTTCCCTGAATCAGACAACCTTTTCAAATGGGTAGGG
SEQ ID




ACCAT
NO:





2992





UBE2M
NM_003969.1
CTCCATAATTTATGGCCTGCAGTATCTCTTCTTGGAGCCCAACCCCGAGGACCCACTGAACA
SEQ ID




AGGAGGCCGCA
NO:





2993





UBL1
NM_003352.3
GTGAAGCCACCGTCATCATGTCTGACCAGGAGGCAAAACCTTCAACTGAGGACTTGGGGGA
SEQ ID




TAAGAAGGAAGG
NO:





2994


UCP2
NM_003355.2
ACCATGCTCCAGAAGGAGGGGCCCCGAGCCTTCTACAAAGGGTTCATGCCCTCCTTTCTCCG
SEQ ID




CTTGGGTT
NO:





2995


UGT1A1
NM_000463.2
CCATGCAGCCTGGAATTTGAGGCTACCCAGTGCCCCAACCCATTCTCCTACGTGCCCAGGCC
SEQ ID




TCTC
NO:





2996





UMPS
NM_000373.1
TGCGGAAATGAGCTCCACCGGCTCCCTGGCCACTGGGGACTACACTAGAGCAGCGGTTAGA
SEQ ID




ATGGCTGAGG
NO:





2997





UNC5A
XM_030300.7
GACAGCTGATCCAGGAGCCACGGGTCCTGCACTTCAAGGACAGTTACCACAACCTGCGCCT
SEQ ID




ATCCAT
NO:





2998





UNC5B
NM_170744.2
AGAACGGAGGCCGTGACTGCAGCGGGACGCTGCTCGACTCTAAGAACTGCACAGATGGGCT
SEQ ID




GTGCATG
NO:





2999





UNC5C
NM_003728.2
CTGAACACAGTGGAGCTGGTTTGCAAACTCTGTGTGCGGCAGGTGGAAGGAGAAGGGCAGA
SEQ ID




TCTTCCAG
NO:





3000





upa
NM_002658.1
GTGGATGTGCCCTGAAGGACAAGCCAGGCGTCTACACGAGAGTCTCACACTTCTTACCCTGG
SEQ ID




ATCCGCAG
NO:





3001





UPP1
NM_003364.2
ACGGGTCCTGCCTCAGTTGGCGGAATGGCGGCCACGGGAGCCAATGCAGAGAAAGCTGAAA
SEQ ID




GTCACAATGATTGCCCCG
NO:





3002





VCAM1
NM_001078.2
TGGCTTCAGGAGCTGAATACCCTCCCAGGCACACACAGGTGGGACACAAATAAGGGTTTTG
SEQ ID




GAACCACTATTTTCTCATCACGACAGCA
NO:





3003





VCL
NM_003373.2
GATACCACAACTCCCATCAAGCTGTTGGCAGTGGCAGCCACGGCGCCTCCTGATGCGCCTAA
SEQ ID




CAGGGA
NO:





3004





VCP
NM_007126.2
GGCTTTGGCAGCTTCAGATTCCCTTCAGGGAACCAGGGTGGAGCTGGCCCCAGTCAGGGCA
SEQ ID




GTGGAG
NO:





3005





VDAC1
NM_003374.1
GCTGCGACATGGATTTCGACATTGCTGGGCCTTCCATCCGGGGTGCTCTGGTGCTAGGTTAC
SEQ ID




GAGGGCTGG
NO:





3006





VDAC2
NM_003375.2
ACCCACGGACAGACTTGCGCGCGTCCAATGTGTATTCCTCCATCATATGCTGACCTTGGCAA
SEQ ID




AGCT
NO:





3007





VDR
NM_000376.1
GCCCTGGATTTCAGAAAGAGCCAAGTCTGGATCTGGGACCCTTTCCTTCCTTCCCTGGCTTGT
SEQ ID




AACT
NO:





3008





VEGF
NM_003376.3
CTGCTGTCTTGGGTGCATTGGAGCCTTGCCTTGCTGCTCTACCTCCACCATGCCAAGTGGTCC
SEQ ID




CAGGCTGC
NO:





3009





VEGF_altsplice1
AF486837.1
TGTGAATGCAGACCAAAGAAAGATAGAGCAAGACAAGAAAATCCCTGTGGGCCTTGCTCAG
SEQ ID




AGCGGAGAAAGC
NO:





3010





VEGF_altsplice2
AF214570.1
AGCTTCCTACAGCACAACAAATGTGAATGCAGACCAAAGAAAGATAGAGCAAGACAAGAA
SEQ ID




AAATGTGACAAGCCGAG
NO:





3011





VEGFB
NM_003377.2
TGACGATGGCCTGGAGTGTGTGCCCACTGGGCAGCACCAAGTCCGGATGCAGATCCTCATG
SEQ ID




ATCCGGTACC
NO:





3012





VEGFC
NM_005429.2
CCTCAGCAAGACGTTATTTGAAATTACAGTGCCTCTCTCTCAAGGCCCCAAACCAGTAACAA
SEQ ID




TCAGTTTTGCCAATCACACTT
NO:





3013





VIM
NM_003380.1
TGCCCTTAAAGGAACCAATGAGTCCCTGGAACGCCAGATGCGTGAAATGGAAGAGAACTTT
SEQ ID




GCCGTTGAAGC
NO:





3014





WIF
NM_007191.2
TACAAGCTGAGTGCCCAGGCGGGTGCCGAAATGGAGGCTTTTGTAATGAAAGACGCATCTG
SEQ ID




CGAGTG
NO:





3015





WISP1
NM_003882.2
AGAGGCATCCATGAACTTCACACTTGCGGGCTGCATCAGCACACGCTCCTATCAACCCAAGT
SEQ ID




ACTGTGGAGTTTG
NO:





3016





Wnt-3a
NM_033131.2
ACAAAGCTACCAGGGAGTCGGCCTTTGTCCACGCCATTGCCTCAGCCGGTGTGGCCTTTGCA
SEQ ID




GTGACACGCTCA
NO:





3017





Wnt-5a
NM_003392.2
GTATCAGGACCACATGCAGTACATCGGAGAAGGCGCGAAGACAGGCATCAAAGAATGCCA
SEQ ID




GTATCAATTCCGACA
NO:





3018





Wnt-5b
NM_032642.2
TGTCTTCAGGGTCTTGTCCAGAATGTAGATGGGTTCCGTAAGAGGCCTGGTGCTCTCTTACTC
SEQ ID




TTTCATCCACGTGCAC
NO:





3019





WNT2
NM_003391.1
CGGTGGAATCTGGCTCTGGCTCCCTCTGCTCTTGACCTGGCTCACCCCCGAGGTCAACTCTTC
SEQ ID




ATGG
NO:





3020





WWOX
NM_016373.1
ATCGCAGCTGGTGGGTGTACACACTGCTGTTTACCTTGGCGAGGCCTTTCACCAAGTCCATG
SEQ ID




CAACAGGGAGCT
NO:





3021





XPA
NM_000380.2
GGGTAGAGGGAAAAGGGTTCAACAAAGGCTGAACTGGATTCTTAACCAAGAAACAAATAAT
SEQ ID




AGCAATGGTGGTGCA
NO:





3022





XPC
NM_004628.2
GATACATCGTCTGCGAGGAATTCAAAGACGTGCTCCTGACTGCCTGGGAAAATGAGCAGGC
SEQ ID




AGTCATTGAAAG
NO:





3023





XRCC1
NM_006297.1
GGAGATGAAGCCCCCAAGCTTCCTCAGAAGCAACCCCAGACCAAAACCAAGCCCACTCAGG
SEQ ID




CAGCTGGAC
NO:





3024





YB-1
NM_004559.1
AGACTGTGGAGTTTGATGTTGTTGAAGGAGAAAAGGGTGCGGAGGCAGCAAATGTTACAGG
SEQ ID




TCCTGGTGGTGTTCC
NO:





3025





YWHAH
NM_003405.2
CATGGCCTCCGCTATGAAGGCGGTGACAGAGCTGAATGAACCTCTCTCCAATGAAGATCGA
SEQ ID




AATCTCC
NO:





3026





zbtb7
NM_015898.2
CTGCGTTCACACCCCAGTGTCACAGGGCGAGCTGTTCTGGAGAGAAAACCATCTGTCGTGGC
SEQ ID




TGAG
NO:





3027





ZG16
NM_152338.1
TGCTGAGCCTCCTCTCCTTGGCAGGGGCACTGTGATGAGGAGTAAGAACTCCCTTATCACTA
SEQ ID




ACCCCCATCC
NO:





3028
















TABLE 4







Most Highly Correlated Genes

















Variable
Rank 1
Rank 2
Rank 3
Rank 4
Rank 5
Rank 6
Rank 7
Rank 8
Rank 9
Rank 10





ADAMTS12
SPARC
TIMP2
COL1A1
ANTXR1
BGN
LOXL2
THY1
CDH11
IGFBP7
COL1A2



0.7317
0.7177
0.7077
0.7022
0.6962
0.6679
0.6665
0.647
0.6433
0.6393


ANTXR1
TIMP2
BGN
COL1A1
THY1
FAP
SFRP4
SPARC
TGFB3
ADAMTS12
PDGFC



0.8358
0.8159
0.7796
0.7696
0.7261
0.7154
0.7138
0.7119
0.7022
0.6992


BGN
COL1A1
SPARC
TIMP2
FAP
ANTXR1
TGFB3
SFRP2
INHBA
WISP1
CTHRC1



0.8986
0.8711
0.8446
0.8177
0.8159
0.8147
0.811
0.7854
0.7682
0.7668


CALD1
IGFBP5
TAGLN
CDH11
TIMP2
MYLK
PDGFC
DLC1
ANTXR1
IGFBP7
SPARC



0.7483
0.7452
0.7339
0.691
0.6846
0.6822
0.6707
0.6524
0.6494
0.649


CDH11
SPARC
TIMP2
IGFBP7
CALD1
TAGLN
IGFBP5
COL1A2
BGN
MMP2
PDGFC



0.7831
0.7629
0.7587
0.7339
0.7338
0.7319
0.7272
0.7265
0.7019
0.6845


COL1A1
BGN
SPARC
TIMP2
FAP
ANTXR1
LOXL2
COL1A2
CTHRC1
TGFB3
WISP1



0.8986
0.8713
0.8071
0.7833
0.7796
0.7724
0.7642
0.7496
0.7491
0.7442


COL1A2
SPARC
MMP2
COL1A1
THBS1
BGN
CDH11
LOXL2
ITGA5
CTHRC1
INHBA



0.8549
0.7886
0.7642
0.7409
0.7368
0.7272
0.7248
0.7243
0.7112
0.7005


CTGF
CYR61
THBS1
INHBA
BGN
COL1A2
SPARC
PAI1
VIM
SFRP2
CXCL12



0.8028
0.7694
0.7078
0.6912
0.6893
0.6886
0.6763
0.6747
0.6688
0.6683


CTHRC1
FAP
BGN
COL1A1
INHBA
COL1A2
TIMP3
SFRP2
SPARC
TIMP2
LOXL2



0.7713
0.7668
0.7496
0.7348
0.7112
0.7078
0.699
0.6964
0.6853
0.67


CTSL
TP
SOD2
ITGA5
UPA
TIMP1
THBS1
PAI1
COL1A2
DPYD
CD68



0.6975
0.6913
0.6748
0.6558
0.6448
0.636
0.6296
0.6152
0.6151
0.6148


CXCL12
BGN
CTGF
SFRP2
TIMP2
TGFB3
VIM
COL1A1
SPARC
CYR61
MCP1



0.6838
0.6683
0.6649
0.6334
0.6254
0.6212
0.6206
0.6173
0.6149
0.6022


CYR61
CTGF
DUSP1
THBS1
PAI1
COL1A2
INHBA
CXCL12
CTHRC1
VIM
GADD45B



0.8028
0.7338
0.6623
0.6477
0.6272
0.6257
0.6149
0.5918
0.576
0.573


DLC1
TIMP2
CALD1
IGFBP5
TGFB3
BGN
ANTXR1
TAGLN
THY1
HSPG2
TLN1



0.6783
0.6707
0.653
0.6465
0.6399
0.6378
0.6075
0.6065
0.6047
0.5982


DUSP1
CYR61
FOS
CTGF
PAI1
EGR1
NR4A1
GADD45B
THBS1
CXCL12
EGR3



0.7338
0.7183
0.6632
0.6545
0.6357
0.5993
0.5877
0.5827
0.5262
0.5184


FAP
BGN
COL1A1
CTHRC1
TIMP2
INHBA
ANTXR1
SFRP2
WISP1
TIMP3
TGFB3



0.8177
0.7833
0.7713
0.7364
0.7286
0.7261
0.7189
0.7147
0.7027
0.7001


HSPG2
TIMP2
THY1
IGFBP7
SPARC
TAGLN
ANTXR1
BGN
IGFBP5
COL1A1
CDH11



0.7455
0.7425
0.7246
0.6959
0.6857
0.6678
0.6625
0.6259
0.608
0.6052


IGFBP5
TAGLN
IGFBP7
CALD1
CDH11
TIMP2
SPARC
MYLK
DLC1
TIMP1
BGN



0.7829
0.764
0.7483
0.7319
0.6893
0.6781
0.6532
0.653
0.6403
0.6374


IGFBP7
TAGLN
SPARC
IGFBP5
CDH11
THY1
HSPG2
TIMP2
SFRP4
ANTXR1
PDGFC



0.8225
0.7715
0.764
0.7587
0.7428
0.7246
0.7139
0.6558
0.6541
0.6538


INHBA
BGN
SPARC
CTHRC1
FAP
COL1A1
CTGF
COL1A2
CDH11
THBS1
LOXL2



0.7854
0.774
0.7348
0.7286
0.7202
0.7078
0.7005
0.6744
0.6685
0.6613


ITGA5
COL1A2
THBS1
MMP2
SPARC
CTSL
PAI1
TIMP1
UPA
NRP2
SNAI2



0.7243
0.7058
0.6969
0.6772
0.6748
0.671
0.6374
0.6357
0.6301
0.623


LOXL2
COL1A1
SPARC
BGN
COL1A2
TIMP2
ANTXR1
CTHRC1
ADAMTS12
INHBA
FAP



0.7724
0.7606
0.7415
0.7248
0.7174
0.6829
0.67
0.6679
0.6613
0.6439


LOX
SPARC
COL1A1
BGN
COL1A2
INHBA
LOXL2
UPA
THY1
GJB2
SFRP2



0.7433
0.7065
0.695
0.62
0.604
0.5981
0.5865
0.5672
0.5664
0.5599


MMP2
COL1A2
SPARC
THBS1
CDH11
ITGA5
TAGLN
PDGFRA
VIM
CALD1
NRP2



0.7886
0.7229
0.7172
0.7019
0.6969
0.6663
0.6662
0.6556
0.6356
0.6188


MYLK
TAGLN
MYH11
CALD1
IGFBP5
IGFBP7
CDH11
TLN1
CRYAB
NRP2
PDGFRA



0.7671
0.7329
0.6846
0.6532
0.6456
0.6347
0.6335
0.6075
0.6057
0.5934


NRP2
TAGLN
SPARC
TIMP2
BGN
THBS1
CDH11
COL1A2
VIM
PDGFC
CALD1



0.6954
0.6845
0.668
0.6663
0.6638
0.6615
0.6601
0.6532
0.6436
0.6417


PAI1
THBS1
CTGF
ITGA5
DUSP1
CYR61
CTSL
INHBA
SPARC
TIMP1
COL1A2



0.6802
0.6763
0.671
0.6545
0.6477
0.6296
0.6138
0.6079
0.6019
0.59


PDGFC
TIMP2
ANTXR1
SPARC
CDH11
CALD1
BGN
COL1A2
TAGLN
IGFBP7
SFRP4



0.707
0.6992
0.6961
0.6845
0.6822
0.6788
0.6684
0.654
0.6538
0.6487


SFRP2
BGN
TGFB3
COL1A1
FAP
SPARC
CTHRC1
TIMP2
CTGF
CXCL12
COL1A2



0.811
0.7782
0.7263
0.7189
0.6994
0.699
0.6864
0.6688
0.6649
0.6536


SFRP4
ANTXR1
CDH11
TIMP2
BGN
IGFBP7
PDGFC
SFRP2
SPARC
FAP
CTHRC1



0.7154
0.6734
0.6702
0.6662
0.6558
0.6487
0.6397
0.6291
0.6256
0.6103


SPARC
COL1A1
BGN
COL1A2
TIMP2
CDH11
INHBA
IGFBP7
TAGLN
LOXL2
THY1



0.8713
0.8711
0.8549
0.7967
0.7831
0.774
0.7715
0.7667
0.7606
0.7512


TAGLN
IGFBP7
IGFBP5
MYLK
SPARC
CALD1
CDH11
TIMP2
NRP2
HSPG2
MYH11



0.8225
0.7829
0.7671
0.7667
0.7452
0.7338
0.7004
0.6954
0.6857
0.6706


TGFB3
BGN
SFRP2
COL1A1
TIMP2
ANTXR1
SPARC
FAP
WISP1
THY1
DLC1



0.8147
0.7782
0.7491
0.7331
0.7119
0.7095
0.7001
0.6652
0.6538
0.6465


THBS1
CTGF
COL1A2
SPARC
MMP2
ITGA5
PAI1
VIM
INHBA
NRP2
CDH11



0.7694
0.7409
0.7207
0.7172
0.7058
0.6802
0.6723
0.6685
0.6638
0.6635


THY1
ANTXR1
SPARC
IGFBP7
HSPG2
BGN
TIMP2
COL1A1
ADAMTS12
TGFB3
TAGLN



0.7696
0.7512
0.7428
0.7425
0.7365
0.7327
0.7241
0.6665
0.6538
0.6334


TIMP1
SPARC
BGN
THBS1
COL1A2
CDH11
CTSL
IGFBP5
ITGA5
NRP2
NRP1



0.7068
0.6713
0.6534
0.6518
0.6452
0.6448
0.6403
0.6374
0.6172
0.6172


TIMP2
BGN
ANTXR1
COL1A1
SPARC
CDH11
HSPG2
FAP
TGFB3
THY1
WISP1



0.8446
0.8358
0.8071
0.7967
0.7629
0.7455
0.7364
0.7331
0.7327
0.7263


TIMP3
CTHRC1
BGN
FAP
TIMP2
ANTXR1
INHBA
COL1A1
LOXL2
PDGFC
SFRP2



0.7078
0.7053
0.7027
0.6967
0.6644
0.6364
0.6306
0.6125
0.6098
0.6064


TK1
MAD2L1
SURV
H2AFZ
RRM2
ENO1
KI_67
CDC2
NME1
TGFBR2
NEK2



0.6019
0.5979
0.5314
0.5176
0.5122
0.5071
0.4933
0.4871
−0.481
0.4805


TLN1
VIM
THBS1
TAGLN
MYLK
NRP2
IGFBP5
CALD1
CTGF
COL1A2
DLC1



0.6549
0.64
0.6343
0.6335
0.6271
0.6221
0.6219
0.616
0.6146
0.5982


TMEPAI
NKD
TGFBI
ATP5E
TS
REG4
ATP5A1
VEGFB
PTCH
STMY3
IGFBP7



0.5264
0.5239
0.4626
−0.4341
−0.4322
−0.4302
0.4282
0.4207
0.4173
0.4093


TMSB10
ENO1
ANXA2
PKR2
TLN1
UBE2M
RHOC
C20ORF126
SBA2
TP
P21



0.6212
0.5169
0.5159
0.478
0.4447
0.4332
−0.4296
0.427
0.422
0.4205


TOP2A
CDC6
CENPF
BRCA1
NME1
SURV
KIFC1
MYBL2
BUB1
AURKB
C20_ORF1



0.6143
0.4655
0.4571
0.4544
0.4375
0.429
0.4194
0.4151
0.3996
0.3958


TP
CTSL
GBP2
CD18
SOD2
DPYD
CIAP2
CTSB
UPA
CD68
TIMP1



0.6975
0.6434
0.6321
0.6191
0.598
0.5636
0.5461
0.5406
0.538
0.5303


TS
ATP5A1
CDC20
AURKB
DHFR
PKR2
TMEPAI
ATP5E
RAD54L
REG4
LMNB1



0.5525
0.4872
0.4854
0.4849
0.4591
−0.4341
−0.4303
0.4291
0.4205
0.417


UBE2C
CSEL1
STK15
MYBL2
C20_ORF1
E2F1
MCM2
CDC2
EREG
C20ORF126
ATP5E



0.6581
0.6551
0.5006
0.4835
0.4385
0.411
0.4031
0.3927
0.3874
0.378


UNC5B
THY1
BGN
ANTXR1
TGFB3
TIMP2
SPARC
IGFBP7
HSPG2
COL1A1
ADAMTS12



0.5755
0.5594
0.5589
0.5417
0.5283
0.5236
0.5191
0.5055
0.4997
0.4958


UPA
CTSL
INHBA
THBS1
ITGA5
COL1A2
SPARC
CTHRC1
BGN
COL1A1
TIMP1



0.6558
0.6399
0.639
0.6357
0.629
0.6223
0.6173
0.6109
0.6014
0.6013


VCL
TAGLN
SPARC
TIMP2
TLN1
NRP2
CDH11
COL1A2
HSPG2
THBS1
IGFBP7



0.6246
0.6024
0.5972
0.581
0.5726
0.5583
0.5515
0.5512
0.5494
0.544


VCP
CAPG
BAD
NOTCH1
GSK3B
H2AFZ
MAD2L1
TUFM
KI_67
IGFBP7
RCC1



0.5823
0.5384
0.4991
0.4936
0.4724
0.4564
0.437
0.4343
0.4286
0.4176


VDAC2
HDAC1
SLC25A3
HNRPAB
PKR2
TS
SEMA4B
CHK1
CKS2
CDC2
CCNB1



0.5109
0.4867
0.4316
0.4196
0.3748
0.3683
0.364
0.3575
0.353
0.3506


VEGFB
IGFBP7
TAGLN
THY1
PTP4A3_V2
IGFBP5
PTCH
CDH11
BAD
CAPG
TMEPAI



0.6369
0.5024
0.4866
0.478
0.4614
0.4445
0.4398
0.4357
0.4327
0.4282


VEGF
VEGF_ALTSPLICE1
VEGF_ALTSPLICE2
HSPA1B
EFNA1
CLAUDIN_4
STC1
AXIN1
TERC
MGAT5
CDCA7_V2



0.6894
0.5931
0.3855
0.358
0.3175
0.3044
0.2826
0.2711
0.258
0.2354


VEGF_ALTSPLICE1
VEGF_ALTSPLICE2
VEGF
CMYC
THBS1
EFNA1
NEDD8
CLIC1
NOTCH1
CDCA7_V2
TMSB10



0.7502
0.6894
0.3686
0.3599
0.3577
−0.3552
0.3464
0.3459
0.3414
0.3389


VEGF_ALTSPLICE2
VEGF_ALTSPLICE1
VEGF
ITGB1
THBS1
CTGF
TP53BP2
CLIC1
MGAT5
EFNA1
HIF1A



0.7502
0.5931
0.4269
0.4235
0.407
0.402
0.3923
0.3788
0.3739
0.3704


VIM
COL1A2
SPARC
CTGF
THBS1
BGN
MMP2
TLN1
NRP2
TAGLN
CDH11



0.6897
0.6773
0.6747
0.6723
0.6625
0.6556
0.6549
0.6532
0.6463
0.6376


WISP1
BGN
COL1A1
TIMP2
FAP
SPARC
ANTXR1
CTHRC1
TGFB3
INHBA
SFRP2



0.7682
0.7442
0.7263
0.7147
0.694
0.6679
0.666
0.6652
0.6599
0.6292


WNT2
THY1
ANTXR1
BGN
SFRP4
CDH11
TIMP2
IGFBP7
SPARC
COL1A1
ADAMTS12



0.5223
0.5044
0.4897
0.4823
0.4823
0.4699
0.4484
0.4412
0.4381
0.4268
















TABLE 5







Results of Identification of Genes Through Gene Module/Clique Analysis of


Validated Gene Biomarkers








Validated



Gene
Co-expressed genes (Pearson co-expression coefficient)

















AXIN2
NKD (0.72)
CDX2
CRIPTO
EPHB2
PTCH
ROCK2
CAD17




(0.66)
[TDGF1]
(0.56)
(0.50)
(0.49)
(0.45)





(0.64)



CDCA7
MGAT5
PTP4A3



(0.45)
(0.41)
(0.40)


BGN
COL1A1
SPARC
TIMP2
FAP
ANTXR1
TGFB3
SFRP2



(0.90)
(0.87)
(0.84)
(0.82)
(0.82)
(0.81)
(0.81)



INHBA
WISP1
CTHRC1
LOXL2
COL1A2
THY1
CDH11



(0.79)
(0.77)
(0.77)
(0.74)
(0.74)
(0.74)
(0.73)



TIMP3
ADAMTS12
LOX
CTGF
CXCL12
PDGFC



(0.71)
(0.70)
(0.70)
(0.69)
(0.68)
(0.68)


cMYC
HSPE1
NME1
TERC
EREG
AREG
NOTCH1
MYBL2



(0.55)
(0.49)
(0.48)
(0.47)
(.046)
(0.46)
(0.45)



CSEL1
C_SRC
SNRPF
E2F1 (0.44)
ATP5E
UMPS
PRDX4



(0.45)
(0.44)
(0.44)

(0.44)
(0.43)
(0.40)



CDX2
MAD2L1



(0.40)
(0.40)


EFNB2
LAMC2
KLF5
SPRY2



(0.46)
(0.43)
(0.42)


FAP
BGN
COL1A1
CTHRC1
TIMP2
INHBA
ANTXR1
SFRP2



(0.82)
(0.78)
(0.77)
(0.74)
(0.73)
(0.73)
(0.72)



WISP1
TIMP3
TGFB3
SPARC
LOXL2
SFRP4
COL1A2



(0.72)
(0.70)
(0.70)
(0.67)
(0.64)
(0.63)
(0.62)



CYP1B1
CDH11
CTSB
PDGFC
CXCL12
MCP1



(0.62)
(0.61)
(0.61)
(0.59)
(0.59)
(0.59)


GADD45B
DUSP1
PAI1
CTGF
CYR61
INHBA
BGN
SPARC



(0.59)
(0.58)
(0.58)
(0.53)
(0.56)
(0.52)
(0.51)



UPA
THBS1
PLK3
TIMP1
SFRP2
CYP1B1
VIM



(0.50)
(0.50)
(0.49)
(0.49)
(0.48)
(0.47)
(0.47)



LOX
TAGLN
CXCL12
WISP1
TGFB3
STC1



(0.46)
(0.46)
(0.46)
(0.46)
(0.45)
(0.45)


HSPE1
CCNB1
CMYC
NME1
SNRPF
HNRPAB
RRM2
RBX1



(0.57)
(0.55)
(0.53)
(0.52)
(0.50)
(0.48)
(0.48)



ODC1
MAD2L1
MSH2
AREG
HSPA8
CD44E
THY1



(0.47)
(0.46)
(0.41)
(0.41)
(0.41)
(0.40)
(0.40)


INHBA
BGN
SPARC
CTHRC1
FAP
COL1A1
CTGF
COL1A2



(0.79)
(0.77)
(0.74)
(0.73)
(0.72)
(0.71)
(0.72)



CDH11
THBS1
LOXL2
TIMP2
WISP1
SFRP2
UPA



(0.67)
(0.67)
(0.66)
(0.66)
(0.66)
(0.64)
(0.64)



TIMP3
ANTXR1
CYR61
PAI1
PDGFC
ADAMTS12



(0.64)
(0.64)
(0.63)
(0.61)
(0.61)
(0.61)


Ki67
CDC2
MAD2L1
H2AFZ
BUB1
CDC20
SURV
TK1



(0.69)
(0.60)
(0.58)
(0.54)
(0.52)
(0.51)
(0.51)



NEK2
LMNB1
RRM2
SNRPF
CCNB1
KIFC1
RAD54L



(0.51)
(0.50)
(0.48)
(0.47)
(0.47)
(0.46)
(0.46)



ESPL1
PCNA
KIF22
CDC25C
VCP
MCM3



(0.46)
(0.45)
(0.44)
(0.44)
(0.43)
(0.43)


MAD2L1
H2AFZ
CDC2
SNRPF
TK1
KI_67
SURV
CCNB1



(0.64)
(0.62)
(0.61)
(0.60)
(0.60)
(0.58)
(0.57)



RRM2
NEK2
BUB1
NME1
MCM3
BAD
HSPE1



(0.56)
(0.55)
(0.53)
(0.51)
(0.49)
(0.47)
(0.46)



VCP
TGFBR2
KRT8
PCNA
CDC20
RCC1



(0.46)
(0.45)
(0.44)
(0.44)
(0.44)
(0.43)


MYBL2
C20_ORF1
E2F1
UBE2C
STK15
CSEL1
CMYC
ATP5E



(0.56)
(0.55)
(0.50)
(0.46)
(0.46)
(0.52)
(0.42)



TOP2A
CDCA7



(0.42)
(0.41)


RUNX1
CDH11
TIMP2
PDGFC
ANTXR1
BGN
CALD1
FZD1



(0.57)
(0.55)
(0.54)
(0.53)
(0.52)
(0.52)
(0.51)



SPARC
IGFBP7
INHBA
NRP2
AKT3
SFRP4
COL1A2



(0.50)
(0.50)
(0.50)
(0.49)
(0.49)
(0.49)
(0.49)



CTHRC1
FAP
WISP1
TGFB3
TAGLN
TIMP3



(0.48)
(0.48)
(0.48)
(0.47)
(0.47)
(0.47)
















TABLE 6







Gene Cliques Identified for Validated Genes











Seeding



Spearman


Gene
AffyProbeID
Weight
Cliqued Gene
Cutoff














FAP
9441
19
FAP
0.5


FAP
13949
4
DKFZp434K191
0.5


FAP
13949
4
POM121L1
0.5


FAP
13949
4
LOC646074
0.5


FAP
13949
4
LOC100133536
0.5


FAP
13949
4
LOC651452
0.5


FAP
13949
4
LOC729915
0.5


FAP
13949
4
DKFZP434P211
0.5


FAP
13949
4
LOC728093
0.5


FAP
7405
3
CALCR
0.5


FAP
9568
3
TPSAB1
0.5


FAP
10493
3
TLX2
0.5


FAP
15164
3

0.5


FAP
15197
3
NUDT7
0.5


FAP
16536
3
IGHA1
0.5


FAP
20381
3
LRRC3
0.5


FAP
4496
2
RDX
0.5


FAP
4839
2
SPI1
0.5


FAP
6242
2
UMOD
0.5


FAP
9590
2
RDH5
0.5


FAP
15576
2
COMT
0.5


FAP
16692
2

0.5


FAP
18423
2
LYVE1
0.5


FAP
6479
1
LPHN2
0.5


FAP
10429
1
HLA-DRA
0.5


FAP
16097
1
STK38
0.5


FAP
19846
1
SERGEF
0.5


FAP
20724
1
OMP
0.5


HSPE1
4660
569
HSPE1
0.5


HSPE1
15676
338
YME1L1
0.5


HSPE1
746
302
CTBP2
0.5


HSPE1
1358
265
NET1
0.5


HSPE1
1697
174
AASDHPPT
0.5


HSPE1
17578
146
C11orf10
0.5


HSPE1
18720
139
CHMP5
0.5


HSPE1
12550
138
SP3
0.5


HSPE1
10354
133
PDCD10
0.5


HSPE1
879
132
YME1L1
0.5


HSPE1
8855
123
MED21
0.5


HSPE1
1181
102
CNIH
0.5


HSPE1
17414
98
MRPL13
0.5


HSPE1
471
97
HMGN1
0.5


HSPE1
17704
96
MRPL22
0.5


HSPE1
13816
95
SHMT2
0.5


HSPE1
10513
85
SUMO1
0.5


HSPE1
22252
81

0.5


HSPE1
8637
79
CLNS1A
0.5


HSPE1
9151
74
CETN3
0.5


HSPE1
92
73
SMNDC1
0.5


HSPE1
437
72
RPLP2
0.5


HSPE1
3713
63
PPID
0.5


HSPE1
3111
62
TTC35
0.5


HSPE1
20668
60
UGT1A9
0.5


HSPE1
20668
60
UGT1A6
0.5


HSPE1
20668
60
UGT1A8
0.5


HSPE1
11526
54
PDS5A
0.5


HSPE1
108
53
TMED2
0.5


HSPE1
12094
52
NUP160
0.5


HSPE1
8110
48
PDIA3
0.5


HSPE1
17336
48
MAP2K1IP1
0.5


HSPE1
11983
47
WDFY3
0.5


HSPE1
17192
45
SPG21
0.5


HSPE1
495
39
PPIB
0.5


HSPE1
17591
39
NDUFB4
0.5


HSPE1
17591
39
LOC727762
0.5


HSPE1
9287
37
PRKAA1
0.5


HSPE1
31
35
RPL11
0.5


HSPE1
19126
30
RPL36
0.5


HSPE1
166
29
YWHAZ
0.5


HSPE1
8914
29
MSH2
0.5


HSPE1
1060
28
PSMA3
0.5


HSPE1
21589
26
LOC441533
0.5


HSPE1
1241
25
RANBP2
0.5


HSPE1
7592
24
ITGB6
0.5


HSPE1
20791
24
TBL1XR1
0.5


HSPE1
2992
23
MRPL19
0.5


HSPE1
4412
23
MSLN
0.5


HSPE1
801
22
hCG_1781062
0.5


HSPE1
801
22
SRP9
0.5


HSPE1
17967
22
FAM29A
0.5


HSPE1
8189
20
PRKDC
0.5


HSPE1
15646
18
SEC11A
0.5


HSPE1
120
16
RPS3A
0.5


HSPE1
120
16
LOC439992
0.5


HSPE1
112
14
RPS25
0.5


HSPE1
395
14
ZNF313
0.5


HSPE1
8347
14
CANX
0.5


HSPE1
11315
14
TUT1
0.5


HSPE1
11315
14
EEF1G
0.5


HSPE1
8766
13
NAB1
0.5


HSPE1
18447
13
SHQ1
0.5


HSPE1
1170
12
IFNGR2
0.5


HSPE1
19696
12
CLDN16
0.5


HSPE1
17528
11
MCTS1
0.5


HSPE1
38
10
RPS27A
0.5


HSPE1
38
10
UBC
0.5


HSPE1
38
10
UBB
0.5


HSPE1
309
10
RPS15A
0.5


HSPE1
10762
10
EEF1G
0.5


HSPE1
10762
10
TUT1
0.5


HSPE1
4819
9
HNRNPA2B1
0.5


HSPE1
10894
9
RPS17
0.5


HSPE1
20002
9
CBLC
0.5


HSPE1
4294
8
FEN1
0.5


HSPE1
417
7
SSR1
0.5


HSPE1
3271
6
HMGB3
0.5


HSPE1
7814
6
C7orf28A
0.5


HSPE1
7814
6
C7orf28B
0.5


HSPE1
11918
6
WEE1
0.5


HSPE1
3474
5
CSTF3
0.5


HSPE1
19605
5
TMCO3
0.5


HSPE1
231
4
DYNLL1
0.5


HSPE1
296
4
MAT2A
0.5


HSPE1
863
4
ARHGEF12
0.5


HSPE1
4185
4
TRA2A
0.5


HSPE1
18483
4
LSM8
0.5


HSPE1
21253
3
ADCK2
0.5


HSPE1
926
2
LOC100130862
0.5


HSPE1
926
2
TRAM1
0.5


HSPE1
4761
2
SLC16A4
0.5


HSPE1
19884
2
NUP62CL
0.5


HSPE1
47
1
RPL34
0.5


HSPE1
1155
1
INSIG1
0.5


HSPE1
2415
1
DDIT4
0.5


HSPE1
3473
1
ARG2
0.5


HSPE1
11997
1
RCOR1
0.5


HSPE1
16678
1

0.5


INHBA
9981
4
INHBA
0.5


INHBA
1386
2
SRGN
0.5


INHBA
21897
2
COL11A1
0.5


INHBA
1320
1
AEBP1
0.5


INHBA
5099
1
ANGPT2
0.5


INHBA
5939
1
TCL6
0.5


INHBA
5939
1
TCL1B
0.5


INHBA
9047
1
CD36
0.5


MAD2L1
2889
5
MAD2L1
0.5


MAD2L1
4862
3
SRP19
0.5


MAD2L1
3962
2
NUPL1
0.5


MAD2L1
4484
2
ORC5L
0.5


MAD2L1
12103
2
PAPOLA
0.5


MAD2L1
2863
1
ITGB1BP1
0.5


KI67
11408
15
KI67
0.5


KI67
11409
15
KI67
0.5


KI67
11406
14
KI67
0.5


KI67
986
13
BUB3
0.5


KI67
9460
10
BUB3
0.5


KI67
8882
9
DBI
0.5


KI67
320
8
XRCC6
0.5


KI67
1717
8
PTBP1
0.5


KI67
7951
8
XPNPEP1
0.5


KI67
8574
7
GLRX3
0.5


KI67
11181
7
SFRS1
0.5


KI67
11407
7
KI67
0.5


KI67
17827
7
BXDC5
0.5


KI67
100
5
KARS
0.5


KI67
2694
5
CFDP1
0.5


KI67
12471
5
DNAJC9
0.5


KI67
484
4
SSRP1
0.5


KI67
791
4
TARS
0.5


KI67
1005
4
RRM1
0.5


KI67
1622
4
BIRC5
0.5


KI67
17411
4
MRPS16
0.5


KI67
424
3
HDGF
0.5


KI67
1083
3
MCM3
0.5


KI67
2427
3
SFRS3
0.5


KI67
2738
3
RFC5
0.5


KI67
3271
3
HMGB3
0.5


KI67
8303
3
HMGB2
0.5


KI67
9311
3
UCK2
0.5


KI67
12916
3
UBE2I
0.5


KI67
17225
3
NDUFA10
0.5


KI67
17225
3
LOC732160
0.5


KI67
17720
3
KIF4A
0.5


KI67
19014
3
ERCC6L
0.5


KI67
1298
2
SNRPA
0.5


KI67
1302
2
NCAPD2
0.5


KI67
1424
2
PSRC1
0.5


KI67
3779
2
CDK2
0.5


KI67
6025
2
SNHG3-RCC1
0.5


KI67
6025
2
RCC1
0.5


KI67
8746
2
HARS2
0.5


KI67
17338
2
DCXR
0.5


KI67
17441
2
ARHGAP17
0.5


KI67
17907
2
CEP55
0.5


KI67
18151
2
CWF19L1
0.5


KI67
899
1
CUL3
0.5


KI67
1381
1
CDC25B
0.5


KI67
3033
1
MED12
0.5


KI67
8957
1
AURKB
0.5


KI67
9538
1
TAF5
0.5


KI67
11401
1
PTBP1
0.5


KI67
13174
1
NGDN
0.5


KI67
18311
1
PAPD1
0.5


KI67
19342
1
NUSAP1
0.5


RUNX1
10265
38
RUNX1
0.6


RUNX1
10621
21
RUNX1
0.6


RUNX1
10624
11
RUNX1
0.6


RUNX1
16111
11

0.6


RUNX1
15586
10

0.6


RUNX1
7955
9
GABRD
0.6


RUNX1
13947
9
TPSD1
0.6


RUNX1
16761
9

0.6


RUNX1
6124
8
INS
0.6


RUNX1
9341
8
KLK2
0.6


RUNX1
15333
8
F12
0.6


RUNX1
15717
8
SEC14L3
0.6


RUNX1
19749
8
JPH2
0.6


RUNX1
2021
7
CSH1
0.6


RUNX1
2021
7
CSH2
0.6


RUNX1
2021
7
GH1
0.6


RUNX1
2021
7
FCHO2
0.6


RUNX1
14776
7
APPBP2
0.6


RUNX1
16935
7

0.6


RUNX1
13242
6
PNPLA2
0.6


RUNX1
17026
6
SIX5
0.6


RUNX1
7844
5
CSH1
0.6


RUNX1
7844
5
GH1
0.6


RUNX1
7844
5
CSH2
0.6


RUNX1
7907
5
GRAP2
0.6


RUNX1
10097
5
SGCA
0.6


RUNX1
4397
4
PCSK2
0.6


RUNX1
8058
4
KCNA10
0.6


RUNX1
9957
4
CLEC4M
0.6


RUNX1
14240
4
DOT1L
0.6


RUNX1
20209
4
ACOXL
0.6


RUNX1
7167
3
CDY2A
0.6


RUNX1
7167
3
CDY1
0.6


RUNX1
7167
3
CDY2B
0.6


RUNX1
7167
3
CDY1B
0.6


RUNX1
7985
3
LMX1B
0.6


RUNX1
8006
3
OR2J2
0.6


RUNX1
8070
3
HIST3H3
0.6


RUNX1
11037
3
IGHG1
0.6


RUNX1
11044
3
IGHG1
0.6


RUNX1
11044
3
LOC100133862
0.6


RUNX1
11044
3
IGHA1
0.6


RUNX1
13294
3
NKG7
0.6


RUNX1
14153
3
IGKV4-1
0.6


RUNX1
14518
3

0.6


RUNX1
16170
3

0.6


RUNX1
16401
3
KRT84
0.6


RUNX1
19748
3
TXNDC3
0.6


RUNX1
19870
3
GUCY1B2
0.6


RUNX1
6932
2
LECT2
0.6


RUNX1
9485
2
SOCS1
0.6


RUNX1
10358
2
ID2B
0.6


RUNX1
11241
2
PVRL1
0.6


RUNX1
11266
2
PCDHGA11
0.6


RUNX1
14875
2

0.6


RUNX1
15862
2
IGHM
0.6


RUNX1
16087
2
FAM48A
0.6


RUNX1
16200
2
LOC390561
0.6


RUNX1
16200
2
LOC730909
0.6


RUNX1
16568
2
RASAL2
0.6


RUNX1
16937
2

0.6


RUNX1
18968
2
ZNF3
0.6


RUNX1
20168
2
TP73
0.6


RUNX1
21214
2
PKP1
0.6


RUNX1
3849
1
GOLIM4
0.6


RUNX1
5706
1
ZNF747
0.6


RUNX1
7412
1
SRY
0.6


RUNX1
7412
1
LOC100130809
0.6


RUNX1
13490
1
OPCML
0.6


RUNX1
13739
1
SMARCA4
0.6


RUNX1
13844
1
ORM1
0.6


RUNX1
13844
1
ORM2
0.6


RUNX1
15714
1
PCDHGA3
0.6


RUNX1
19633
1
ZBBX
0.6


RUNX1
20562
1
GFRA4
0.6


RUNX1
21537
1
SCAND2
0.6


RUNX1
21554
1
LOC100132923
0.6
















TABLE 7







Datasets used for gene clique analysis of


prognostic and predictive genes










GEO Accession
Number of



Number
Tumor Samples













GSE1323
6



GSE2138
20



GSE2509
6



GSE2742
27



GSE5364
9
















TABLE 8







Association of gene expression and risk of recurrence in


surgery alone patients from the QUASAR study
















HR
LR



Gene
N
HR
95% CI
p-value
















Axin_2
711
1.13
(1.00, 1.28)
0.046



BIK
711
0.61
(0.47, 0.80)
0.0002



EFNB2
711
1.71
(1.40, 2.08)
3.9E−07



HSPE1
711
0.75
(0.56, 1.00)
0.054



MAD2L1
711
0.66
(0.52, 0.84)
0.0006



RUNX1
711
1.76
(1.37, 2.26)
7.6E−06



BGN
711
1.31
(1.11, 1.55)
0.001



FAP
711
1.48
(1.16, 1.87)
0.002



INHBA
711
1.35
(1.13, 1.62)
0.001



Ki_67
711
0.63
(0.47, 0.83)
0.001



MYBL2
711
0.98
(0.74, 1.28)
0.86



cMYC
711
0.93
(0.79, 1.11)
0.44



GADD45B
711
1.17
(0.95, 1.44)
0.14
















TABLE 9







Results of the meta analysis and stratified Cox models












META

Stratified




analysis

Cox Model














Gene
HR
95% CI
HR
95% CI






Axin_2
0.99
(0.89, 1.09)
1.00
(0.95, 1.05)



BIK
0.75
(0.64, 0.88)
0.74
(0.65, 0.83)



EFNB2
1.37
(1.23, 1.54)
1.38
(1.26, 1.52)



HSPE1
0.77
(0.67, 0.88)
0.80
(0.73, 0.89)



MAD2L1
0.67
(0.61, 0.75)
0.67
(0.61, 0.75)



RUNX1
1.38
(1.14, 1.68)
1.38
(1.23, 1.55)



BGN
1.29
(1.19, 1.39)
1.28
(1.19, 1.38)



INHBA
1.29
(1.19, 1.39)
1.29
(1.19, 1.39)



FAP
1.23
(1.15, 1.31)
1.24
(1.15, 1.34)



Ki_67
0.74
(0.69, 0.81)
0.75
(0.68, 0.84)



cMYC
0.84
(0.78, 0.90)
0.83
(0.76, 0.90)



MYBL2
0.86
(0.79, 0.93)
0.86
(0.80, 0.94)



GADD45B
1.20
(1.12, 1.29)
1.23
(1.11, 1.37)








Claims
  • 1. A method for obtaining a Recurrence Score (RS) result for a patient with colorectal cancer, comprising: measuring levels of RNA transcripts of a set of genes consisting of BGN, FAP, INHBA, MYBL2, Ki-67, cMYC, and GADD45B, and at least one reference gene in a tumor sample obtained from the patient;normalizing levels of the RNA transcripts of BGN, FAP, INHBA, MYBL2, Ki-67, cMYC, and GADD45B against the levels of the RNA transcripts of at the least one reference gene to provide normalized levels of the RNA transcripts of BGN, FAP, INHBA, MYBL2, Ki-67, cMYC, and GADD45B;assigning the normalized levels to gene subsets comprising a stromal group and a cell cycle group and a cell signaling group, wherein the stromal group comprises FAP, BGN, and INHBA, and the cell cycle group comprises Ki-67, cMYC, and MYBL2 and the cell signaling group comprises GADD45B;wherein the level of normalized RNA transcripts from the stromal group selected from BGN, FAP, and INHBA is measured to obtain a stromal group score, the level of normalized RNA transcripts from the cell cycle group selected from MYBL2, Ki-67, and cMYC is measured to obtain a cell cycle group score, and the level of the normalized RNA transcript of GADD45B is measured to obtain a cell signaling group score, wherein the stromal group score, cell cycle group score, and cell signaling group score equal the sum of the normalized RNA transcript levels for each gene of the group divided by the number of genes in the group;weighting the stromal group score by +0.15, weighting the cell cycle group score by −0.3 and weighting the cell signaling group score by +0.15;calculating a Recurrence Score (RS) result for the patient using the weighted gene group scores; andgenerating a report comprising the RS result.
  • 2. The method of claim 1, wherein the normalized levels of the RNA transcripts are further calculated as a ratio of the normalized levels to tumor region, wherein the tumor region is tumor-associated stroma unit area or tumor epithelia unit area.
  • 3. The method of claim 1, further comprising: measuring a surface area of tumor-associated stroma in the tumor sample and calculating a Stromal Risk Score based on the surface area of the tumor-associated stroma,wherein increased Stromal Risk Score is positively correlated to increased risk of recurrence of cancer for said patient; andwherein the report further comprises the Stromal Risk Score.
  • 4. The method of claim 1, wherein the tumor sample is obtained from a biopsy.
  • 5. The method of claim 1, wherein the tumor sample is fresh or frozen.
  • 6. The method of claim 1, wherein the levels of the RNA transcripts are measured by reverse transcription polymerase chain reaction (RT-PCR).
  • 7. The method of claim 1, further comprising scaling the RS result on a scale of 0 to 100, wherein the scaled RS result=0 if 44×(RS+0.82)<0, the RS=100 if 44×(RS+0.82)>100, and wherein the scaled RS result=44×(RS+0.82) when 44×(RS+0.82) has a value ≥0 and ≤100.
  • 8. The method of claim 1, further comprising determining a recurrence risk group tier for the patient based on the patient's scaled RS result in comparison to a set of at least three previously defined recurrence risk group tiers.
  • 9. The method of claim 8, wherein the recurrence risk group tiers comprise a low risk group tier if the patient's scaled RS result is <30, an intermediate risk group tier if the patient's scaled RS result is ≥30 to <41, and a high risk group tier if the patient's scaled RS result is ≥41.
  • 10. The method of claim 1, wherein the RS result for the patient is calculated from the sum of the weighted stromal group score, the weighted cell cycle group score, and the weighted cell signaling group score.
  • 11. The method of claim 1, wherein the tumor sample is a paraffin embedded and fixed sample.
  • 12. The method of claim 1, wherein the at least one reference gene comprises one or more of ATP5E, PGK1, GPX1, UBB, and VDAC2.
  • 13. The method of claim 1, wherein the at least one reference gene consists of one to five genes.
  • 14. A method for obtaining a Recurrence Score (RS) result for a patient with colorectal cancer, comprising: extracting RNA from a tumor sample obtained from the patient;reverse transcribing RNA transcripts of a set of genes consisting of BGN, FAP, INHBA, MYBL2, Ki-67, cMYC, and GADD45B, and at least one reference gene to produce cDNAs;amplifying the cDNAs to produce amplicons of the RNA transcripts of the genes;assaying levels of the amplicons;normalizing the levels of the amplicons of BGN, FAP, INHBA, MYBL2, Ki-67, cMYC, and GADD45B against the level of the amplicon of the at least one reference RNA transcript in said tumor sample to provide normalized amplicon levels of the BGN, FAP, INHBA, MYBL2, Ki-67, cMYC, and GADD45B RNA transcripts;assigning the normalized amplicon levels to gene subsets comprising a stromal group and a cell cycle group and a cell signaling group to obtain a stromal group score and a cell cycle group score and a cell signaling group score, wherein the stromal group score equals the sum of the normalized amplicon levels of FAP, BGN, and INHBA divided by three, the cell cycle group score equals the sum of the normalized amplicon levels of Ki-67, cMYC, and MYBL2 divided by three, and the cell signaling group score equals the normalized amplicon level of GADD45B;weighting the stromal group score by +0.15, weighting the cell cycle group score by −0.3, and weighting the cell signaling group score by +0.15;calculating a recurrence score (RS) result for the patient from the sum of the weighted stromal group score, the weighted cell cycle group score, and the weighted cell signaling group score; andgenerating a report comprising the RS result.
  • 15. The method of claim 14, wherein the tumor sample is fresh, frozen.
  • 16. The method of claim 14, further comprising: measuring a surface area of tumor-associated stroma in the tumor sample and calculating a Stromal Risk Score based on the surface area of the tumor-associated stroma,wherein increased Stromal Risk Score is positively correlated to increased risk of recurrence of cancer for said patient; andwherein the report further comprises the Stromal Risk Score.
  • 17. The method of claim 14, wherein the tumor sample is obtained from a biopsy.
  • 18. The method of claim 14, further comprising scaling the RS result on a scale of 0 to 100, wherein the scaled RS result =0 if 44×(RS+0.82)<0, the RS=100 if 44×(RS+0.82)>100, and wherein the scaled RS result=44×(RS+0.82) when 44×(RS+0.82) has a value ≥0 and ≤100.
  • 19. The method of claim 14, further comprising determining a recurrence risk group tier for the patient based on the patient's scaled RS in comparison to a set of at least three previously defined recurrence risk group tiers.
  • 20. The method of claim 19, wherein the recurrence risk group tiers comprise a low risk group tier if the patient's scaled RS is <30, an intermediate risk group tier if the patient's scaled RS is ≥30 to <41, and a high risk group tier if the patient's scaled RS is ≥41.
  • 21. The method of claim 14, wherein the tumor sample is a paraffin embedded and fixed sample.
  • 22. The method of claim 14, wherein the at least one reference gene comprises one or more of ATP5E, PGK1, GPX1, UBB, and VDAC2.
  • 23. The method of claim 14, wherein the at least one reference gene consists of one to five genes.
  • 24. A method of analyzing the expression of RNA transcripts of genes in a colorectal cancer patient, comprising: extracting RNA from a tumor sample obtained from the patient;reverse transcribing RNA transcripts of a set of genes consisting of BGN, FAP, INHBA, MYBL2, Ki-67, cMYC, and GADD45B, and at least one reference gene, in the tumor sample to produce cDNAs, wherein a reference gene is a gene that does not exhibit a significantly different RNA expression level in in cancerous colorectal tissue compared to non-cancerous colorectal tissue; andamplifying the cDNAs to produce amplicons of the RNA transcripts of the genes for use in determining expression levels of the RNA transcripts.
  • 25. The method of claim 24, wherein the at least one reference gene comprises one or more of ATP5E, PGK1, GPX1, UBB, and VDAC2.
CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority benefit of U.S. Provisional Application Ser. No. 61/174,890 filed on May 1, 2009 and U.S. Provisional Application Ser. No. 61/239,420 filed Sep. 2, 2009, each of which is incorporated herein by reference in its entirety.

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Related Publications (1)
Number Date Country
20100285980 A1 Nov 2010 US
Provisional Applications (2)
Number Date Country
61174890 May 2009 US
61239420 Sep 2009 US