Patent Application
20180187267
The field of application of the present invention is the medical sector, in the field of Molecular Biology. More specifically, the invention addresses a method for the early diagnosis of colorectal cancer and the kit for performing the method. This invention further relates to methods for disease diagnosis, including the early detection of colon cancer in patients. More particularly the invention also to methods for preparing samples derived from tissue, stools, circulating DNA and circulating tumor cells for disease diagnosis, including the detection of colon cancer, so as to assure or increase the likelihood that the sample will contain the diagnostically relevant information if the patient has a disease, for example a cancerous or precancerous lesion, and to methods for sample analysis regardless of its source.
The invention further relates to a method of non-invasive early detection of colon cancer and/or of colon cancer precursor cells. It also relates to XNA clamps and primers allowing to perform mutational analyses in selected regions of the genes responsible for colon cancer in a combined fashion, to a kit comprising said XNA clamps primers, and, in addition, to the use of said primers and said kit in mutational analysis, particularly in early detection of colon cancer and/or colon cancer precursor cells.
Polymerase chain reaction (PCR) is a widely used technique for the detection of pathogens. The technique uses a DNA polymerase used to amplify a piece of DNA by in vitro enzymatic replication. The PCR process generates DNA that is used as a template for replication. This results in a chain reaction that exponentially amplifies the DNA template.
Technologies for genomic detection most commonly use DNA probes to hybridize to target sequences. To achieve required sensitivity, the use of PCR to amplify target sequences has remained standard practice in many labs. While PCR has been the principle method to identify genes associated with disease states, the method has remained confined to use within a laboratory environment. Most current diagnostic applications that can be used outside of the laboratory are based on antibody recognition of protein targets and use ELISA-based technologies to signal the presence of a disease. These methods are fast and fairly robust, but they can lack the specificity associated with nucleic acid detection.
With the advent of molecular diagnostics and the discovery of numerous nucleic acid biomarkers useful in the diagnosis and treatment of conditions and diseases, detection of nucleic acid sequences, and sequence variants, mutations and polymorphisms has become increasingly important. In many instances, it is desirable to detect sequence variants or mutations (which may in some instances, differ by one a single nucleotide) present in low copy numbers against a high background of wild-type sequences. For example, as more and more somatic mutations are shown to be biomarkers for cancer prognosis and prediction of therapeutic efficacy, the need for efficient and effective methods to detect rare mutations in a sample is becoming more and more critical. In the case in which one or more allelic variants is/are present in low copy number compared to wild-type sequences, the presence of excess wild-type target sequence creates challenges to the detection of the less abundant variant target sequence. Nucleic acid amplification/detection reactions almost always are performed using limiting amounts of reagents. A large excess of wild-type target sequences, thus competes for and consumes limiting reagents. As a result amplification and/or detection of rare mutant or variant alleles under these conditions is substantially suppressed, and the methods may not be sensitive enough to detect the rare variants or mutants. Various methods to overcome this problem have been attempted. These methods are not ideal, however, because they either require the use of a unique primer for each allele, or the performance of an intricate melt-curve analysis. Both of these shortcomings limit the ability and feasibility of multiplex detection of multiple variant alleles from a single sample.
Additionally, it is also known that colorectal cancer is a leading cause of death in Western society. However, if diagnosed early, it may be treated effectively by surgical removal of the cancerous tissue. Colorectal cancers originate in the colorectal epithelium and typically are not extensively vascularized (and therefore not invasive) during the early stages of development. Colorectal cancer is thought to result from the clonal expansion of a single mutant cell in the epithelial lining of the colon or rectum. The transition to a highly vascularized, invasive and ultimately metastatic cancer which spreads throughout the body commonly takes ten years or longer. If the cancer is detected prior to invasion, surgical removal of the cancerous tissue is an effective cure. However, colorectal cancer is often detected only upon manifestation of clinical symptoms, such as pain and black tarry stool. Generally, such symptoms are present only when the disease is well established, often after metastasis has occurred, and the prognosis for the patient is poor, even after surgical resection of the cancerous tissue. Early detection of colorectal cancer therefore is important in that detection may significantly reduce its morbidity.
Invasive diagnostic methods such as endoscopic examination allow for direct visual identification, removal, and biopsy of potentially cancerous growths such as polyps. Endoscopy is expensive, uncomfortable, inherently risky, and therefore not a practical tool for screening populations to identify those with colorectal cancer. Non-invasive analysis of stool samples for characteristics indicative of the presence of colorectal cancer or precancer is a preferred alternative for early diagnosis, but no known diagnostic method is available which reliably achieves this goal.
Complex signal pathways are involved in the colorectal cancer pathogenesis such as the WNT and RAS/RAF/MAPK pathways. Genetic and epigenetic changes in the pathway components have been studied extensively in relation to their roles in the initiation and development of CRC. KRAS mutations are found in several cancers including colorectal, lung, thyroid, and pancreatic cancers and cholangiocarcinoma. More than 90% KRAS mutations are located within codons 12 and 13 of exon 2, which may lead to abnormal growth signaling by the p21− ras protein. These alterations in cell growth and division may trigger cancer development as signaling is excessive. KRAS mutations have also been detected in many colorectal cancer patients.
The B-type Raf Kinase (BRAF) protein is a serine/threonine kinase that has important roles in regulating the MAP kinase/ERK signaling pathways, affecting cellular proliferation, differentiation, and programmed cell death. A BRAF mutation is commonly found in many human cancers including melanoma, colorectal cancer, lung cancer, and papillary thyroid carcinoma. The most common mutations in BRAF occur in codon 600, where an amino acid substitution in the activation segment of the kinase domain creates a constitutively active form of the protein. The V600E and V600K mutations are found in high frequencies in human cancer V600E 70-90% and V600K 10-15%. BRAF mutations are generally found in tumors that are wild-type for KRAS.
The adenomatous polyposis coli (APC) gene is a key tumor suppressor gene and APC mutation has been found in most colon cancers. The gene encodes a multi-domain protein that binds to various proteins, including -catenin, axin, CtBP, Asefs, IQGAP1, EB1 and microtubules. Most (˜60%) cancer-linked APC mutations occur in a region referred to as the mutation cluster region (MCR) and result in C-terminal truncation of the protein. Mutations in the tumor suppressor gene APC result in the accumulation of catenin which activates the Wnt signaling pathway, leading to tumorigenesis. APC also plays roles in other fundamental cellular processes including cell adhesion and migration, organization of the actin and microtubule networks, spindle formation and chromosome segregation. Mutations in APC cause deregulation of theses cellular process, leading to the initiation and expansion of colon cancer. APC has been used as a biomarker for early colon cancer detection.
The β-catenin gene (CTNNB1) is also an important component of the Wnt pathway. Mutations in the serine or threonine phosphorylation sites in the regulatory domain (exon 3, codon 29-48) of the gene leads to accumulation of the gene product (β-catenin) which activates the Wnt pathway.
The invention provides a method for detecting the presence or absence of a known mutated gene contained in a biological sample, said method comprising the steps of: (1) allowing a mixture of a clamp primer consisting of XNA which hybridizes with all or part of a target site having a sequence of a wild-type gene or a sequence complementary to the wild-type gene, a primer capable of amplifying a region comprising a target site having a sequence of the mutated gene, and the biological sample to coexist in a reaction solution for gene amplification, and selectively amplifying the region comprising a target site of the mutated gene by a gene amplification method, and (2) selectively detecting a detection region comprising the target site of the mutated gene by a gene detection method, using an amplified product obtained in step (1) or part thereof as a template, to detect the presence or absence of the mutated gene.
The invention also relates to a method for screening for the presence of colorectal cancer in a patient, the method comprising the steps of: (a) obtaining a biological sample from said patient; and (b) performing an assay that screen for DNA mutations in said sample employing a Xenonucleic acid clamp to detect mutations indicative of the presence of colorectal cancer.
The invention further relates to a method of detecting a mutant gene associated with colorectal cancer, comprising: providing a sample containing DNA and a xenonucleic acid clamp capable of hybridizing to a wild-type gene; and detecting a mutant of the gene in the sample with a xeno-nucleic acid probe capable of hybridizing to the mutant gene.
The present invention additionally provides a method for screening and/or monitoring a patient for mutations associated with colorectal cancer, the method comprising: isolating DNA from a stool sample, fresh peripheral blood (PB), plasma, and formalin-fixed, paraffin-embedded (FFPE) tissues sample obtained from the patient suspected of having a condition associated with colorectal cancer mutations; performing PCR on the extracted DNA to produce amplified DNA while using a xenonucleic acid clamp for blocking amplification of wild-type DNA; sequencing the amplified DNA in an automated sequencer; analyzing an output of the automated sequencer to identify mutations in the sequence.
The invention also provides a kit for detecting the presence or absence of mutations in the selected regions of the target genes associated with colorectal cancer, comprising XNA clamps and primers; wherein the XNA clamps are capable of hybridizing with the selected regions having wild-type sequences in the target genes, and the primers are capable of amplifying the selected regions containing each of the mutations in the target genes.
The invention further provides kits that include novel xenonucleic acid clamps.
The invention is a real-time PCR based in vitro diagnostic assay for qualitative detection of colorectal cancer associated biomarkers including APC (codons 877, 1309, 1367, 1450, 1465, 1556), KRAS (codons 12 and 13), BRAF (codon 600), CTNNB1 (codons 41 and 45) and TGFBR2 (codon 449). The detection kit identifies the presence or absence of mutations in the targeted regions but does not specify the exact nature of the mutation. The detection kits are designed to detect any mutation at or near the stated codon site without specifying the exact nucleotide change.
The mutation detection assay of the invention is based on xenonucleic acid (XNA) mediated PCR clamping technology. Xeno-nucleic acids (XNAs) are synthetic genetic polymers containing non-natural components such as alternative nucleobases, sugars, or a connecting backbone with a different chemical structure. This introduction of a wider selection of functional building blocks could enable XNA sequences to participate in a wider selection of chemical reactions than their DNA or RNA equivalents. XNA is a synthetic DNA analog in which the phosphodiester backbone has been replaced by a repeat formed by units of (2-aminoethyl)-glycine. XNAs hybridize tightly to complementary DNA target sequences only if the sequence is a complete match. Binding of XNA to its target sequence blocks strand elongation by DNA polymerase. When there is a mutation in the target site, and therefore a mismatch, the XNA:DNA duplex is unstable, allowing strand elongation by DNA polymerase. Addition of an XNA, whose sequence with a complete match to wild-type DNA, to a PCR reaction, blocks amplification of wild-type DNA allowing selective amplification of mutant DNA. XNA oligomers are not recognized by DNA polymerases and cannot be utilized as primers in subsequent real-time PCR reactions.
The invention relates to a method for conducting the early detection of and/or monitoring recurrence of colon cancer and for the detection of colon cancer precursory cells, employing polymerase chain reaction (PCR) using primers and xenonucleic acid (XNA) clamp oligomers with which mutation analyses can be carried out in selected regions of genes APC, K-ras, β-catenin B-raf and Transforming Growth Factor Beta Receptor II. The invention also relates to a kit containing said primers and xenonucleic acid (XNA) clamp oligomers and the use of these primers and xenonucleic acid (XNA) clamp oligomers and of the kit for analyzing mutations, particularly for conducting the early detection of and/or monitoring recurrence of colon cancer and for the detection of colon cancer precursory cells.
The invention further discloses means and methods for analysis of mutations in tumor DNA derived from colorectal cancer tumor tissue biopsies, circulating free tumor DNA derived from patient plasma samples or tumor DNA derived from stool samples.
The invention uses nucleic acid molecular oligomers that hybridize by Watson-Crick base pairing to target DNA sequences yet have a modified chemical backbone. The xenonucleic acid oligomers (
The invention allows for a new way to screen for somatic mutations that utilizes a sequence-specific XNA clamp that suppresses PCR amplification of wild-type template DNA. The clamp allows selective PCR amplification of only mutant templates, which allows the detection of mutant DNA in the presence of a large excess of wild-type templates from a variety of samples including FFPE, liquid biopsy, and traditionally challenging cytology samples.
The molecular clamps for qPCR are synthetic oligomers containing natural A,T,C,G or modified nucleosides (15 to 25 nt long) and have hydrophilic and neutral backbone (no phosphate group like PNA) and undergo hybridization by Watson-Crick pairing. The benefits of XNA include resistance to any known nucleases, much higher binding affinity as DNA binding is independent of salt concentration and large melting temperature differential (ΔTm=15-20° C.) in single-nucleotide (SNP's) and insertion/deletions (indels) (5-7° C. for natural DNA).
The assay of the invention utilizes sequence-specific clamps (Xeno-Nucleic Acid XNA probe) that suppresses PCR amplification of wild-type DNA template and selectively amplifies only mutant template. The assay and kits of the invention represent a rapid, reproducible solution which employs a simple workflow and PCR machines that are commonly used in research and clinical labs.
The xenonucleic acids that can be used in the present invention include functionality selected from the group consisting of azide, oxaaza and aza. Many XNA's are disclosed in Applicant's pending U.S. application Ser. No. 15/786,591 filed Oct. 17, 2017; the entire contents of which are incorporated by reference herewith.
The biological samples useful for conducting the assay of the invention include, but are not limited to, whole blood, lymphatic fluid, serum, plasma, buccal cells, sweat, tears, saliva, sputum, hair, skin, biopsy, cerebrospinal fluid (CSF), amniotic fluid, seminal fluid, vaginal excretions, serous fluid, synovial fluid, pericardial fluid, peritoneal fluid, pleural fluid, transudates, exudates, cystic fluid, bile, urine, gastric fluids, intestinal fluids, fecal samples, and swabs, aspirates (e.g., bone marrow, fine needle, etc.), washes (e.g., oral, nasopharyngeal, bronchial, bronchialalveolar, optic, rectal, intestinal, vaginal, epidermal, etc.), and/or other specimens.
Any tissue or body fluid specimen may be used as a source for nucleic acid for use in the technology, including forensic specimens, archived specimens, preserved specimens, and/or specimens stored for long periods of time, e.g., fresh-frozen, methanol/acetic acid fixed, or formalin-fixed paraffin embedded (FFPE) specimens and samples. Nucleic acid template molecules can also be isolated from cultured cells, such as a primary cell culture or a cell line. The cells or tissues from which template nucleic acids are obtained can be infected with a virus or other intracellular pathogen. A sample can also be total RNA extracted from a biological specimen, a cDNA library, viral, or genomic DNA. A sample may also be isolated DNA from a non-cellular origin, e.g. amplified/isolated DNA that has been stored in a freezer.
Nucleic acid molecules can be obtained, e.g., by extraction from a biological sample, e.g., by a variety of techniques such as those described by Maniatis, et al. (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y. (see, e.g., pp. 280-281).
The XNA-PCR chemistry is also the most reliable tool and it is the only technology that provides detection sensitivity of 0.1% or lower, a level that cannot be achieved by droplet digital PCR and Sanger sequencing. The assays can be completed in two hours for a variety of specimens, including solid tumors (e.g. FFPE tissues) and liquid biopsies (e.g. circulating tumor DNA).
Mutations Interrogated by primers and XNAs:
KRAS codon 12 any non-synonymous other than wild-type GGT->GXT, XGT etc. Gly->Asp, Ser, Val, Arg, Ala, Cys
KRAS codon 13—GGC->GAC Gly>Asp
BRAF codon 600 GTG->GAG, V600E (17600K, D, R or M)
codon 33 TCT->TAT, Ser->Tyr,
codon 41 ACC>GCC Thr>Ala, ACC>ATC Thr>Ile
codon 45 TCT>CCT Ser>Pro, TCT>TTT Ser>Phe
APC codon 1309 delAAAAG
codon 1367 CAG>TAG Glu>Stop
codon 1450 CGA>TGA Arg>Stop, 7bpdel
Primers designed to amplify regions containing each of the target mutations in the target genes are used together with wild-type sequence specific PCR clamp oligomers: peptide nucleic acid (PNA) locked nucleic acids (LNA), bridged nucleic acid (BNA) or more preferably xenonucleic acid clamp oligomers as previously disclosed (Ref DiaCarta XNA patent filings). The PCR reaction is performed and the resulting amplicons generated are detected by real-time fluorescence based PCR using SYBR green intercalating dye or fluorescent 5′-exonuclease hydrolysis probes (taqman). Alternatively the amplicons can be detected employing sequence specific hybridization capture and detection and solid-phase separation techniques.
The gene mutation specific primers and PCR clamp reactions are performed together with primers that are designed to amplify a housekeeping gene such as β-Actin (ACTB). The housekeeping gene provides a means to monitor the quality and quantity of the input DNA that is obtained from colon cancer tissue biopsy samples, circulating free tumor DNA in patients plasma or tumor DNA extracted from patient stool samples.
QIAamp DNA Stool Mini Kit. Ca#51504. Good for 50×200 mg stool samples.
Buffer ASL. Ca#1014755. Buffer AL, Ca#1014600, Buffer AW1 Ca#1014792, Buffer AW2 Ca#1014592, InhibitEx tablets, Ca#19590, RNAseA Ca#1007885, Proteinase K Ca#19131.
Our storage buffer: 10 mM NaCl, 500 mM TrisHCl pH9.5, 100 mM EDTA. Neutralization buffer: 1M MES pH 5.76 (Teknova). Silica maxi spin columns. Epoch BioSciences (Ca#2040-050).
Streptavidin coated Magnetic Dynabeads MyOne (Thermo Fisher Scientific, Ca#00351575) are the best for DNA capturing. 20×SSC buffer. Beckman Coulter Sorvall centrifuge with JA25.50 rotor and 50 ml centrifugation tubes with screw caps (Ca#357003). BeckmanCoulter AllegraX-15 bench top centrifuge with SX4750 rotor for maxi columns.
The procedure described below is for the whole stool covered with the storage buffer added by patient. If stool is in the frozen state we recommend to take about 10×2 g pieces and add 10 volumes (20 ml) of ASL buffer to each piece. Allow stool to thaw and continue as described.
Add the minimal volume of storage buffer to the fresh stool just to cover stool surface (no more!) Mix suspension with glass rod for few minutes to make it more homogeneous. Close the container and incubate for 16-24 h at room temperature.
Mix stool and transfer 2-3 spoons of stool suspension into the graduated 50 ml conical tube to determine the volume of an aliquot.
Spin the aliquot at ˜20000 g for 5 min. Discard the supernatant and determine the weight of the pellet.
Discard the tube with the pellet.
To start DNA purification from 2 g of stool take 2 g/0.55 g/ml=3.6 ml of the liquid stool. To start with 200 mg use 360 μl of stool.
Isolation of Human DNA from 200 mg of Stool in the Storage Buffer.
This procedure is modification of Qiagen's QIAamp protocol. It is recommended for the training purposes. It is quick and may be performed using DNA stool mini kit (Ca#51504). Mix the liquid stool and transfer 360 μl (200 mg) into 15 ml graduated conical tube. Add 3.6 ml (10 volumes) of ASL buffer. Vortex. Incubate at room temperature for 5 min. Add 360 ul 1M MES pH5.76 buffer. Vortex. Volume=4.32 ml
Distribute 2 ml×2 into two 2 ml centrifugation tubes. Spin at 10000-13000 g for 5 min in the bench top centrifuge. Combine supernatants in 15 ml conical tube. Add 1 ul RNAseA (100 mg/ml, Qiagen). Mix and incubate for 5 min. Add 1 InhibitEx tablet (Qiagen). Vortex for about 1 min until tablet is completely dispersed. Transfer the whole mix into two 2 ml tubes. Spin at 13000 g for 5 min. Combine the supernatants in 15 ml conical tube. Add 25 ul Proteinase K. Mix. Add the equal volume of AL buffer. Mix. Incubate at 70 C for 20 min in the water bath. Cool the mix to the room temperature. Add the volume of ethanol equal to that of AL buffer.
Mix. Load 0.7 ml mix repeatedly onto one silica column. (It may take more than 10 loadings. See details in instruction to the kit).
a). Perform each loading of sample at 6000 g for 1 min.
500 μl of AW1 buffer at 6000 g for 1 min.
500 μl of AW2 buffer at 10000 for 1 min, twice.
c). Spin dry column at 13000 g for 2 min.
d). Elution. Load 50-100 μl AE buffer onto silica column. Incubate for 1 min. Spin at 13000 g for 2 min.
Isolation of Human DNA from 2 g of Stool in the Storage Buffer.
Mix the liquid stool and transfer 3.6 ml (2 g) into 50 ml graduated conical tube. Add 36 ml (10 volumes) of ASL buffer. Vortex. Incubate at room temperature for 5 min. Add 3.6 ml of 1M MES pH5.76 buffer. Vortex. Volume=43.2 ml. Transfer mix into 50 ml centrifugation tube (Beckman Coulter, Ca#357003). Spin at 20000 g for 10 min. Collect supernatant in 50 ml conical tube. Add 4 μl RNAseA (100 mg/ml, Qiagen). Mix and incubate for 5 min. Add 4 InhibitEx tablets (Qiagen). Vortex for about 1 min until tablets are completely dispersed. Transfer the whole mix into 50 ml centrifugation tube. Spin at 20000 g for 10 min. Collect the supernatant in 50 ml conical tube. Add 250 μl Proteinase K. Mix. Add the equal volume of AL buffer. Mix. Incubate at 70° C. for 20 min in the water bath. Cool the mix to the room temperature. Add the volume of ethanol equal to that of AL buffer.
1. Use the beads from the bead vial of the Promega Maxwell® RSC Whole Blood DNA Kit
1.1. Resuspend the Bead Mix in the 2nd well of the kit cartridge and
1.2. transfer the whole content of the bead mixture to the solution from step 3.7
1.3. Incubate for 0.5 hour at RT on an orbital shaker at moderate speed to bind NA to the NA Binding Beads.
1.4. Pull down the beads with the magnet (optional: Spin down and discard supernatant). Save about 500 ul supernatant with beads.
1.5. Transfer bead suspension into the bead compartment of the kit cartridge and proceed with the kit-specific program.
1.6. Use 150 ul elution volume
The DNA is ready for qPCR.
Mix. Load ˜20 ml mix repeatedly onto one Maxi silica column inserted into 50 ml conical tube. (It may take more than 5 loadings).
a) Perform each loading of sample at 1850 g for 3 min in “Allegra X-15R centrifuge, bucket rotor SX4750, Beckman Coulter)
5 ml of AW1 buffer at 4500 g for 1 min.
5 ml of AW2 buffer at 4500 g for 15 min.
d) Elution. Load 1 ml of AE buffer onto silica column. Incubate for 5 min. Spin at 4500 g for 2 min.
Concentration of DNA Isolated from 2 g of Stool Before the Sequence Dependent Capture.
The volume of DNA eluted from maxi column is about 700 μl. Denature DNA by heating at 95 C for 5 min.
Transfer DNA into 2 ml centrifugation tube. Add 70 ul of 5M NaCl+70 ul of 5N NH4Ac+700 μl isopropanol. Incubate for 1 h at room temperature. Precipitate DNA by centrifugation at 13000 g for 15 min in the bench top centrifuge. Wash pellet with 70% EtOH. Dry pellet at 55 C for 5 min. Dissolve DNA in 35 μl of 10 mM Tris pH8.0.
Enrichment of Eluted DNA with the Target Specific Capture 5′-BIOprobe on the Magnetic Beads.
Put 35 μl of eluted DNA into 0.2 ml tube and incubate at 95° C. for 2 minutes in thermo cycler with the preheated lid. Chill the tube on ice for 2 minutes. Transfer denatured DNA into the new 0.2 ml tube. Assemble hybridization mix as shown in the Table below.
Perform hybridization in thermo cycler at: 95° C. 4 min-58 C 1 h.
Prepare magnetic beads during hybridization.
Vortex beads in bottle for 20 sec. Transfer 10 μl (10̂9 beads) to the bottom of 0.5 ml tube. Place tube on the magnet for 1 min. Remove the liquid covering the concentrated beads. Remove tube from the magnet. Add 100 μl of 1× B&W buffer and suspend beads by gentle aspiration. Put the tube on the magnet. Repeat the washing step with 50 ul of 1× B&W. Cover beads with 50 μl of 1× B&W to prevent beads from drying.
Put the tube with the washed beads covered with 1× B&W on magnet and remove supernatant without disturbing beads. Remove tube from the magnet and immediately suspend beads in 10 ul of B&W buffer. Remove the post hybridization mix from the thermo cycler. Add 7 μl of washed beads. Suspend beads by the gentle aspiration. Place tubes into shaker for 2 hours at 1100 rpm. The speed of the shaking should be high enough to don't allow beads to precipitate.
Washing of Beads with Captured DNA.
Collect beads on the magnet. Aspirate the supernatant. Suspend beads in 100 μl B&W. Repeat this wash step with 50 μl of B&W. Repeat the step with suspending beads in 50 μl of 10 mM NaCl+20 mM TrisHCl pH7.5 (high stringency wash buffer).
Elution of DNA from the Beads.
Aspirate the low stringency wash buffer from beads. Suspend beads in 20 μl of 20 ng/μl of polyA or other homopolymer carrier. Place tubes into thermo cycler and heat at 70 C for 5 min to elute DNA. Place tube on magnet and collect ˜20 μl of captured human DNA.
55 blinded samples of DNA extracted from plasma and FFPE of patients with known clinical and mutational status were provided as 15 ul aliquots in microcentrifuge tubes. Some samples were from tumor tissue of colon cancer patients. Samples were labeled from 1 to 55 with the ID# on the sides of tubes.
The goal of the test was for detection of mutations in plasma of colon cancer patients. Samples were accessioned according to accessioning and sample traceability SOPs.
The quantity and qPCR readiness of the DNA was checked by qPCR using the reference amplicon from the internal control of the assay. The samples then were diluted accordingly and tested using the assay. All positive calls for any of the target mutations were confirmed by Sanger sequencing of the amplicons.
The Colorectal Cancer Mutation Detection Kit of the invention is based on xenonucleic acid (XNA) mediated PCR clamping technology. XNA is a synthetic DNA analog in which the phosphodiester backbone has been replaced by a repeat formed by units of (2-aminoethyl)-glycine. XNAs hybridize tightly to complementary DNA target sequences only if the sequence is a complete match. Binding of XNA to its target sequence blocks strand elongation by DNA polymerase. When there is a mutation in the target site, and therefore a mismatch, the XNA:DNA duplex is unstable, allowing strand elongation by DNA polymerase. Addition of an XNA, whose sequence with a complete match to wild-type DNA, to a PCR reaction, blocks amplification of wild-type DNA allowing selective amplification of mutant DNA. XNA oligomers are not recognized by DNA polymerases and cannot be utilized as primers in subsequent real-time PCR reactions. The qPCR detection is Taqman-based.
qPCR Assay
The assay of the invention is a real-time PCR based in vitro diagnostic assay for qualitative detection of colorectal cancer-associated biomarkers including APC (codons 1309, 1367, 1450), KRAS (codons 12 and 13), BRAF (codon 600) and CTNNB1 (codons 41 and 45). The detection kit identifies the presence or absence of mutations in the targeted regions but does not specify the exact nature of the mutation. The detection kits are designed to detect any mutation at or near the stated codon site without specifying the exact nucleotide change.
Table 1 above shows a list of mutations commonly found in the targeted gene that can be detected by the kit. The assay and kit is to be used by trained laboratory professionals within a laboratory environment.
QIAamp DSP DNA FFPE Tissue Kit (QIAGEN, Cat. No. 60404) or equivalent
QIAamp Circulating Nucleic Acid Kit (QIAGEN, Cat. No. 55114) or equivalent
0.2 ml DNase-free PCR tubes or plates, nuclease-free, low-binding micro centrifuge tubes and nuclease-free pipet tips with aerosol barriers.
Permanent marker, real time PCR instrument, dedicated pipettes* (adjustable) for sample preparation, dedicated pipettes* (adjustable) for PCR master mix preparation, dedicated pipettes* (adjustable) for dispensing of template DNA, micro centrifuge, bench top centrifuge* with rotor for 1.5 ml tubes, vortexer, PCR rack, reagent reservoir, distilled water.
* Prior to use ensure that instruments have been maintained and calibrated according to the manufacturer's recommendations.
The assays have been developed and validated on the instruments shown in the table below. Instrument platforms not listed in the table should be validated by the individual labs. Guidance for validation can be obtained from DiaCarta upon request.
The kits of the invention should be stored at −20° C. immediately upon receipt, in a constant-temperature freezer and protected from light. When stored under the specified storage conditions, the kit is stable until the stated expiration date. It is recommended to store the PCR reagents (Box land 2) in a pre-amplification area and the controls (Box 3) in a postamplification (DNA template-handling) area. The kit can undergo up to 6 freeze-thaw cycles without affecting performance.
Human genomic DNA must be extracted from fixed paraffin-embedded tissue, frozen tissue or plasma prior to use. Several methods exist for DNA isolation. For consistency, we recommend using a commercial kit, such as Qiagen DNA extraction kit (QIAamp DNA FFPE Tissue Kit, cat No. 56404, for paraffin embedded specimens; DNeasy Blood & Tissue kit, cat. No. 69504 or 69506, for tissue and blood specimens, QIAamp Circulating Nucleic Acid Kit, cat. No. 55114 for plasma). Follow the genomic DNA isolation procedure according to manufacturer's protocol. Sufficient amounts of DNA can be isolated from FFPE blocks or fresh frozen sections as well as plasma (approx. 2-10 μg).
This assay requires a total of 22.5-35 ng of DNA per sample (2.5-5 ng/reaction). After DNA isolation, measure the concentration using fluorometric analysis (i.e. Qubit) and dilute to 1.25-2.5 ng/μ1. If using spectrophotometric analysis, make sure the A260/A230 value is greater than 2.0 and A260/A280 value between 1.8 and 2.0.
A 24-test kit contains enough control material for 3 runs. Thaw all primer and probe mixes, XNAs, Positive Control, WT Negative Control, Nuclease-Free Water and 2×PCR mastermix provided. Thaw all reaction mixes at room temperature for a minimum of 30 minutes. Vortex all components except the PCR Master Mix and Primer and probe Mix for 5 seconds and perform a quick spin. The PCR Master Mix and Primer/probe mix should be mixed gently by inverting the tube a few times. Prior to use, ensure that any precipitate in the PCR Master Mix is re-suspended by pipetting up and down multiple times. Do not leave kit components at room temperature for more than 2 hours. The PCR reactions are set up in a total volume of 10 μl/reaction.
Table 4 shows the component volumes for each 10 ul reaction.
For accuracy, 2×PCR Mastermix, primers and XNA should be pre-mixed into assay mixes as described in Table 5 below.
Assay mixes should be prepared just prior to use. Label a micro centrifuge tube (not provided) for each reaction mix, as shown in Table 5. For each control and mutation detection reaction, prepare sufficient working assay mixes for the DNA samples, one Positive Control, one Nuclease-Free Water for No-Template Control (NTC), and one WT Negative Control, according to the volumes in Table 5. Include reagents for 1 extra sample to allow sufficient overage for the PCR set up. The assay mixes contain all of the components needed for PCR except the sample.
Negative Control, Positive Control and Non template control must be run with each reaction mix, every time the assay is run.
The Internal Control assay uses ACT-B housekeeping gene as a reference gene to assess the quality of amplifiable DNA and demonstrating if the reagents are working correctly. When assessed using the HEX channel, this control should make amplicons efficiently for all samples and controls except NTC, providing another way to monitor performance of the primers, probes, polymerase, and sample DNA quality/quantity.
Please always use white plates, strips, or tubes. In pre-amplification area, add 8 μl of the appropriate assay mix to the plate or tubes. In designated template area, add 2 μl of template to each well.
Table 6 is a suggested plate set-up for a single experiment analyzing 3 unknown samples. Please disregard any assay mixes listed below that are not part of your kit. When all reagents have been added to the plate, tightly seal the plate to prevent evaporation. Spin at 1000 rpm for 1 minute to collect all the reagents. Place in the real-time PCR instrument immediately.
Roche Light cycler 96 and Light cycler 480, Bio-Rad CFX 384 and ABI QuantStudio 5
1) Selection of Detectors:
2) Setup the cycling parameters as shown in Table 7a or Table 7b
3) Start the run
The real-time PCR instrument generates a cycle threshold (Cq, also called as Ct) value for each sample. Cq is the cycle number at which a signal is detected above the set threshold for fluorescence. The lower the cycle number at which signal rises above background, the stronger the PCR reaction it represents and the higher initial template concentration (**please see MIQE Guidelines under References for more information).
Data Analysis for Light Cycler 480
For the Light Cycler 480, open the LightCycler480 SW 1.5.1.61 and select Abs Quant/2nd Derivative Max algorithm to analyze the run file data.
Data Analysis for Bio-Rad CFX384
For the BioRad CFX384, open the qPCR run file using BioRad CFX manager. In the Log scale view, adjust the threshold to 100±20 for HEX and 300±60 for FAM. Export the Cq data to excel. Exact threshold setting may be different for individual instruments.
Data Analysis for ABI QuantStudio 5
For the ABI Quant Studio 5 instrument, adjust the threshold according to Table 8. Exact threshold setting may be different for individual instruments.
Export the Cq data to excel. For each control or sample, calculate the difference in Cq value between the mutation assay and the Internal Control Assay as follows: Cq difference (ΔCq)=Mutation Assay Cq−Internal Control Assay Cq
Verify that no amplification is observed in the non-template controls (NTC) for each of the reaction mixes. Cq should be Undetermined. For each control or sample, calculate the difference in Cq value between the mutation assay and the External Control Assay as follows:
Cq difference (ΔCq)=Mutation Assay Cq−Internal Control Assay Cq
For the assay to be valid, the Negative Control and Positive Control must meet the criteria in Table 9a and Table 9b.
The Cq value of the Internal Control Mix serve as an indication of the purity and concentration of DNA in each well. Thus, the validity of the test can be decided by the Cq value of the Internal Control mix. Cq values of any sample with Internal Control Mix should be in the range of 25<Cq<31 (Roche Light cycler 480 and Bio-Rad CFX 384) or 25<Cq<30 (ABI QuantStudio 5). If the Cq values fall outside this range, the test results should be considered invalid. The experiment should be repeated following the recommendations in Table 10.
If a Cq value is Undetermined, assign a Cq of 50 and proceed to analysis. The tables below should be used to determine mutational status based on ΔCq values.
Note: If the Cq value of FAM is 50, the mutational status will be scored as “Negative” regardless of the ΔCq values.
Differentiating KRAS c12/KRAS c13 Mutational Status
The KRAS c12 reaction mix detects both KRAS c12 and KRAS c13 mutations, whereas the KRAS c13 reaction mix detects only KRAS c13 mutations. Therefore, in order to differentiate between KRAS c12 and KRAS c13 mutations a combination of results from the two mixes should be used as described in Table 14 below.
The performance characteristics of the assay were established on the Roche LightCycler 96, Roche LightCycler 480, Bio-Rad CFX 384 and ABI QuantStudio 5 real-time PCR instruments. The studies were performed using genetically defined reference standards (genomic DNA and FFPE) from cell lines with defined mutations obtained from Horizon Discovery (Cambridge, England) and cfDNA reference standards from SeraCare (Massachusetts, US). These samples have been characterized genetically as containing heterozygous or homozygous mutations in the coding sequence of the respective target regions. These single nucleotide polymorphisms in the target regions have been confirmed by genomic DNA sequencing and/or ddPCR. Additional samples consisted of cancer patient tissue, plasma samples and normal healthy donor DNA from tissue and plasma.
Reproducibility of the assay was determined with defined analytical levels of genomic DNA with known mutational status and allelic frequencies.
Reproducibility is demonstrated based on % CV of Cq values and rate of % correct mutation calls for all assays on two lots and operators for Roche and Bio-Rad instruments.
The intra-assay data demonstrated good reproducibility with low % CV (Table 16).
To determine the limit of detection (LOD) and analytical sensitivity of the kit, the studies were performed using serial dilutions of mutant DNA (reference FFPE and cfDNA) in wild-type background. The wild-type DNA used for dilution was obtained from mutant-free FFPE and normal human plasma respectively. Mutant allelic frequencies tested were 1%, 0.5% and 0.1% at 2.5, 5 and 10 ng/reaction DNA input levels. The mutant copy numbers present in genomic DNA with 1%, 0.5% and 0.1% allelic frequency at different DNA input levels are shown in Table 17a.
Recommended input of FFPE should not be higher than 20 ng/well due to possible PCR inhibition. Optimal FFPE sample input is between 25 and 31 Cq of the Internal Control.
Analytical specificity of the kit was determined as the correct calling of the samples with no mutation at different concentrations of WT template. There were no false positive calls for up to 320 ng of gDNA per well and up to 20 ng FFPE DNA.
Cross-reactivity of the assays within the kit was tested with one or more mutations present in a mixed positive control at 50% allelic frequency.
The data demonstrates that the present invention Kit can correctly identify several mutations within one template. There is cross reactivity between KRAS12 and KRAS13, due to the proximity of the mutations, which can be differentiated (Refer to Table 13).
Clinical sensitivity and specificity was tested on the samples extracted from FFPE and plasma of patients with different stages of CRC from normal to advanced adenomas (AA), to colorectal cancer stages 1 through 4.
A sample was considered positive if at least one of the target mutations tested positive based on the cutoffs presented in Tables 10-12.
1 Products used in this study
Summary of the qPCR test results is presented in Table 20 below:
In the column listing the overall assay calls (second from the right) samples highlighted in green were positive by Light green—weak positive. Negative calls—orange. Since the samples were blinded and most of them were expected to be extracted from plasma, we have used positive, negative and weak positive calls due to un-validated cutoffs for the plasma sample type. The column also shows all the genes that were found positive/weak positive for target mutations. Overall there were 29 positive calls, 16 negative calls and 10 weak positive calls.
Samples s22, s24, s34, s36, s39, s44, s52 and s55 had insufficient DNA as evidenced by the Cq of the IC over 30. These samples were processed by present invention assay, but results of these tests should be interpreted with caution, especially the negative calls on Samples s24, s34 and s55.
qPCR results of all positive and weak positive samples were further confirmed by Sanger sequencing of the qPCR amplicons. Some BRAF samples were also tested by alternative BRAF qPCR DiaCarta kit.
Results are presented in the last column to the right. Out of the 49 samples tested for all the relevant targets, Sanger sequencing produced no satisfactory data for 6 samples. 2 BRAF weak positive samples were found to be negative (either WT by Sanger sequencing or Negative by the alternative qPCR DiaCarta assay for BRAF c600). Several BRAF mutations outside of the V600E were shown to be present in the other weak positive cases that did not change the overall calls for the samples carrying these mutations. 100% of the Positive present invention calls were confirmed by Sanger sequencing with available data. 3 calls could not be confirmed due to poor Sanger data.
3 out of 10 weak positive calls were negative by Sanger, 5 did not produce sequencing or qPCR data and 2 BRAF WP calls tested positive for mutations other than V600E.
The test results clearly demonstrate that the assay can be used to detect mutations in the CRC DNA samples extracted from patient plasma. As little as 30 ng of DNA is sufficient to provide test results as evidenced by concordance rate of 100% for positive calls with available Sanger data. Most of the samples with low quantity/quality of DNA are difficult to test, but these can be identified by using the internal control data.
The table above shows the assay performance from FFPE samples. Pre-cancer detection sensitivity is 60% (6 out of 10 samples).
The Table below compares the technical details and performance characteristics of assay of the invention with prior art assays.
This example describes the feasibility studies of the Assay for qualitative detection of mutations in targeted genes of APC (codons 1309, 1367, 1450), KRAS (codons 12 and 13), BRAF (codon 600) and CTNNB1 (codons 41 and 45) genes associated with colorectal cancer initiating events.
The Assay is a real-time qPCR-based in vitro diagnostic test intended for use in the detection of mutations in the APC (codons 1309, 1367, 1450), KRAS (codons 12 and 13), BRAF (codon 600) and CTNNB1 (codons 41 and 45) genes in DNA extracted from FFPE sections and human stool samples.
Since clinical samples from cancer patients frequently contain trace amounts of mutant allele in a large excess of wild-type DNA, DiaCarta's proprietary QClamp® XNA-PCR technology is employed in the present invention Taqman assays to suppress amplification of WT alleles to improve the sensitivity of mutation detection.
A panel of target genes were selected based on their mutation frequency in early-stage colorectal cancer patients (UP patent 0,172,823 A1 licensed from Pottsdam University), preliminary clinical trials by Dr. Sholttka (publications). These early colorectal cancer related biomarkers include APC (codons 1309, 1367, 1450), KRAS (codons 12 and 13), BRAF (codon 600), CTNNB1 (codons 41 and 45) genes and TGFβ (to be included). A housekeeping gene, beta-actin (ACTβ), was selected as internal control based on preliminary data from B. Sholttka and because competitor assay (ColoGuard from Exact Sciences) also uses that same gene for internal control. ACTβ assay is used to monitor sample DNA extraction efficiency and presence of PCR inhibitors as well as to provide a way of quantitation of amplifiable template in each reaction well to prevent false positive/negative results.
3.2.1. Primers and probes were designed using PrimerQuest Tool following the qPCR primer and probe design rules. The primers were designed with a Tm of 62-64° C. while the probes were designed with Tm of 66-68° C.
3.2.2. The amplicon sizes were designed under 150 bp if possible.
3.2.3. Primers and probes were checked in-silico for specificity (BLAST), primer dimers/secondary structure (autoDimer) and amplicon secondary structure (M-fold).
3.2.4. The XNAs were designed to be between the forward and reverse primers or overlap a few bases with the forward primer.
3.2.5. The probes were designed to be parallel (on the same strand as) to XNAs and either overlap with the XNA (mutant-specific probes) or be distal to the XNA (locus specific probes).
3.3. Design Selection strategy
3.3.1. Primer, probe and XNA combinations and concentration optimization tests were performed to find the optimal conditions for differentiating mutant and WT alleles for each targeted somatic mutation.
3.3.2. Several qPCR master mixes are tested to find the best one that gives the lowest Ct and highest delta Ct for best performance in differentiating mutant and WT.
3.3.3. For efficient clamping by the XNA, a XNA annealing step at 70° C. before the binding of primers and probes is included in the qPCR cycling program. Optimal annealing temperature for primers and probes will be tested by gradient analysis.
4.1. Composition of the PCR reaction Mix
1.1. Reference templates:
CTNNB1 CD 41: IDT gBlock, custom
CTNNB1 CD 45: ATCC CCL-247_D1
BRAF C600: BRAF C600 Reference standard (Horizon Cat#: HD238)
KRAS c13: KRAS G13D Reference Standard (Horizon Cat#: HD290)
KRAS c12: KRAS G12D Reference Standard (Horizon Cat#: HD272)
APC 1309: ATCC CRL-2158_D1
APC 1367: ATCC CRL-2101_D1
APC 1450: ATCC CCL-235_D1
Roche LC96 DC2034, Cat. No. 05 815 916 001
Roche LC480II DC2035, Cat. No. 05015243001
BioRad CFX384 DC2044, Cat. No. 4329001
Takara Bio Premix Ex Taq (Probe qPCR) 2× master mix, Clontech/TAKARA, Cat. # RR390A
SensiFAST Probe No-ROX mix (2×), Bioline, Cat. # BIO-86002
STAT-NAT-DNA—Mix (lyophilized), SENTINEL, Cat. #1N001)
KAPA Probe Fast qPCR Master Mix (2×) Universal (Cat. #: KK4703)
SensiFAST Probe No-ROX mix (2×), Bioline, Cat.# BIO-86002
PrimerQuestTool/IDT
Autodimer
M-fold
CLC sequence viewer 7
1.3. Browser based tools
UCSC Genome Browser
NCBI
dbSNP
dbVar
COSMIC
DDC.0007_present invention qPCR Project Plan
DDC.0006_Product Requirements for present invention multiplex qPCR Test C0.0001 Product development and Commercialization
Based on previous tests on master mixes for Taqman based qPCR assays, KAPA Probe Fast qPCR Master Mix (2×) Universal was selected as the primary master mix for Taqman probe based qPCR reactions for mutation detection assay development. The following additional master mixes were compared with the KAPA master mix:
1) Takara Bio Premix Ex Taq (Probe qPCR) 2× master mix, Clontech/TAKARA, Cat.# RR390A
3) STAT-NAT-DNA—Mix (lyophilized), SENTINEL, Cat. #1N001)
3.1.1. Lyophilized master mix can be conveniently stored and shipped at room temperature, so lyophilized Bioline master mix was also evaluated and compared with KAPA probe Fast qPCR Master Mix (2×) Universal (Table 23)
Bioline master mix and KAPA Probe Fast qPCR master Mix (2×) were further compared using samples with different mutation frequency and on different qPCR machines (Roche LC 480 vs BioradCFX 384). The control is in HEX channel while all the targeted mutations are in Fam. Delta Ct was calculated for each sample as follows: Ct difference (ACt)=Mutation Assay Ct−Control Assay Ct. The data were summarized in Table 24.
3.1.1.
Bioline master mix and KAPA Probe Fast qPCR Master Mix (2×) Universal are comparable when the mutation frequency is 5% or higher while when mutation frequency is lower (0.5% or 0.1% or lower), KAPA Probe Fast qPCR Master Mix (2×) Universal performed better in regarding to differentiating mutant and WT alleles. Therefore, KAPA Probe Fast qPCR Master Mix (2×) Universal will be used in the present invention assay.
5.2. Optimization of the assay reagent composition and thermocycling conditions.
5.2.1. Primers for BRAF c600 and KRAS c12, c13 were designed and optimized previously in existing QClamp SYBR commercial products (DC-10-1066, DC-10-0036, DC-10-0039, DC-10-1039, DC-10-0197, DC-10-0169).
5.2.2. The APC, CTNNB1, beta-ACT primers were designed to have annealing temperatures same as BRAF and KRAS primer pairs (64 C for Roche and BioRad instruments).
5.2.3. Annealing temperature gradients (60-70 C) were performed using the Roche LC96 with KAPA Probe Fast qPCR Master Mix (2×) Universal to find the optimal annealing temperature of each target primers and probes. The results of the gradient analysis were summarized in Table 25 and Table 26.
5.2.1. PCR annealing temperature conclusion: 63-64 C annealing temperatures were demonstrated to be optimal for differentiation of mutant and WT alleles for all the invention assay targets.
XNAs are employed in the invention Taqman mutation detection assays to suppress wt amplification in order to improve mutation detection sensitivity. For efficient clamping by the XNA, a XNA annealing step at 70° C. before the binding of primers and probes is included in the qPCR cycling program. Based on gradient analysis of the primer and probe annealing temperature, the thermo cycling conditions for the invention Taqman mutation detection assays is optimized as follows:
5.2.3. 95° C. for 5 min followed by 50 cycles of 95° C. 20 seconds, 70° C. 40 seconds, 64° C. 30 seconds and 72° C. 30 seconds (data acquisition).
5.3.1. Primer and probe matrix dilution experiments were conducted to find the optimal concentrations for differentiating mutant and WT alleles of targeted genes.
5.3.1. The use of XNA combined with limited primer/probe concentration resulted in less or no WT background Amplification for selected locus specific probes. The results of optimization of primer, probe and XNA concentrations are summarized in Tables 28-36.
3.1.2.
5.3.1. Optimal concentrations are 0.1 uM primer and 0.05 uM probe for differentiating mutant and WT of CTNNB1 c45, BRAF c600 on Roche LightCycler 96, Roche LightCycler480 and BioRadCFX384.
5.3.2. For CTNNB1 c41, 0.2 um primer and 0.1 um probe are optimal for differentiating mutant and WT alleles on Roche Light cycler 96, Roche Light Cycler 480.
5.3.1. For KRAS12 and 13, 0.4/0.2 um primer and probe are optimal for differentiating mutant and WT on LC 96, 0.2 um primer and 0.1 um probe are optimal for differentiating mutant and WT on LC 480 and BioRadCFX384.
5.3.2. In general, using limited primers and locus specific probes concentration ((100 Nm to 200 Nm/50 to 100 nM) result in less or no WT background amplification with XNA. Primer/probe conc. above 0.4/0.2 um usually result in WT background amplification with XNA. The use of limited primer/probe conc. combined with XNA will result in less or no WT background amplification for selected locus specific probes.
5.4. Optimization of XNA Concentration with Primer-Probes
5.4.1. Primers and probes were screened for differentiating mutant and WT alleles in presence of XNA. For optimization, XNA titration and limited primer and probe concentration (100 Nm to 200 nM/50 to 100 nM) were used.
5.4.2. The following primers were screened by SYBR assay to find the primer pairs that result in best ACt between mutant and WT alleles (Tables 37-39).
A Primer/XNA Matrix was run to find the optimal Primer/XNA concentrations which gave the best differential between WT and 5% MT of BCT c41. The primer/XNA matrix analysis was summarized in Table 40.
5.3.1. For the other targeted mutations including BRAF V600 and KRAS c12 and c13, the primer pairs that were used in DiaCarta Qclamp SYBR Kits of BRAF and KRAS c12 and KRAS c13 assays were also used in the development of the Taqman probe based BRAF and KRAS c12 and KRAS c13 mutation detection assays.
5.3.2. Primer, probe and XNA combinations and concentrations that resulted in highest delta Ct (measured as the difference between Cts of the mutation detection assay for the WT and 5% Mut samples) were selected for each targeted mutation detection assay.
5.3.3. The following primers and probes and XNA showed the best performance in regarding to differentiating mutant and WT alleles. For more details in the screening of primers by SYBR assay, please see the attached file with this document.
5.3.1. The following figures illustrate the performance examples present invention assays with optimal primer, probe, XNA concentration and ACt between Wt and mutant.
Based on experiments on each of the invention target primers, probe and XNA combination and titration, optimal conditions were obtained for each targeted mutation detection assay as listed in Table 22 and illustrated in figures above. The finalized assays of the invention were assessed for test specificity, sensitivity and reproducibility.
A set of cell lines with known mutation status were tested to evaluate the assay of the invention accuracy. The invention assays were run on the Roche LC 96 instrument. Only expected mutations were detected in all tested cell lines.
Analytical Sensitivity was determined by testing of DNA samples with a serial dilutions of DNA into wild type DNA. Mutation detection assays were performed on DNA samples with 5%, 1%, 0.5%, 0.1%, mutation DNA in wt background respectively. The lowest percentage of mutated DNA in wild type background that can be detected is determined. At least 0.5% of mutation DNA in wild type background can be detected by the invention Taqman assays (See Table 18) and Table 19.
Reproducibility (Precision) of the invention assays was demonstrated by comparing test results from mutation detection assays on 5% AF sample from multiple runs throughout the feasibility study period (See Table 46 and 47). % CV values were calculated within runs and between runs to test inter-assay and intra-assay precision (Table 47 and 48).
Data presented in tables 47 and 48 indicated that all the invention assays have good intra- and inter-assay precision with % CV<10.
Analytical specificity was tested by performing the assay on reference samples with known mutation negative status. All the test results were as expected (see Table 43).
5.7.1. Limit of blank was tested by performing the assay on the NTC samples.
All tested NTC samples were called negative.
1.1. The final design is presented in the Tables 41 and 42.
1.2. Final assay PCR cycling parameters are presented in section 5.2.3:
95° C. for 5 min followed by 50 cycles of 95° C. 20 seconds, 70° C. 40 seconds, 64° C. 30 seconds and 72° C. 30 seconds (data acquisition).
1.3. The present invention design demonstrated that the performance parameters of the tested design met or exceeded specifications set in the product requirement document (DDC.0006) and the assay is ready for the development stage.
1.3.1. Product requirement 1 for the sample types tested will be tested in the Matrix interference test of the Verification study. Requirements 11-15 will be also tested in Verification and Stability studies of the Development stage.
1.3.2. Product requirement 2 is met: under 60 min for reaction setup and under 2.5 h for the reaction PCR run on the three qPCR instruments tested.
1.3.3. Product requirement 3 will be addressed in a separate stool DNA preparation study
1.3.4. Product requirement 4 is met by having 7 reaction mixes where each gene is tested in a separate reaction mix, KRAS 12 and KRAS 13 are in two separate reactions; CTNNB 41 and 45 are also in 2 separate reactions. APC is tested in 2 tubes.
1.3.5. Product requirement 5 is met by testing the assay on all three listed qPCR instruments—Roce LC96 and LC480 and BioRad CFX
1.3.6. Product requirement 6 is met by including the internal control assay in each reaction tube that provides evidence of the sufficient quantity of amplifyable DNA in each reaction well.
1.3.7. Product requirement 7 is met, kit contains NTC, WT control and mixed positive control.
1.3.8. At least 0.5% of mutatnt DNA in wild type background can be detected by the present inventionTaqman assays (high sensitivity) with total DNA input of 2.5 ng/well. Exceeds Product requirement 8 set for detection of 1% mutant DNA.
1.3.9. The data presented in this report demonstrate the feasibility of the present invention design to detect intended mutations with no cross-reactivity observed. Product requirement 9
1.3.10. The design also showed good intra and inter-assay reproducibility (CV<10%). Product requirement 10 is met.
1.4. The final design is presented in the Tables 41 and 42.
1.5. Final assay PCR cycling parameters are presented in section 5.2.3:
95° C. for 5 min followed by 50 cycles of 95° C. 20 seconds, 70° C. 40 seconds, 64° C. 30 seconds and 72° C. 30 seconds (data acquisition
This example further describes the verification and validation studies of the assay of the invention for qualitative detection of mutations in targeted genes of APC (codons 1309, 1367, 1450), KRAS (codons 12 and 13), BRAF (codon 600) and CTNNB1 (codons 41 and 45) genes associated with colorectal cancer initiating events. The assay and kit has been validated for precision, limit of detection (LOD), stability, specificity/cross-reactivity and matrix interference.
The verification and validation studies were performed on two development lots of the assays and kits. Mixed positive controls were used as test samples except that positive controls for APC 1309 and APC 1367 were prepared individually for the LOD studies. The mutation detection protocol is as described in the present invention for doing the test samples. The validation tests were run on LC 480 (for instrument comparison, the tests were also run on BioRad384).
The assay of the invention is a real-time qPCR-based in vitro diagnostic test intended for use in the detection of mutations in the APC (codons 1309, 1367, and 1450), KRAS (codons 12 and 13), BRAF (codon 600) and CTNNB1 (codons 41 and 45) genes in DNA extracted from FFPE sections and Human stool samples.
Test analytic sensitivity of the assay (LOD) and allelic frequency
Test Limit of Blank of the assay
Test matrix interference (e.g. FFPE extraction, add ethanol) for the potential inhibitory effect of
several substances that would most probably be encountered in the real patient samples
Test cross-reactivity (detection of each of the present invention target DNA).
Intra-assay: replicate samples representative of all mutations near LOD
Inter-assay: 3×3 samples in 3 runs per instrument
Lot-to-lot variation tested by repeating 1.5.1 and 1.5.2 on second lot, on same run
Instrument comparison on Roche LC480, BioRad CFX384
Operator variability (2 operators test same lot on the same day on same instrument)
Test analytic specificity on both lots
Analytic Specificity test on high concentration of WT reference samples
Invention stability studies Accelerated Stability Studies
Freeze-thaw stability studies
Real-time stability studies
Deviations from the planned V&V of the invention assay analytical performance
Sensifast lyophilized Bioline mastermix was reverted to KAPA Universal 2× liquid formulation for the two reasons: The timelines of the manufacturing on the Bioline side were too long and The assay sensitivity at 1% mutation was not as good as with KAPA
Manufacturing: Reagents for some primer-probe mixes were purchased separately for lot 2, others-same
The tubes used to aliquote the kits were from USA scientific, planned to be change to the stock of approved tubes from Fisher Scientific that are used for all the current product manufacturing.
The run time for the BioRad CFX 384 instrument exceeds 2 h limit set as Product Requirement #5. The requirement was not an essential one and 2.5 h run time was considered acceptable.
Composition of the PCR Reaction Mix
CTNNB1 CD 41: IDT gBlock, custom
BRAF C600: BRAF C600 Reference standard (Horizon Cat#: HD238)
2 development lots (DL-1 and DL-2) of the Multiplexed Colorectal Cancer detection Kits including:
Analytical sensitivity of the assay was evaluated by testing 1%, 0.5% and 0.1% mutand DNA template at 2.5 ng, 5 ng and 10 ng input for all the present invention targets. For each target, 1%, 0.5% and 0.1% mutation at each of the three DNA input level were tested in triplicates and on 3 separate runs on LC 480. No template control (NTC), wild type DNA (clamping control) and mixed positive controls (APC 1309 and APC 1367 positive controls were prepared individually) were included in each run. Average Ct values, standard deviation (SD) and coefficient of variation (% CV) were calculated for both FAM (target) and HEX (internal control). The ACt values (ΔCt=Ct Fam−Ct Hex) were calculated from the averaged Ct values (Table 51 to Table). The average ΔCt values over all 3 DNA input levels for all three runs were calculated. The cut-off ΔCt is set to be the average ΔCt values—1.5ΔCt SD (Table). Correct call percentage were calculated for 1%, 0.5% and 0.1% mutation detection of all target at 2.5 ng, 5 ng and 10 ng DNA input (Table 53 and Table 54). Correct call percentage were also calculated for 1% mutation detection of all target at 5 ng DNA input with all runs during the V&V period and results were incorporated in Tables 53 and 54.
0.5% mutation frequency in APC (c1367, c1450), BCT(c41,c45), KRAS(c12, c13) can be reliably detected (100% correct call) at as low as 2.5 ng DNA input per PCR reaction.
at 5 ng DNA input 1% mutation in APC 1309 and BRAF V600 can be detected with 94% and 100% correct calls respectively. For APC (c1367, c1450), BCT(c41,c45) and KRAS(c12, c13) analytic sensitivity is 0.5% at this input with 100% correct calls.
Non-template controls (nuclease free water) were run with each validation test to monitor for contamination in the PCR. The data for NTC from 50 replicates from multiple runs were compiled (Table 56) and analyzed to estimate level of background noise of the present invention assays.
For present invention targets including APC 1450, BCT 41, BCT 45, KRAS 12 and BRAF V600, there is no background amplification noise with no detected amplification for these targets when testing NTC. For APC 1309/1367 and KRAS13, there is minimal background noise with average Ct over 48 and 49 respectively.
To determine whether residual common substance in DNA isolated from FFPE has interfering inhibitory effect on the performance of the present invention assay, Ethanol (ETOH) was spiked in the DNA samples at 2%, 5% and 10% concentration and tested in 5 replicates on Roche LC 480. The average Ct values were calculated for each sample. The average Ct difference between each sample spiked with alcohol and the unspiked sample was calculated and summarized in Table 57.
The Ct difference between the unspiked and spiked test was used to determine if the tested ETOH amount caused inhibition of the present invention qPCR reactions. Data in Table showed that there is no EHOH interference on the present invention assays with up to 10% ETOH spiked in samples for most present invention targets including APC 1309/1367, APC 1450, BCT 41, BCT 45 and BRAF V600. KRAS 13amplification was inhibited by as little as 2% ETOH (dCT over 2).
There are 8 target mutation detection reactions in the present invention assay. Each target assay was tested against all positive reference material to evaluate the cross-reactivity. Each assay mix was tested with three replicates of the eight individual 1% mutation standards. Some of the reference materials carry more than one target mutations (e.g. the BRAF reference standard from Horizon carries BRAF V600E, BCT 45 and KRAS 13 mutations at 50% frequency, the BCT 45 standard from ATCC also carries KRAS 13 mutation at 50% frequency). ΔCt (Ct Fam−CtHex) was calculated for each standard with all the mutation reactions and summarized in Table 58. Mutational status (Positive or Negative) of each test sample was determined on the basis of the cut-off dCT values (see Table 53).
All target mutations including APC 1309, APC 1367, APC 1450, BCT 41, BCT 45, BRAF V600 were detected as expected by present invention assay, indicating there is no cross-reactivity of the different target detection. KRAS 12 is producing a signal in KRAS13 positive samples, but there is 6 Ct difference between the true KRAS 13 signal and the cross-talk signal from KRAS 12. This pattern can be used to differentiate between true KRAS 12 and KRAS 13 positive samples. Since the kit is to detect KRAS 12 and KRAS 13 mutations but not to differentiate them, the cross-talk will not have impact on the performance of the kit. Therefore, only intended target mutations can be detected by the present invention kit.
Based on the analytical sensitivity studies (section 5.1), 2.5 ng or 5 ng was found to be the minimum DNA input for the present invention kit to detect 1% mutations. To determine the maximum permissible DNA sample input for the present invention qPCR assays, high amounts of wild-type human genomic DNA were tested. Present invention qPCR assays (Fam and Hex) with different WT DNA inputs were performed for all targets in triplicates. The upper LOD was expected to be determined as the lowest DNA input levels producing false positive test results. qPCR with β-actin (Hex) was used to estimate the DNA amount and demonstrate PCR efficiency (
The DNA input amount (control Ct value) between 31≤Ct≤24, was shown to be acceptable for the present invention assay corresponding to 2.5 ng to 320 ng per gDNA per well. ΔCt analysis of different DNA input amounts showed 100% correct calls. No false positive results were observed with up to 320 ng DNA input. Since the recommended DNA input for present invention mutation detection assays is only 5 ng/per reaction, it is unlikely that there will be false positive result due to sample overloading at this level of input.
Two development lots of present invention Kit reagents were used in the reproducibility experiments—DL1 and DL2. Two operators (Qing Sun and Larry Pastor) were testing the kits on two different instruments. The main instrument was LC480 from Roche, the second test instrument was BioRad CFX384. These tests were performed to assess that the product meets requirements set in DDC.0006.
Experiments were performed to evaluate the reproducibility of the present invention assays including intra-assay, inter-assay, lot-to-lot, instrument comparison and operator reproducibility. For intra-assay reproducibility and instrument comparison, 9 replicates of each sample including NTC, WT and PC were tested in one run of each lot on one plate. To assess inter-assay, lot-to-lot and operator reproducibility, 3 replicates of each sample including NTC, WT and PC were tested in one run of each lot for all present invention targets on one plate. The intra-assay and inter-assay reproducibility experiments were repeated on DL2. The mean, SD, % CV value were calculated for each marker or each lot and test sample. The data are summarized in Tables 50 to 66 below.
All target Ct values are FAM signals, Control—from the internal control measured on HEX channel. Control values were calculated as averages for all replicates for each run.
The data on precision testing of present invention kit reagents summarized in Tables 10 to 16 demonstrated that all the present invention assays have good intra-assay, inter-assay, lot-to-lot and operator reproducibility with % CV<10 (Product requirement PR10 met).
All planned tests of the sources of variation that could affect the reproducibility of the present invention assay were tested and results show that the assay is robust and meets product requirements as set in DDC.0007.
7.7 Assay Sensitivity and Specificity with FFPE Samples (Matrix Interference).
DNA from positive reference FFPE (KRAS G12D, Horizon Diagnostics) and negative (WT) FFPE was extracted with the QIAamp DSP DNA FFPE Tissue Kit (Catalog, Qiagen, REF 60604. QIAGEN GmbH, Hilden, Germany) following manufacturer's instructions. To determine the upper FFPE DNA input limit for the present invention assay (the maximum amount of WT DNA that can be tested without producing false positive results), different amounts of WT FFPE DNA (10 and 20 ng/well based on Qubit data) were used in the present invention reactions and tested on LC 480 instrument. Data are summarized in Table 67.
To estimate the assay sensitivity using DNA from FFPE, DNA input was set at 5 ng/well by Qubit data. DNA samples containing KRAS G12D mutation at 2% and 4% allelic frequency were tested and data were summarized in Table 68.
10.11
Test results of different FFPE DNA input indicated that FFPE DNA input up to 20 ng/per well produced no false positive results.
Initial testing on FFPE DNA with 2% and 4% KRAS G12D mutation suggested 2% of KRAS G12D can be detected with 100% accuracy at 5 ng input FFPE DNA level.
All patents, patent applications and publications cited in this application including all cited references in those patents, applications and publications, are hereby incorporated by reference in their entirety for all purposes to the same extent as if each individual patent, patent application or publication were so individually denoted.
Although the foregoing description (Angres) contains many specifics, these should not be construed as limiting the scope of the present invention, but merely as providing illustrations of some of the presently preferred embodiments. Similarly, other embodiments may be devised without departing from the spirit or scope of the present invention. Features from different embodiments may be employed in combination. The scope of the invention is, therefore, indicated and limited only by the appended claims and their legal equivalents rather than by the foregoing description. All additions, deletions and modifications to the invention as disclosed herein which fall within the meaning and scope of the claims are to be embraced thereby.
This application claims the priority benefit under 35 U.S.C. section 119 of U.S. Provisional Patent Application No. 62/442,898 entitled “Method For Conducting Early Detection Of Colon Cancer And/Or Of Colon Cancer Precursor Cells And For Monitoring Colon Cancer Recurrence” filed Jan. 5, 2017, which is in its entirety herein incorporated by reference.
| Number | Date | Country | |
|---|---|---|---|
| 62442898 | Jan 2017 | US |
