Methods and materials for identifying malignant skin lesions

Abstract

This document provides methods and materials for identifying malignant skin lesions (e.g., malignant pigmented skin lesions). For example, methods and materials for using quantitative PCR results and correction protocols to reduce the impact of basal keratinocyte contamination on the analysis of test sample results to identify malignant skin lesions are provided.

Description

STATEMENT ACCORDING TO 37 C.F.R. § 1.821(c) or (e)—REQUEST TO TRANSFER COMPUTER-READABLE FORM OF SEQUENCE LISTING FROM PARENT APPLICATION

Pursuant to 37 C.F.R. § 1.821(c) or (e), the transmittal documents of this application include a Request to Transfer Computer-Readable Form of the Sequence Listing from the parent application, the contents of the Sequence Listing are incorporated herein by this reference.

TECHNICAL FIELD

This document relates to methods and materials for identifying malignant skin lesions (e.g., malignant pigmented skin lesions). For example, this document relates to methods and materials for using quantitative PCR results and correction protocols to reduce the impact of basal keratinocyte contamination on the analysis of test sample results to identify malignant skin lesions.

BACKGROUND

Malignant skin lesions are typically identified by obtaining a skin biopsy and morphologically assessing the biopsy's melanocytes under a microscope. Such a procedure can be difficult to standardize and can lead to overcalling of melanomas.

Once a diagnosis of melanoma is made by morphological assessment, the risk of metastasis is typically determined by the invasion depth of malignant cells into the skin (i.e., the Breslow depth). The Breslow depth can dictate further work-up such as a need for an invasive sentinel lymph node (SLN) procedure. Such procedures, however, can lead to inaccurate determinations of the true malignant potential of a pigmented lesion.

BRIEF SUMMARY

Provided are methods and materials for identifying malignant skin lesions (e.g., malignant pigmented skin lesions). For example, this document provides methods and materials for using quantitative PCR results and correction protocols to reduce the impact of basal keratinocyte contamination on the analysis of test sample results to identify malignant skin lesions.

As described herein, quantitative PCR can be performed using a routine skin biopsy sample (e.g., a paraffin-embedded tissue biopsy) to obtain expression data (e.g., gene copy numbers) for one or more marker genes. Correction protocols can be used to reduce the impact of basal keratinocyte contamination on the analysis of the expression data from the test sample. For example, the contribution of gene expression from basal keratinocytes present within the test skin sample can be determined and removed from the overall gene expression values to determine the final gene expression value for a particular gene as expressed from cells other than basal keratinocytes (e.g., melanocytes). An assessment of the final gene expression values, which include minimal, if any, contribution from basal keratinocytes, for a collection of marker genes can be used to determine the benign or malignant biological behavior of the tested skin lesion.

In general, one aspect hereof features a method for identifying a malignant skin lesion. The method comprises, or consists essentially of, (a) determining, within a test sample, the expression level of a marker gene selected from the group consisting of PLAT, SPP1, TNC, ITGB3, COL4A1, CD44, CSK, THBS1, CTGF, VCAN, FARP1, GDF15, ITGB1, PTK2, PLOD3, ITGA3, IL8, and CXCL1 to obtain a measured expression level of the marker gene for the test sample, (b) determining, within the test sample, the expression level of a keratinocyte marker gene to obtain a measured expression level of the keratinocyte marker gene for the test sample, (c) removing, from the measured expression level of the marker gene for the test sample, a level of expression attributable to keratinocytes present in the test sample using the measured expression level of the keratinocyte marker gene for the test sample and a keratinocyte correction factor to obtain a corrected value of marker gene expression for the test sample, and (d) identifying the test sample as containing a malignant skin lesion based, at least in part, on the corrected value of marker gene expression for the test sample. The keratinocyte marker gene can be K14. The marker gene can be SPP1. The step (c) can comprise (i) multiplying the measured expression level of the keratinocyte marker gene for the test sample by the keratinocyte correction factor to obtain a correction value and (ii) subtracting the correction value from the measured expression level of the marker gene for the test sample to obtain the corrected value of marker gene expression for the test sample.

Unless otherwise defined, all 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 pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flow chart of an exemplary process for determining the gene expression value, which includes minimal, if any, contribution from basal keratinocytes, for a marker gene by cells within a tested sample (e.g., a tested skin biopsy sample).

FIG. 2 is a flow chart of an exemplary process for determining a keratinocyte correction factor for a marker gene of interest.

FIG. 3 is a flow chart of an exemplary process for removing copy number contamination from basal keratinocytes from a copy number value for a marker gene to determine the gene expression value, which includes minimal, if any, contribution from basal keratinocytes, for that marker gene by cells within a tested sample (e.g., a tested skin biopsy sample).

FIG. 4 is a diagram of an example of a generic computer device and a generic mobile computer device that can be used as described herein.

FIG. 5 is a flow chart of an exemplary process for using FN1 and SPP1 expression levels to determine the benign or malignant nature of a skin lesion.

FIG. 6 is a flow chart of an exemplary process for using FN1 and ITGB3 expression levels to determine the benign or malignant nature of a skin lesion.

FIG. 7 is a network diagram.

DETAILED DESCRIPTION

This document provides methods and materials for identifying malignant skin lesions (e.g., malignant pigmented skin lesions). For example, this document provides methods and materials for using quantitative PCR results and correction protocols to reduce the impact of basal keratinocyte contamination on the analysis of test sample results to identify malignant skin lesions.

FIG. 1 shows an exemplary process 100 for determining a gene expression value, which includes minimal, if any, contribution from basal keratinocytes, for a marker gene by cells within a tested sample (e.g., a tested skin biopsy sample). The process begins at box 102, where quantitative PCR using a collection of primer sets and a test sample is used to obtain a Ct value for the target of each primer set. Each gene of interest can be assessed using a single primer set or multiple different primer sets (e.g., two, three, four, five, six, seven, or more different primer sets). In some cases, quantitative PCR is performed using each primer set and control nucleic acid of the target of each primer set (e.g., linearized cDNA fragments) to obtain a standard curve for each primer set as set forth in box 104. In some cases, quantitative PCR is performed using each primer set and a known sample as an internal control (e.g., a stock biological sample) to obtain an internal control value for each primer set as set forth in box 106. This internal control can be used to set values for each primer set across different assays. In some cases, the quantitative PCR performed according to boxes 102, 104, and 106 can be performed in parallel. For example, the quantitative PCR performed according to boxes 102, 104, and 106 can be performed in a single 96 well format.

At box 108, the quality of the obtained standard curves can be confirmed. In some cases, a gene of interest included in the assay format can be a melanocyte marker (e.g., levels of MLANA and/or MITF expression) to confirm the presence of melanocytes in the test sample. Other examples of melanocyte markers that can be used as described herein include, without limitation, TYR, TYRP1, DCT, PMEL, OCA2, MLPH, and MC1R.

At box 110, the raw copy number of each target present in the test sample is determined using the Ct values and the standard curve for each target. In some cases, the averaged, corrected copy number for each gene is calculated using the raw copy number of each target of a particular gene and the internal control value for each primer set (box 112). This averaged, corrected copy number value for each gene can be normalized to a set number of one or more housekeeping genes as set forth in box 114. For example, each averaged, corrected copy number value for each gene can be normalized to 100,000 copies of the combination of ACTB, RPL8, RPLP0, and B2M. Other examples of housekeeping genes that can be used as described herein include, without limitation, RRN18S, GAPD, PGK1, PPIA, RPL13A, YWHAZ, SDHA, TFRC, ALAS1, GUSB, HMBS, HPRT1, TBP, and TUPP. Once normalized, the copy number values for each gene can be referred to as the averaged, corrected, normalized copy number for that gene as present in the test sample.

At box 116, the averaged, corrected, normalized copy number for each gene can be adjusted to remove the copy number contamination from basal keratinocytes present in the test sample. In general, copy number contamination from basal keratinocytes can be removed by (a) determining a keratinocyte correction factor for the gene of interest using one or more keratinocyte markers (e.g., keratin 14 (K14)) and one or more normal skin samples (e.g., FFPE-embedded normal skin samples), (b) determining the averaged, corrected, normalized copy number value for the one or more keratinocyte markers of the test sample and multiplying that value by the keratinocyte correction factor to obtain a correction value for the gene of interest, and (c) subtracting that correction value from the averaged, corrected, normalized copy number value of the gene of interest to obtain the final copy number for the gene of interest. Examples of keratinocyte markers that can be used as described herein include, without limitation, KRT5, KRT1, KRT10, KRT17, ITGB4, ITGA6, PLEC, DST, and COL17A1.

With reference to FIG. 2, process 200 can be used to obtain a keratinocyte correction factor for a gene of interest. At box 202, the averaged, corrected, normalized copy number for one or more genes of interest (e.g., Gene X) and one or more basal keratinocyte marker genes (e.g., K14) are determined using one or more normal skin samples and procedures similar to those described in FIG. 1. As box 204, the keratinocyte correction factor for each gene of interest (e.g., Gene X) is determined by dividing the averaged, corrected, normalized copy number for each gene of interest present in a normal skin sample by the averaged, corrected, normalized copy number of a basal keratinocyte marker gene present in a normal skin sample. Examples of keratinocyte correction factors for particular genes of interest are set forth in Table E under column “AVG per copy K14.”

With reference to FIG. 3, once a keratinocyte correction factor in determined for a particular gene of interest (e.g., Gene X), then the averaged, corrected, normalized copy number for the basal keratinocyte marker gene present in the test sample can be multiplied by the keratinocyte correction factor for the gene of interest (e.g., Gene X) to obtain a correction value for the gene of interest (e.g., Gene X). See, e.g., box 302. At box 304, the correction value for the gene of interest (e.g., Gene X) is subtracted from the averaged, corrected, normalized copy number for the gene of interest (e.g., Gene X) present in the test sample to obtain a final copy number value of the gene of interest (e.g., Gene X) present in the test sample.

FIG. 4 is a diagram of an example of a generic computer device 1400 and a generic mobile computer device 1450, which may be used with the techniques described herein. Computing device 1400 is intended to represent various forms of digital computers, such as laptops, desktops, workstations, personal digital assistants, servers, blade servers, mainframes, and other appropriate computers. Computing device 1450 is intended to represent various forms of mobile devices, such as personal digital assistants, cellular telephones, smart phones, and other similar computing devices. The components shown here, their connections and relationships, and their functions, are meant to be exemplary only, and are not meant to limit implementations of the inventions described and/or claimed in this document.

Computing device 1400 includes a processor 1402, memory 1404, a storage device 1406, a high-speed interface 1408 connecting to memory 1404 and high-speed expansion ports 1410, and a low speed interface 1415 connecting to low speed bus 1414 and storage device 1406. Each of the components 1402, 1404, 1406, 1408, 1410, and 1415, are interconnected using various busses, and may be mounted on a common motherboard or in other manners as appropriate. The processor 1402 can process instructions for execution within the computing device 1400, including instructions stored in the memory 1404 or on the storage device 1406 to display graphical information for a GUI on an external input/output device, such as display 1416 coupled to high speed interface 1408. In other implementations, multiple processors and/or multiple buses may be used, as appropriate, along with multiple memories and types of memory. Also, multiple computing devices 1400 may be connected, with each device providing portions of the necessary operations (e.g., as a server bank, a group of blade servers, or a multi-processor system).

The memory 1404 stores information within the computing device 1400. In one implementation, the memory 1404 is a volatile memory unit or units. In another implementation, the memory 1404 is a non-volatile memory unit or units. The memory 1404 may also be another form of computer-readable medium, such as a magnetic or optical disk.

The storage device 1406 is capable of providing mass storage for the computing device 1400. In one implementation, the storage device 1406 may be or contain a computer-readable medium, such as a floppy disk device, a hard disk device, an optical disk device, or a tape device, a flash memory or other similar solid state memory device, or an array of devices, including devices in a storage area network or other configurations. A computer program product can be tangibly embodied in an information carrier. The computer program product may also contain instructions that, when executed, perform one or more methods, such as those described herein. The information carrier is a computer- or machine-readable medium, such as the memory 1404, the storage device 1406, memory on processor 1402, or a propagated signal.

The high speed controller 1408 manages bandwidth-intensive operations for the computing device 1400, while the low speed controller 1415 manages lower bandwidth-intensive operations. Such allocation of functions is exemplary only. In one implementation, the high-speed controller 1408 is coupled to memory 1404, display 1416 (e.g., through a graphics processor or accelerator), and to high-speed expansion ports 1410, which may accept various expansion cards (not shown). In the implementation, low-speed controller 1415 is coupled to storage device 1406 and low-speed expansion port 1414. The low-speed expansion port, which may include various communication ports (e.g., USB, Bluetooth, Ethernet, or wireless Ethernet) may be coupled to one or more input/output devices, such as a keyboard, a pointing device, a scanner, an optical reader, a fluorescent signal detector, or a networking device such as a switch or router, e.g., through a network adapter.

The computing device 1400 may be implemented in a number of different forms, as shown in FIG. 4. For example, it may be implemented as a standard server 1420, or multiple times in a group of such servers. It may also be implemented as part of a rack server system 1424. In addition, it may be implemented in a personal computer such as a laptop computer 1422. In some cases, components from computing device 1400 may be combined with other components in a mobile device (not shown), such as device 1450. Each of such devices may contain one or more of computing device 1400, 1450, and an entire system may be made up of multiple computing devices 1400, 1450 communicating with each other.

Computing device 1450 includes a processor 1452, memory 1464, an input/output device such as a display 1454, a communication interface 1466, and a transceiver 1468, among other components (e.g., a scanner, an optical reader, a fluorescent signal detector). The device 1450 may also be provided with a storage device, such as a microdrive or other device, to provide additional storage. Each of the components 1450, 1452, 1464, 1454, 1466, and 1468, are interconnected using various buses, and several of the components may be mounted on a common motherboard or in other manners as appropriate.

The processor 1452 can execute instructions within the computing device 1450, including instructions stored in the memory 1464. The processor may be implemented as a chipset of chips that include separate and multiple analog and digital processors. The processor may provide, for example, for coordination of the other components of the device 1450, such as control of user interfaces, applications run by device 1450, and wireless communication by device 1450.

Processor 1452 may communicate with a user through control interface 1458 and display interface 1456 coupled to a display 1454. The display 1454 may be, for example, a TFT LCD (Thin-Film-Transistor Liquid Crystal Display) or an OLED (Organic Light Emitting Diode) display, or other appropriate display technology. The display interface 1456 may comprise appropriate circuitry for driving the display 1454 to present graphical and other information to a user. The control interface 1458 may receive commands from a user and convert them for submission to the processor 1452. In addition, an external interface 1462 may be provide in communication with processor 1452, so as to enable near area communication of device 1450 with other devices. External interface 1462 may provide, for example, for wired communication in some implementations, or for wireless communication in other implementations, and multiple interfaces may also be used.

The memory 1464 stores information within the computing device 1450. The memory 1464 can be implemented as one or more of a computer-readable medium or media, a volatile memory unit or units, or a non-volatile memory unit or units. Expansion memory 1474 may also be provided and connected to device 1450 through expansion interface 1472, which may include, for example, a SIMM (Single In Line Memory Module) card interface. Such expansion memory 1474 may provide extra storage space for device 1450, or may also store applications or other information for device 1450. For example, expansion memory 1474 may include instructions to carry out or supplement the processes described herein, and may include secure information also. Thus, for example, expansion memory 1474 may be provide as a security module for device 1450, and may be programmed with instructions that permit secure use of device 1450. In addition, secure applications may be provided via the SIMM cards, along with additional information, such as placing identifying information on the SIMM card in a non-hackable manner.

The memory may include, for example, flash memory and/or NVRAM memory, as discussed below. In one implementation, a computer program product is tangibly embodied in an information carrier. The computer program product contains instructions that, when executed, perform one or more methods, such as those described herein. The information carrier is a computer- or machine-readable medium, such as the memory 1464, expansion memory 1474, memory on processor 1452, or a propagated signal that may be received, for example, over transceiver 1468 or external interface 1462.

Device 1450 may communicate wirelessly through communication interface 1466, which may include digital signal processing circuitry where necessary. Communication interface 1466 may provide for communications under various modes or protocols, such as GSM voice calls, SMS, EMS, or MMS messaging, CDMA, TDMA, PDC, WCDMA, CDMA2000, or GPRS, among others. Such communication may occur, for example, through radio-frequency transceiver 1468. In addition, short-range communication may occur, such as using a Bluetooth, WiFi, or other such transceiver (not shown). In addition, GPS (Global Positioning System) receiver module 1470 may provide additional navigation- and location-related wireless data to device 1450, which may be used as appropriate by applications running on device 1450.

Device 1450 may also communicate audibly using audio codec 1460, which may receive spoken information from a user and convert it to usable digital information. Audio codec 1460 may likewise generate audible sound for a user, such as through a speaker, e.g., in a handset of device 1450. Such sound may include sound from voice telephone calls, may include recorded sound (e.g., voice messages, music files, etc.) and may also include sound generated by applications operating on device 1450.

The computing device 1450 may be implemented in a number of different forms, as shown in FIG. 4. For example, it may be implemented as a cellular telephone 1480. It may also be implemented as part of a smartphone 1482, personal digital assistant, or other similar mobile device.

Various implementations of the systems and techniques described herein can be realized in digital electronic circuitry, integrated circuitry, specially designed ASICs (application specific integrated circuits), computer hardware, firmware, software, and/or combinations thereof. These various implementations can include implementation in one or more computer programs that are executable and/or interpretable on a programmable system including at least one programmable processor, which may be special or general purpose, coupled to receive data and instructions from, and to transmit data and instructions to, a storage system, at least one input device, and at least one output device.

These computer programs (also known as programs, software, software applications or code) include machine instructions for a programmable processor, and can be implemented in a high-level procedural and/or object-oriented programming language, and/or in assembly/machine language. As used herein, the terms “machine-readable medium” and “computer-readable medium” refer to any computer program product, apparatus and/or device (e.g., magnetic discs, optical disks, memory, and Programmable Logic Devices (PLDs)) used to provide machine instructions and/or data to a programmable processor, including a machine-readable medium that receives machine instructions as a machine-readable signal. The term “machine-readable signal” refers to any signal used to provide machine instructions and/or data to a programmable processor.

To provide for interaction with a user, the systems and techniques described herein can be implemented on a computer having a display device (e.g., a CRT (cathode ray tube) or LCD (liquid crystal display) monitor) for displaying information to the user and a keyboard and a pointing device (e.g., a mouse or a trackball) by which the user can provide input to the computer. Other kinds of devices can be used to provide for interaction with a user as well; for example, feedback provided to the user can be any form of sensory feedback (e.g., visual feedback, auditory feedback, or tactile feedback); and input from the user can be received in any form, including acoustic, speech, or tactile input.

The systems and techniques described herein can be implemented in a computing system that includes a back end component (e.g., as a data server), or that includes a middleware component (e.g., an application server), or that includes a front end component (e.g., a client computer having a graphical user interface or a Web browser through which a user can interact with an implementation of the systems and techniques described herein), or any combination of such back end, middleware, or front end components. The components of the system can be interconnected by any form or medium of digital data communication (e.g., a communication network).

Examples of communication networks include a local area network (“LAN”), a wide area network (“WAN”), and the Internet.

The computing system can include clients and servers. A client and server are generally remote from each other and typically interact through a communication network. The relationship of client and server arises by virtue of computer programs running on the respective computers and having a client-server relationship to each other.

The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES

Example 1—Marker Genes that Discriminate Between Benign and Malignant Tissue

Marker genes were ordered by their ability to differentiate benign from malignant tissue (Table A). This was based on the analysis of 73 benign and 53 malignant tissues, and the hypothesis that changes in expression of fibronectin-associated gene networks are indicative of malignant cell behavior. Values of the test statistic were for the Wilcoxon rank sum test. The values of the test statistic for a Winsorized two-sample test (trimmed outliers were replaced with actual values) and for the chi-square test for the zero vs. >zero versions of each variable were included. The top 5 discriminatory genes based on each statistical test were highlighted in bold.

	TABLE A
	Test statistic value
	Wilcoxon rank	Winsorized two-
gene	sum test	sample t-test	Chi- square test
FN1	−10.2312	−8.04081	106.714
SPP1	−9.0279	−4.9374	86.774
COL4A1	−8.8807	−7.27171	83.711
TNC	−8.7511	−8.31049	75.549
ITGA3	−8.6008	−5.86334	79.788
LOXL3	−8.1978	−6.75327	75.144
AGRN	−8.1243	−7.91238	62.611
VCAN	−8.0812	−6.24088	67.388
PLOD3	−8.0384	−6.89248	62.691
ITGB1	−8.0021	−7.38143	59.973
PTK2	−7.5279	−7.19889	54.446
CTGF	−7.4997	−5.581	57.79
PLOD1	−7.332	−7.36126	44.87
LAMC1	−7.2425	−6.1057	54.233
THBS1	−7.2425	−5.60331	54.233
LOXL2	−7.2241	−6.33208	55.909
IL6	−7.1777	−6.41883	56.966
LOXL1	−7.1279	−6.34431	52.878
IL8	−7.1194	−5.76042	57.296
CYR61	−6.741	−6.97388	43.866
ITGAV	−6.5947	−6.27571	47.021
YAP	−6.4848	−6.36431	42.417
BGN	−6.3419	−6.01066	25.387
LAMB1	−6.3293	−5.68826	37.061
ITGB3	−6.3142	−5.13158	40.835
CXCL1	−6.1077	−5.66564	40.137
THBS2	−6.0427	−5.02003	37.413
COL18A1	−6.0379	−4.9125	41.339
SPARC	−6.0272	−6.39324	38.098
TP53	−6.0182	−6.18554	34.945
PLOD2	−5.9082	−3.50272	47.576
CCL2	−5.8844	−5.38758	30.69
FBLN2	−5.5848	−4.59826	31.913
LAMA1	−5.4876	−4.2817	31.071
THBS4	−5.3971	−3.88786	35.27
COL1A1	−5.325	−4.37617	34.693
ITGA5	−4.9847	−3.56695	25.243
TAZ	−4.036	−3.26011	18.313
POSTN	−3.8054	−2.78378	19.813
LOX	−3.728	−2.8677	17.157
CSRC	−3.7078	−3.71759	13.983
LAMA3	−3.5805	−2.99652	13.391
CDKN1A	−3.5766	−3.20447	17.228
CDKN2A	−3.5491	−2.90903	15.938
ITGA2	−3.4083	−2.72495	11.766
LAMC2	−3.4083	−2.53784	11.766
PCOLCE2	−3.3469	−3.53676	14.449
LOXL4	−3.2079	−2.76128	10.943
PCOLCE	−2.2172	−1.13805	7.993
LAMB3	−1.2822	0.89459	7.028
CSF2	2.175	1.93095	4.522

Example 2—Marker Panel Revision after Statistical Analysis

The candidate gene list from Example 1 was modified to include other FN1 network genes as well as four housekeeping genes (ACTB, RPLP0, RPL8, and B2M), two keratinocyte markers (K10 and K14) to assess keratinocyte contamination, and four melanocyte markers (MITF, TYR, MLANA and PMEL) to assess melanocyte content in the skin sections. Genes from Example 1 with low discriminatory value and a more distant neighborhood to FN1 were excluded from the test setup (LAMC1, LOXL2, CYR61, YAP, BGN, LAMB1, THBS2, COL18A1, SPARC, TP53, PLOD2, CCL2, FBLN2, LAMA1, THBS4, COL1A1, TAZ, POSTN, LOX, CSRC, LAMA3, CDKN1A, CDKN2A, LAMC2, PCOLCE2, LOXL4, PCOLCE, LAMB3, and CSF2). Instead, the discriminatory ability of other FN1 network genes was determined (PLAT, CSK, GDF15, FARP1, ARPC1B, NES, NTRK3, SNX17, L1CAM, and CD44). The following results were based on the analysis of 26 benign nevi and 52 primary cutaneous melanomas with documented subsequent metastasis or skin lesions of melanoma metastasis (Table B). The top 5 genes were highlighted.

TABLE B
	Test Statistic value
	Wilcoxon	Winsorized
gene	rank sum test	two-sample t-test	Chi-square test
COL4A1	−5.85975	−5.42545	46.3273
FN1	−5.50862	−3.63639	35.1951
PLAT	−4.82670	−3.13568	25.7234
IL8	−4.61443	−4.41668	28.6000
SPP1	−4.60153	−3.08137	23.0816
PLOD3	−4.37001	−3.91553	18.8036
TNC	−4.26431	−3.14128	19.5000
CXCL1	−4.24452	−3.76681	20.6471
CSK	−4.15178	−2.96444	18.3962
GDF15	−4.01364	−2.99752	13.7083
ITGB3	−3.92608	−2.80068	16.3091
CCL2	−3.61870	−3.45423	17.5176
VCAN	−3.46906	−2.26781	12.5593
ITGB1	−3.40897	−3.63399	5.0221
PLOD1	−3.40380	−3.20309	9.2625
CTGF	−3.11725	−2.20507	10.0645
THBS1	−3.11721	−2.01257	10.0645
ITGA3	−3.04915	−2.65398	7.5341
FARP1	−2.99724	−2.28024	9.2857
AGRN	−2.92104	−3.30679	1.8838
IL6	−2.85960	−3.05600	10.6257
LOXL3	−2.84999	−2.70498	5.1096
LOXL1	−2.69957	−2.11477	8.1250
ARPC1B	−2.57571	−2.82320	All but 1 value > 0
NES	−2.45264	−2.70056	2.4375
PTK2	−2.22328	−2.26180	4.4057
ITGA2	−2.08353	−1.50078	4.4571
ITGA5	−1.93478	−1.39663	3.8451
ITGAV	−1.29341	−0.81964	3.5615
NTRK3	−1.22485	75 of the 78 values are = 0
MITF	0.58305	0.73916	0.4274
SNX17	0.74754	0.90733	0.0785
L1CAM	1.61125	0.27151	2.1081
MLANA	2.96258	2.92548	All values > 0
CD44	5.23089	7.17590	All but 1 value > 0

Based on the results of Example 1 and above, FN1 was identified as a component of the melanoma phenotype that is at the core of a gene network that discriminates between benign and malignant melanocytic skin lesions (FIG. 7). The modeling was based on the STRING 9.0 database (string-db.org).

The list of all 71 genes tested is provided in Table 1.

TABLE 1
List of genes used to discriminate benign skin tissue lesions from
malignant skin tissue lesions.
Gene Name	GenBank ® Accession No.	GenBank ® GI No.
FN1	NM_212482	47132556
	NM_002026	47132558
	NM_212474	47132548
	NM_212476	47132552
	NM_212478	47132554
	NM_054034	47132546
SPP1	NM_001040058	91206461
	NM_001040060	91598938
	NM_000582	38146097
COL4A1	NM_001845	148536824
TNC	NM_002160	340745336
ITGA3	NM_005501	171846264
	NM_002204	171846266
LOXL3	NM_032603	22095373
AGRN	NM_198576	344179122
VCAN	NM_004385	255918074
	NM_001164098	255918078
	NM_001164097	255918076
PLOD3	NM_001084	62739167
ITGB1	NM_002211	182519230
	NM_133376	182507162
	NM_033668	182507160
PTK2	NM_001199649	313851043
	NM_005607	313851042
	NM_153831	313851041
CTGF	NM_001901	98986335
PLOD1	NM_000302	324710986
LAMC1	NM_002293	145309325
THBS1	NM_003246	40317625
LOXL2	NM_002318	67782347
IL6	NM_000600	224831235
LOXL1	NM_005576	67782345
IL8	NM_000584	324073503
CYR61	NM_001554	197313774
ITGAV	NM_001144999	223468594
	NM_001145000	223468596
	NM_002210	223468593
YAP	NM_001130145	303523503
	NM_001195045	303523626
	NM_006106	303523510
	NM_001195044	303523609
BGN	NM_001711	268607602
LAMB1	NM_002291	167614503
ITGB3	NM_000212	47078291
CXCL1	NM_001511	373432598
THBS2	NM_003247	40317627
COL18A1	NM_030582	110611234
	NM_130445	110611232
SPARC	NM_003118	365777426
TP53	NM_000546	371502114
	NM_001126112	371502115
	NM_001126114	371502117
	NM_001126113	371502116
PLOD2	NM_182943	62739164
	NM_000935	62739165
CCL2	NM_002982	56119169
FBLN2	NM_001998	51873054
	NM_001004019	51873052
	NM_001165035	259013546
LAMA1	NM_005559	329112585
THBS4	NM_003248	291167798
COL1A1	NM_000088	110349771
ITGA5	NM_002205	56237028
TAZ	NM_000116	195232764
	NM_181311	195232766
	NM_181312	195232765
	NM_181313	195232767
POSTN	NM_001135934	209862910
	NM_006475	209862906
	NM_001135935	209863010
LOX	NM_001178102	296010939
	NM_002317	296010938
CSRC	NM_005417	38202215
	NM_198291	38202216
LAMA3	NM_198129	38045909
	NM_001127717	189217424
CDKN1A	NM_000389	310832422
	NM_001220777	334085239
	NM_078467	310832423
	NM_001220778	334085241
CDKN2A	NM_000077	300863097
	NM_058195	300863095
	NM_001195132	304376271
ITGA2	NM_002203	116295257
LAMC2	NM_005562	157419137
	NM_018891	157419139
PCOLCE2	NM_013363	296317252
LOXL4	NM_032211	67782348
PCOLCE	NM_002593	157653328
LAMB3	NM_000228	62868214
	NM_001017402	62868216
	NM_001127641	189083718
CSF2	NM_000758	371502128
ACTB	NM_001101	168480144
RPLP0	NM_053275	49087137
	NM_001002	49087144
RPL8	NM_000973	72377361
	NM_033301	15431305
B2M	NM_004048	37704380
K10	NM_000421	195972865
K14	NM_000526	197313720
MITF	NM_198158	296841082
	NM_198177	296841080
	NM_006722	296841079
	NM_198159	296841078
	NM_000248	296841081
	NM_001184967	296841084
	NM_198178	296923803
TYR	NM_000372	113722118
MLANA	NM_005511	5031912
PMEL	NM_001200054	318037594
	NM_001200053	318037592
	NM_006928	318068057
NES	NM_006617	38176299
L1CAM	NM_024003	221316758
	NM_001143963	221316759
	NM_000425	221316755
GDF15	NM_004864	153792494
ARPC1B	NM_005720	325197176
FARP1	NM_005766	48928036
	NM_001001715	159032536
NTRK3	NM_001007156	340745351
	NM_001012338	340745349
	NM_001243101	340745352
	NM_002530	340745350
CSK	NM_001127190	187475372
	NM_004383	187475371
CD44	NM_001001391	48255940
	NM_001001392	48255942
	NM_001202556	321400139
	NM_001001389	48255936
	NM_000610	48255934
	NM_001001390	48255938
	NM_001202555	321400137
	NM_001202557	321400141
SNX17	NM_014748	388596703
PLAT	NM_000930	132626665
	NM_033011	132626641

Gene expression of target genes was assessed by SYBR/EVA-Green based RT-PCR. All tested genes were accompanied by a standard curve for quantification of absolute copy number per a defined number of housekeeping genes. mRNA extraction from paraffin-embedded biospecimen was performed using an extraction protocol (Qiagen RNA FFPE extraction kit) and an extraction robot (Qiacube from Qiagen). mRNA was transcribed into cDNA using a commercially available kit (iScript kit from BioRad), and Fluidigm technology was used for PCR cycling.

The primer design was performed using web-based open access software. The primers were HPLC purified to minimize background and were optimized for formalin-fixed, paraffin-embedded (FFPE) tissue (i.e., highly degraded tissue). The primers were designed to detect a maximum number of gene transcripts and were designed to be cDNA specific (i.e., not affected by genomic DNA contamination of the total, tissue-derived cDNA). The housekeeping genes, keratin genes, melanocyte-specific genes, and selected high interest genes were detected using four separate and individually designed primer pairs. The primer pairs are set forth in Table 2.

TABLE 2
Primer sets for indicated genes.
Gene Name	Forward primer	Reverse primer
ACTB	5′-GCCAACCGCGAGAAGATG-3′;	5′-GGCTGGGGTGTTGAAGGT-3′;
	SEQ ID NO: 1	SEQ ID NO: 2
	5′-CGCGAGAAGATGACCCAGAT-3′;	5′-GGGGTGTTGAAGGTCTCAAA-3′;
	SEQ ID NO: 3	SEQ ID NO: 4
	5′-TGACCCAGATCATGTTTGAGA-3′;	5′-GTACATGGCTGGGGTGTTG-3′;
	SEQ ID NO: 5	SEQ ID NO: 6
	5′-CTGAACCCCAAGGCCAAC-3′;	5′-TGATCTGGGTCATCTTCTCG-3′;
	SEQ ID NO: 7	SEQ ID NO: 8
RPLP0	5′-AACTCTGCATTCTCGCTTCC-3′;	5′-GCAGACAGACACTGGCAACA-3′;
	SEQ ID NO: 9	SEQ ID NO: 10
	5′-GCACCATTGAAATCCTGAGTG-3′;	5′-GCTCCCACTTTGTCTCCAGT-3′;
	SEQ ID NO: 11	SEQ ID NO: 12
	5′-TCACAGAGGAAACTCTGCATTC-3′;	5′-GGACACCCTCCAGGAAGC-3′;
	SEQ ID NO: 13	SEQ ID NO: 14
	5′-ATCTCCAGGGGCACCATT-3′;	5′-AGCTGCACATCACTCAGGATT-3′;
	SEQ ID NO: 15	SEQ ID NO: 16
RPL8	5′-ACTGCTGGCCACGAGTACG-3′;	5′-ATGCTCCACAGGATTCATGG-3′;
	SEQ ID NO: 17	SEQ ID NO: 18
	5′-ACAGAGCTGTGGTTGGTGTG-3′;	5′-TTGTCAATTCGGCCACCT-3′;
	SEQ ID NO: 19	SEQ ID NO: 20
	5′-TATCTCCTCAGCCAACAGAGC-3′;	5′-AGCCACCACACCAACCAC-3′;
	SEQ ID NO: 21	SEQ ID NO: 22
	5′-GTGTGGCCATGAATCCTGT-3′;	5′-CCACCTCCAAAAGGATGCTC-3′;
	SEQ ID NO: 23	SEQ ID NO: 24
B2M	5′-TCTCTCTTTCTGGCCTGGAG-3′;	5′-GAATCTTTGGAGTACGCTGGA-3′;
	SEQ ID NO: 25	SEQ ID NO: 26
	5′-TGGAGGCTATCCAGCGTACT-3′;	5′-CGTGAGTAAACCTGAATCTTTGG-3′;
	SEQ ID NO: 27	SEQ ID NO: 28
	5′-CCAGCGTACTCCAAAGATTCA-3′;	5′-TCTCTGCTGGATGACGTGAG-3′;
	SEQ ID NO: 29	SEQ ID NO: 30
	5′-GGCTATCCAGCGTACTCCAA-3′;	5′-GCTGGATGACGTGAGTAAACC-3′;
	SEQ ID NO: 31	SEQ ID NO: 32
KRT14	5′-ACCATTGAGGACCTGAGGAA-3′;	5′-GTCCACTGTGGCTGTGAGAA-3′;
	SEQ ID NO: 33	SEQ ID NO: 34
	5′-CATTGAGGACCTGAGGAACA-3′;	5′-AATCTGCAGAAGGACATTGG-3′;
	SEQ ID NO: 35	SEQ ID NO: 36
	5′-GATGACTTCCGCACCAAGTA-3′;	5′-CGCAGGTTCAACTCTGTCTC-3′;
	SEQ ID NO: 37	SEQ ID NO: 38
	5′-TCCGCACCAAGTATGAGACA-3′;	5′-ACTCATGCGCAGGTTCAACT-3′;
	SEQ ID NO: 39	SEQ ID NO: 40
KRT10	5′-GAGCCTCGTGACTACAGCAA-3′;	5′-GCAGGATGTTGGCATTATCAGT-3′;
	SEQ ID NO: 41	SEQ ID NO: 42
	5′-AAAACCATCGATGACCTTAAAAA-3′;	5′-GATCTGAAGCAGGATGTTGG-3′;
	SEQ ID NO: 43	SEQ ID NO: 44
MITF	5′-TTCCCAAGTCAAATGATCCAG-3′;	5′-AAGATGGTTCCCTTGTTCCA-3′;
	SEQ ID NO: 45	SEQ ID NO: 46
	5′-CGGCATTTGTTGCTCAGAAT-3′;	5′-GAGCCTGCATTTCAAGTTCC-3′;
	SEQ ID NO: 47	SEQ ID NO: 48
TYR	5′-TTCCTTCTTCACCATGCATTT-3′;	5′-GGAGCCACTGCTCAAAAATA-3′;
	SEQ ID NO: 49	SEQ ID NO: 50
	5′-TCCAAAGATCTGGGCTATGA-3′;	5′-TTGAAAAGAGTCTGGGTCTGAA-3′;
	SEQ ID NO: 51	SEQ ID NO: 52
MLANA	5′-GAGAAAAACTGTGAACCTGTGG-3′;	5′-ATAAGCAGGTGGAGCATTGG-3′;
	SEQ ID NO: 53	SEQ ID NO: 54
	5′-GAAGACGAAATGGATACAGAGC-3′;	5′-GTGCCAACATGAAGACTTTTATC-3′;
	SEQ ID NO: 55	SEQ ID NO: 56
PMEL	5′-GTGGTCAGCACCCAGCTTAT-3′;	5′-CCAAGGCCTGCTTCTTGAC-3′;
	SEQ ID NO: 57	SEQ ID NO: 58
	5′-GCTGTGGTCCTTGCATCTCT-3′;	5′-GCTTCATAAGTCTGCGCCTA-3′;
	SEQ ID NO: 59	SEQ ID NO: 60
FN1	5′-CTCCTGCACATGCTTTGGA-3′;	5′-AGGTCTGCGGCAGTTGTC-3′;
	SEQ ID NO: 61	SEQ ID NO: 62
	5′-AGGCTTTGGAAGTGGTCATT-3′;	5′-CCATTGTCATGGCACCATCT-3′;
	SEQ ID NO: 63	SEQ ID NO: 64
	5′-GAAGTGGTCATTTCAGATGTGATT-3′;	5′-CCATTGTCATGGCACCATCT-3′;
	SEQ ID NO: 65	SEQ ID NO: 66
	5′-TGGTCATTTCAGATGTGATTCAT-3′;	5′-CATTGTCATGGCACCATCTA-3′;
	SEQ ID NO: 67	SEQ ID NO: 68
SPP1	5′-GTTTCGCAGACCTGACATCC-3′;	5′-TCCTCGTCTGTAGCATCAGG-3′;
	SEQ ID NO: 69	SEQ ID NO: 70
	5′-CCTGACATCCAGTACCCTGA-3′;	5′-TGAGGTGATGTCCTCGTCTG-3′;
	SEQ ID NO: 71	SEQ ID NO: 72
	5′-GAATCTCCTAGCCCCACAGA-3′;	5′-GGTTTCTTCAGAGGACACAGC-3′;
	SEQ ID NO: 73	SEQ ID NO: 74
	5′-CCCATCTCAGAAGCAGAATCTC-3′;	5′-ACAGCATTCTGTGGGGCTA-3′;
	SEQ ID NO: 75	SEQ ID NO: 76
COL4A1	5′-GGAAAACCAGGACCCAGAG-3′;	5′-CTTTTTCCCCTTTGTCACCA-3′;
	SEQ ID NO: 77	SEQ ID NO: 78
	5′-AGAAAGGTGAACCCGGAAAA-3′;	5′-GGTTTGCCTCTGGGTCCT-3′;
	SEQ ID NO: 79	SEQ ID NO: 80
	5′-GAGAAAAGGGCCAAAAAGGT-3′;	5′-CATCCCCTGAAATCCAGGTT-3′;
	SEQ ID NO: 81	SEQ ID NO: 82
	5′-AAAGGGCCAAAAAGGTGAAC-3′;	5′-CCTGGCATCCCCTGAAAT-3′;
	SEQ ID NO: 83	SEQ ID NO: 84
TNC	5′-GTGTCAACCTGATGGGGAGA-3′;	5′-GTTAACGCCCTGACTGTGGT-3′;
	SEQ ID NO: 85	SEQ ID NO: 86
	5′-GGTACAGTGGGACAGCAGGT-3′;	5′-GATCTGCCATTGTGGTAGGC-3′;
	SEQ ID NO: 87	SEQ ID NO: 88
	5′-AACCACAGTCAGGGCGTTA-3′;	5′-GTTCGTGGCCCTTCCAGT-3′;
	SEQ ID NO: 89	SEQ ID NO: 90
	5′-AAGCTGAAGGTGGAGGGGTA-3′;	5′-GAGTCACCTGCTGTCCCACT-3′;
	SEQ ID NO: 91	SEQ ID NO: 92
ITGA3	5′-TATTCCTCCGAACCAGCATC-3′;	5′-CACCAGCTCCGAGTCAATGT-3′;
	SEQ ID NO: 93	SEQ ID NO: 94
	5′-CCACCATCAACATGGAGAAC-3′;	5′-AGTCAATGTCCACAGAGAACCA-3′;
	SEQ ID NO: 95	SEQ ID NO: 96
LOXL3	5′-CAACTGCCACATTGGTGATG-3′;	5′-AAACCTCCTGTTGGCCTCTT-3′;
	SEQ ID NO: 97	SEQ ID NO: 98
	5′-TGACATCACGGATGTGAAGC-3′;	5′-GGGTTGATGACAACCTGGAG-3′;
	SEQ ID NO: 99	SEQ ID NO: 100
AGRN	5′-TGTGACCGAGAGCGAGAAG-3′;	5′-CAGGCTCAGTTCAAAGTGGTT-3′;
	SEQ ID NO: 101	SEQ ID NO: 102
	5′-CGGACCTTTGTCGAGTACCT-3′;	5′-GTTGCTCTGCAGTGCCTTCT-3′;
	SEQ ID NO: 103	SEQ ID NO: 104
VCAN	5′-GACTTCCGTTGGACTGATGG-3′;	5′-TGGTTGGGTCTCCAATTCTC-3′;
	SEQ ID NO: 105	SEQ ID NO: 106
	5′-ACGTGCAAGAAAGGAACAGT-3′;	5′-TCCAAAGGTCTTGGCATTTT-3′;
	SEQ ID NO: 107	SEQ ID NO: 108
PLOD3	5′-GCAGAGATGGAGCACTACGG-3′;	5′-CAGCCTTGAATCCTCATGC-3′;
	SEQ ID NO: 109	SEQ ID NO: 110
	5′-GGAAGGAATCGTGGAGCAG-3′;	5′-CAGCAGTGGGAACCAGTACA-3′;
	SEQ ID NO: 111	SEQ ID NO: 112
ITGB1	5′-CTGATGAATGAAATGAGGAGGA-3′;	5′-CACAAATGAGCCAAATCCAA-3′;
	SEQ ID NO: 113	SEQ ID NO: 114
	5′-CAGTTTGCTGTGTGTTTGCTC-3′;	5′-CATGATTTGGCATTTGCTTTT-3′;
	SEQ ID NO: 115	SEQ ID NO: 116
PTK2	5′-GCCCCACCAGAGGAGTATGT-3′;	5′-AAGCCGACTTCCTTCACCA-3′;
	SEQ ID NO: 117	SEQ ID NO: 118
	5′-GAGACCATTCCCCTCCTACC-3′;	5′-GCTTCTGTGCCATCTCAATCT-3′;
	SEQ ID NO: 119	SEQ ID NO: 120
CTGF	5′-CGAAGCTGACCTGGAAGAGA-3′;	5′-TGGGAGTACGGATGCACTTT-3′;
	SEQ ID NO: 121	SEQ ID NO: 122
	5′-GTGTGCACCGCCAAAGAT-3′;	5′-CGTACCACCGAAGATGCAG-3′;
	SEQ ID NO: 123	SEQ ID NO: 124
PLOD1	5′-CTACCCCGGCTACTACACCA-3′;	5′-GACAAAGGCCAGGTCAAACT-3′;
	SEQ ID NO: 125	SEQ ID NO: 126
	5′-AGTCGGGGTGGATTACGAG-3′;	5′-ACAGTTGTAGCGCAGGAACC-3′;
	SEQ ID NO: 127	SEQ ID NO: 128
LAMC1	5′-ATGATGATGGCAGGGATGG-3′;	5′-GCATTGATCTCGGCTTCTTG-3′;
	SEQ ID NO: 129	SEQ ID NO: 130
THBS1	5′-CTGTGGCACACAGGAAACAC-3′;	5′-ACGAGGGTCATGCCACAG-3′;
	SEQ ID NO: 131	SEQ ID NO: 132
	5′-GCCAAAGACGGGTTTCATTA-3′;	5′-GCCATGATTTTCTTCCCTTC-3′;
	SEQ ID NO: 133	SEQ ID NO: 134
LOXL2	5′-CTCCTCCTACGGCAAGGGA-3′;	5′-TGGAGATTGTCTAACCAGATGGG-3′;
	SEQ ID NO: 135	SEQ ID NO: 136
	5′-CTCCTACGGCAAGGGAGAAG-3′;	5′-TTGCCAGTACAGTGGAGATTG-3′;
	SEQ ID NO: 137	SEQ ID NO: 138
IL6	5′-CCAGAGCTGTCAGATGAGT-3′;	5′-TGCATCTAGATTCTTTGCCTTTT-3′;
	SEQ ID NO: 139	SEQ ID NO: 140
LOXL1	5′-AGGGCACAGCAGACTTCCT-3′;	5′-TCGTCCATGCTGTGGTAATG-3′;
	SEQ ID NO: 141	SEQ ID NO: 142
	5′-GCATGCACCTCTCATACCC-3′;	5′-CGCATTGTAGGTGTCATAGCA-3′;
	SEQ ID NO: 143	SEQ ID NO: 144
IL8	5′-CTTGGCAGCCTTCCTGATT-3′;	5′-GCAAAACTGCACCTTCACAC-3′;
	SEQ ID NO: 145	SEQ ID NO: 146
CYR61	5′-CGCTCTGAAGGGGATCTG-3′;	5′-ACAGGGTCTGCCCTCTGACT-3′;
	SEQ ID NO: 147	SEQ ID NO: 148
	5′-GAGCTCAGTCAGAGGGCAGA-3′;	5′-AACTTTCCCCGTTTTGGTAGA-3′;
	SEQ ID NO: 149	SEQ ID NO: 150
ITGAV	5′-GACCTTGGAAACCCAATGAA-3′;	5′-TCCATCTCTGACTGCTGGTG-3′;
	SEQ ID NO: 147	SEQ ID NO: 148
	5′-GGTGGTATGTGACCTTGGAAA-3′;	5′-GCACACTGAAACGAAGACCA-3′;
	SEQ ID NO: 149	SEQ ID NO: 150
YAP	5′-TGAACAGTGTGGATGAGATGG-3′;	5′-GCAGGGTGCTTTGGTTGATA-3′;
	SEQ ID NO: 151	SEQ ID NO: 152
BGN	5′-AAGGGTCTCCAGCACCTCTAC-3′;	5′-AAGGCCTTCTCATGGATCTT-3′;
	SEQ ID NO: 153	SEQ ID NO: 154
	5′-GAGCTCCGCAAGGATGACT-3′;	5′-AGGACGAGGGCGTAGAGGT-3′;
	SEQ ID NO: 155	SEQ ID NO: 156
LAMB1	5′-CATTCAAGGAACCCAGAACC-3′;	5′-GCGTTGAACAAGGTTTCCTC-3′;
	SEQ ID NO: 157	SEQ ID NO: 158
ITBG3	5′-AAGAGCCAGAGTGTCCCAAG-3′;	5′-ACTGAGAGCAGGACCACCA-3′;
	SEQ ID NO: 159	SEQ ID NO: 160
	5′-CTTCTCCTGTGTCCGCTACAA-3′;	5′-CATGGCCTGAGCACATCTC-3′;
	SEQ ID NO: 161	SEQ ID NO: 162
	5′-TGCCTGCACCTTTAAGAAAGA-3′;	5′-CCGGTCAAACTTCTTACACTCC-3′;
	SEQ ID NO: 163	SEQ ID NO: 164
	5′-AAGGGGGAGATGTGCTCAG-3′;	5′-CAGTCCCCACAGCTGCAC-3′;
	SEQ ID NO: 165	SEQ ID NO: 166
CXCL1	5′-AAACCGAAGTCATAGCCACAC-3′;	5′-AAGCTTTCCGCCCATTCTT-3′;
	SEQ ID NO: 167	SEQ ID NO: 168
THBS2	5′-AGGCCCAAGACTGGCTACAT-3′;	5′-CTGCCATGACCTGTTTTCCT-3′;
	SEQ ID NO: 169	SEQ ID NO: 170
	5′-GGCAGGTGCGAACCTTATG-3′;	5′-CCTTCCAGCCAATGTTCCT-3′;
	SEQ ID NO: 171	SEQ ID NO: 172
COL18A1	5′-GATCGCTGAGCTGAAGGTG-3′;	5′-CGGATGCCCCATCTGAGT-3′;
	SEQ ID NO: 173	SEQ ID NO: 174
SPARC	5′-CCCATTGGCGAGTTTGAGAAG-3′;	5′-AGGAAGAGTCGAAGGTCTTGTT-3′;
	SEQ ID NO: 175	SEQ ID NO: 176
	5′-GGAAGAAACTGTGGCAGAGG-3′;	5′-GGACAGGATTAGCTCCCACA-3′;
	SEQ ID NO: 177	SEQ ID NO: 178
TP53	5′-ACAACGTTCTGTCCCCCTTG-3′;	5′-GGGGACAGCATCAAATCATC-3′;
	SEQ ID NO: 179	SEQ ID NO: 180
PLOD2	5′-TGGATGCAGATGTTGTTTTGA-3′;	5′-CACAGCTTTCCATGACGAGTT-3′;
	SEQ ID NO: 181	SEQ ID NO: 182
	5′-TTGATTGAACAAAACAGAAAGATCA-3′;	5′-TGACGAGTTACAAGAGGAGCAA-3′;
	SEQ ID NO: 183	SEQ ID NO: 184
CCL2	5′-CTGCTCATAGCAGCCACCTT-3′;	5′-AGGTGACTGGGGCATTGATT-3′;
	SEQ ID NO: 185	SEQ ID NO: 186
FBLN2	5′-ACGTGGAGGAGGACACAGAC-3′;	5′-GGAGCCTTCAGGGCTACTTC-3′;
	SEQ ID NO: 187	SEQ ID NO: 188
LAMA1	5′-AGCACTGCCAAAGTGGATG-3′;	5′-TTGTTGACATGGAACAAGACC-3′;
	SEQ ID NO: 189	SEQ ID NO: 190
THBS4	5′-GTGGGCTACATCAGGGTACG-3′;	5′-CAGAGTCAGCCACCAACTCA-3′;
	SEQ ID NO: 191	SEQ ID NO: 192
	5′-CATCATCTGGTCCAACCTCA-3′;	5′-GTCCTCAGGGATGGTGTCAT-3′;
	SEQ ID NO: 193	SEQ ID NO: 194
COL1A1	5′-TGACCTCAAGATGTGCCACT-3′;	5′-TGGTTGGGGTCAATCCAGTA-3′;
	SEQ ID NO: 195	SEQ ID NO: 196
	5′-GATGGATTCCAGTTCGAGTATG-3′;	5′-ATCAGGCGCAGGAAGGTC-3′;
	SEQ ID NO: 197	SEQ ID NO: 198
ITGA5	5′-CCCAAAAAGAGCGTCAGGT-3′;	5′-TTGTTGACATGGAACAAGACC-3′;
	SEQ ID NO: 199	SEQ ID NO: 200
TAZ	5′-CTTCCTAACAGTCCGCCCTA-3′;	5′-CCCGATCAGCACAGTGATTT-3′;
	SEQ ID NO: 201	SEQ ID NO: 202
POSTN	5′-CTGCTTCAGGGAGACACACC-3′;	5′-TGGCTTGCAACTTCCTCAC-3′;
	SEQ ID NO: 203	SEQ ID NO: 204
	5′-AGGAAGTTGCAAGCCAACAA-3′;	5′-CGACCTTCCCTTAATCGTCTT-3′;
	SEQ ID NO: 205	SEQ ID NO: 206
LOX	5′-GCGGAGGAAAACTGTCTGG-3′;	5′-AAATCTGAGCAGCACCCTGT-3′;
	SEQ ID NO: 207	SEQ ID NO: 208
	5′-ATATTCCTGGGAATGGCACA-3′;	5′-CCATACTGTGGTAATGTTGATGA-3′;
	SEQ ID NO: 209	SEQ ID NO: 210
CSRC	5′-TGTCAACAACACAGAGGGAGA-3′;	5′-CACGTAGTTGCTGGGGATGT-3′;
	SEQ ID NO: 211	SEQ ID NO: 212
	5′-TGGCAAGATCACCAGACGG-3′;	5′-GGCACCTTTCGTGGTCTCAC-3′;
	SEQ ID NO: 213	SEQ ID NO: 214
LAMA3	5′-CATGTCGTCTTGGCTCACTC-3′;	5′-AAATTCTGGCCCCAACAATAC-3′;
	SEQ ID NO: 215	SEQ ID NO: 216
CDKN1A	5′-CATGTCGTCTTGGCTCACTC-3′;	5′-AAATTCTGGCCCCAACAATAC-3′;
	SEQ ID NO: 217	SEQ ID NO: 218
CDKN2A	5′-AGGAGCCAGCGTCTAGGG-3′;	5′-CTGCCCATCATCATGACCT-3′;
	SEQ ID NO: 219	SEQ ID NO: 220
	5′-AACGCACCGAATAGTTACGG-3′;	5′-CATCATCATGACCTGGATCG-3′;
	SEQ ID NO: 221	SEQ ID NO: 222
ITGA2	5′-CACTGTTACGATTCCCCTGA-3′;	5′-CGGCTTTCTCATCAGGTTTC-3′;
	SEQ ID NO: 223	SEQ ID NO: 224
LAMC2	5′-ATTAGACGGCCTCCTGCATC-3′;	5′-AGACCAGCCCCTCTTCATCT-3′;
	SEQ ID NO: 225	SEQ ID NO: 226
PCOLCE2	5′-TACTTGGAAAATCACAGTTCCCG-3′;	5′-TGAATCGGAAATTGAGAACGACT-3′;
	SEQ ID NO: 225	SEQ ID NO: 226
LOXL4	5′-GGCCCCGGGAATTATATCT-3′;	5′-CCACTTCATAGTGGGGGTTC-3′;
	SEQ ID NO: 227	SEQ ID NO: 228
	5′-CTGCACAACTGCCACACAG-3′;	5′-GTTCTGCATTGGCTGGGTAT-3′;
	SEQ ID NO: 229	SEQ ID NO: 230
PCOLCE	5′-CGTGGCAAGTGAGGGGTTC-3′;	5′-CGAAGACTCGGAATGAGAGGG-3′;
	SEQ ID NO: 231	SEQ ID NO: 232
	5′-GAGGCTTCCTGCTCTGGT-3′;	5′-CGCAAAATTGGTGCTCAGT-3′;
	SEQ ID NO: 233	SEQ ID NO: 234
LAMB3	5′-GTCCGGGACTTCCTAACAGA-3′;	5′-GCTGACCTCCTGGATAGTGTG-3′;
	SEQ ID NO: 235	SEQ ID NO: 236
PMEL	5′-GTGGTCAGCACCCAGCTTAT-3′;	5′-CCAAGGCCTGCTTCTTGAC-3′;
	SEQ ID NO: 237	SEQ ID NO: 238
	5′-GCTGTGGTCCTTGCATCTCT-3′;	5′-GCTTCATAAGTCTGCGCCTA-3′;
	SEQ ID NO: 239	SEQ ID NO: 240
NES	5′-CTTCCCTCAGCTTTCAGGAC-3′;	5′-TCTGGGGTCCTAGGGAATTG-3′;
	SEQ ID NO: 241	SEQ ID NO: 242
	5′-ACCTCAAGATGTCCCTCAGC-3′;	5′-CAGGAGGGTCCTGTACGTG-3′;
	SEQ ID NO: 243	SEQ ID NO: 244
L1CAM	5′-GAGACCTTCGGCGAGTCACAG-3′;	5′-AAAGGCCTTCTCCTCGTTGT-3′;
	SEQ ID NO: 245	SEQ ID NO: 246
	5′-GGCGGCAAATACTCAGTGAA-3′;	5′-CCTGGGTGTCCTCCTTATCC-3′;
	SEQ ID NO: 247	SEQ ID NO: 248
GDF15	5′-CGGATACTCACGCCAGAAGT-3′;	5′-AGAGATACGCAGGTGCAGGT-3′;
	SEQ ID NO: 249	SEQ ID NO: 250
	5′-AAGATTCGAACACCGACCTC-3′;	5′-GCACTTCTGGCGTGAGTATC-3′;
	SEQ ID NO: 251	SEQ ID NO: 252
ARPC1B	5′-CACGCCTGGAACAAGGAC-3′;	5′-ATGCACCTCATGGTTGTTGG-3′;
	SEQ ID NO: 253	SEQ ID NO: 254
	5′-CAGGTGACAGGCATCGACT-3′;	5′-CGCAGGTCACAATACGGTTA-3′;
	SEQ ID NO: 255	SEQ ID NO: 256
FARP1	5′-TGAGGCCCTGAGAGAGAAGA-3′;	5′-ATTCCGAAACTCCACACGTC-3′;
	SEQ ID NO: 257	SEQ ID NO: 258
	5′-TCAAGGAAATTGAGCAACGA-3′;	5′-TCTGATTTGGGCATTTGAGC-3′;
	SEQ ID NO: 259	SEQ ID NO: 260
NTRK3	5′-TATGGTCGACGGTCCAAAT-3′;	5′-TCCTCACCACTGATGACAGC-3′;
	SEQ ID NO: 261	SEQ ID NO: 262
	5′-CACTGTGACCCACAAACCAG-3′;	5′-GCAAGTCCAACTGCTATGGA-3′;
	SEQ ID NO: 263	SEQ ID NO: 264
CSK	5′-TGAGGCCCTGAGAGAGAAGA-3′;	5′-ATTCCGAAACTCCACACGTC-3′;
	SEQ ID NO: 265	SEQ ID NO: 266
	5′-TCTACTCCTTTGGGCGAGTG-3′;	5′-CGTCCTTCAGGGGAATTCTT-3′;
	SEQ ID NO: 267	SEQ ID NO: 268
CD44	5′-TAAGGACACCCCAAATTCCA-3′;	5′-GCCAAGATGATCAGCCATTC-3′;
	SEQ ID NO: 269	SEQ ID NO: 270
	5′-GCAGTCAACAGTCGAAGAAGG-3′;	5′-AGCTTTTTCTTCTGCCCACA-3′;
	SEQ ID NO: 271	SEQ ID NO: 272
SNX17	5′-AGCCAGCAAGCAGTGAAGTC-3′;	5′-TCAGGTGACTCAAGCAGTGG-3′;
	SEQ ID NO: 273	SEQ ID NO: 274
	5′-CCGGGAGTCTATGGTCAAAC-3′;	5′-CACGGCACTCAGCTTACTTG-3′;
	SEQ ID NO: 275	SEQ ID NO: 276
PLAT	5′-TGGAGCAGTCTTCGTTTCG-3′;	5′-CTGGCTCCTCTTCTGAATCG-3′;
	SEQ ID NO: 277	SEQ ID NO: 278
	5′-GCCCGATTCAGAAGAGGAG-3′;	5′-TCATCTCTGCAGATCACTTGG-3′;
	SEQ ID NO: 279	SEQ ID NO: 280

The following was performed to generate a standard curve for the target of each primer pair. The standard was generated with a defined number of amplicons per volume for each primer pair. In particular, a standard (S7) was designed to contain about 5 million copies of amplicon-containing cDNA in a bacterial expression vector backbone (pJET1.2 obtained from Fermentas) per one microliter volume for each primer pair. From this, six 1:10 dilutions were generated such that seven standards S1 to S7 were obtained ranging from 5 to 5 million copies of amplicon. To obtain fragments of cDNA, total RNA was extracted from the human HaCaT, A431, and A375 cell lines, and the RNA was reverse transcribed into cDNA. Cell line-derived cDNA was used as a template to amplify fragments of cDNA that contained the desired amplicons for the real time-PCR primer pairs. A list of primers used to generate the desired cDNA fragments is listed in Table 3.

TABLE 3
Primer sets for generating cDNA fragments of the indicated genes.
Gene Name	Forward primer	Reverse primer
FN1	5′-CCAGCAGAGGCATAAGGTTC-3′;	5′-AGTAGTGCCTTCGGGACTGG-3′;
	SEQ ID NO: 281	SEQ ID NO: 282
SPP1	5′-AGGCTGATTCTGGAAGTTCTGAGG-3′;	5′-AATCTGGACTGCTTGTGGCTG-3′;
	SEQ ID NO: 283	SEQ ID NO: 284
COL4A1	5′-GTTGGGCCTCCAGGATTTA-3′;	5′-GCCTGGTAGTCCTGGGAAAC-3′;
	SEQ ID NO: 285	SEQ ID NO: 286
TNC	5′-TGGATGGATTGTGTTCCTGA-3′;	5′-GCCTGCCTTCAAGATTTCTG-3′;
	SEQ ID NO: 287	SEQ ID NO: 288
ITGA3	5′-CTGAGACTGTGCTGACCTGTG-3′;	5′-CTCTTCATCTCCGCCTTCTG-3′;
	SEQ ID NO: 289	SEQ ID NO: 290
LOXL3	5′-GAGACCGCCTACATCGAAGA-3′;	5′-GGTAGCGTTCAAACCTCCTG-3′;
	SEQ ID NO: 291	SEQ ID NO: 292
AGRN	5′-ACACCGTCCTCAACCTGAAG-3′;	5′-AATGGCCAGTGCCACATAGT-3′;
	SEQ ID NO: 293	SEQ ID NO: 294
VCAN	5′-GGTGCACTTTGTGAGCAAGA-3′;	5′-TTGGTATGCAGATGGGTTCA-3′;
	SEQ ID NO: 295	SEQ ID NO: 296
PLOD3	5′-AGCTGTGGTCCAACTTCTGG-3′;	5′-GTGTGGTAACCGGGAAACAG-3′;
	SEQ ID NO: 297	SEQ ID NO: 298
ITGB1	5′-TTCAGTTTGCTGTGTGTTTGC-3′;	5′-CCACCTTCTGGAGAATCCAA-3′;
	SEQ ID NO: 299	SEQ ID NO: 300
PTK2	5′-GGCAGTATTGACAGGGAGGA-3′;	5′-TACTCTTGCTGGAGGCTGGT-3′;
	SEQ ID NO: 301	SEQ ID NO: 302
CTGF	5′-GCCTATTCTGTCACTTCGGCTC-3′;	5′-GCAGGCACAGGTCTTGATGAAC-3′;
	SEQ ID NO: 303	SEQ ID NO: 304
PLOD1	5′-GACCTCTGGGAGGTGTTCAG-3′;	5′-TTAGGGATCGACGAAGGAGA-3′;
	SEQ ID NO: 305	SEQ ID NO: 306
LAMC1	5′-ATTCCTGCCATCAACCAGAC-3′;	5′-CCTGCTTCTTGGCTTCATTC-3′;
	SEQ ID NO: 307	SEQ ID NO: 308
THBS1	5′-CAAAGGGACATCCCAAAATG-3′;	5′-GAGTCAGCCATGATTTTCTTCC-3′;
	SEQ ID NO: 309	SEQ ID NO: 310
LOXL2	5′-TACCCCGAGTACTTCCAGCA-3′;	5′-GATCTGCTTCCAGGTCTTGC-3′;
	SEQ ID NO: 311	SEQ ID NO: 312
IL6	5′-CACACAGACAGCCACTCACC-3′;	5′-CAGGGGTGGTTATTGCATCT-3′;
	SEQ ID NO: 313	SEQ ID NO: 314
LOXL1	5′-CAGACCCCAACTATGTGCAA-3′;	5′-CGCATTGTAGGTGTCATAGCA-3′;
	SEQ ID NO: 315	SEQ ID NO: 316
IL8	5′-CTCTCTTGGCAGCCTTCCT-3′;	5′-TGAATTCTCAGCCCTCTTCAA-3′;
	SEQ ID NO: 317	SEQ ID NO: 318
CYR61	5′-TCGCCTTAGTCGTCACCCTT-3′;	5′-TGTTTCTCGTCAACTCCACCTCG-3′;
	SEQ ID NO: 319	SEQ ID NO: 320
ITGAV	5′-CTGATTTCATCGGGGTTGTC-3′;	5′-TGCCTTGCTGAATGAACTTG-3′;
	SEQ ID NO: 321	SEQ ID NO: 322
YAP	5′-CCAGTGAAACAGCCACCAC-3′;	5′-CTCCTTCCAGTGTTCCAAGG-3′;
	SEQ ID NO: 323	SEQ ID NO: 324
BGN	5′-GGACTCTGTCACACCCACCT-3′;	5′-CAGGGTCTCAGGGAGGTCTT-3′;
	SEQ ID NO: 325	SEQ ID NO: 326
LAMB1	5′-TGCCAGAGCTGAGATGTTGTT-3′;	5′-TGTAGCATTTCGGCTTTCCT-3′;
	SEQ ID NO: 327	SEQ ID NO: 328
ITGB3	5′-GGCAAGTACTGCGAGTGTGA-3′;	5′-ATTCTTTTCGGTCGTGGATG-3′;
	SEQ ID NO: 329	SEQ ID NO: 330
CXCL1	5′-CACTGCTGCTCCTGCTCCT-3′;	5′-TGTTCAGCATCTTTTCGATGA-3′;
	SEQ ID NO: 331	SEQ ID NO: 332
THBS2	5′-TGACAATGACAACATCCCAGA-3′;	5′-TGAGTCTGCCATGACCTGTT-3′;
	SEQ ID NO: 333	SEQ ID NO: 334
COL18A1	5′-CCCTGCTCTACACAGAACCAG-3′;	5′-ACACCTGGCTCCCCTTTCT-3′;
	SEQ ID NO: 335	SEQ ID NO: 336
SPARC	5′-GCCTGGATCTTCTTTCTCCTTTGC-3′;	5′-CATCCAGGGCGATGTACTTGTC-3′;
	SEQ ID NO: 337	SEQ ID NO: 338
TP53	5′-CCCCCTCTGAGTCAGGAAAC-3′;	5′-TCATGTGCTGTGACTGCTTG-3′;
	SEQ ID NO: 339	SEQ ID NO: 340
PLOD2	5′-TGGACCCACCAAGATTCTCCTG-3′;	5′-GACCACAGCTTTCCATGACGAG-3′;
	SEQ ID NO: 341	SEQ ID NO: 342
CCL2	5′-TCTGTGCCTGCTGCTCATAG-3′;	5′-GAGTTTGGGTTTGCTTGTCC-3′;
	SEQ ID NO: 343	SEQ ID NO: 344
FBLN2	5′-CGAGAAGTGCCCAGGAAG-3′;	5′-AGTGAGAAGCCAGGAAAGCA-3′;
	SEQ ID NO: 345	SEQ ID NO: 346
LAMA1	5′-TGGAAATATCACCCACAGCA-3′;	5′-AGGCATTTTTGCTTCACACC-3′;
	SEQ ID NO: 347	SEQ ID NO: 348
THBS4	5′-GCTCCAGCTTCTACGTGGTC-3′;	5′-TTAATTATCGAAGCGGTCGAA-3′;
	SEQ ID NO: 349	SEQ ID NO: 350
COL1A1	5′-AGCCAGCAGATCGAGAACAT-3′;	5′-CCTTCTTGAGGTTGCCAGTC-3′;
	SEQ ID NO: 351	SEQ ID NO: 352
ITGA5	5′-CACCAATCACCCCATTAACC-3′;	5′-GCTTGAGCTGAGCTTTTTCC-3′;
	SEQ ID NO: 353	SEQ ID NO: 354
TAZ	5′-CCAGGTGCTGGAAAAAGAAG-3′;	5′-GAGCTGCTCTGCCTGAGTCT-3′;
	SEQ ID NO: 355	SEQ ID NO: 356
POSTN	5′-GCAGACACACCTGTTGGAAA-3′;	5′-GAACGACCTTCCCTTAATCG-3′;
	SEQ ID NO: 357	SEQ ID NO: 358
LOX	5′-CCTACTACATCCAGGCGTCCAC-3′;	5′-ATGCAAATCGCCTGTGGTAGC-3′;
	SEQ ID NO: 359	SEQ ID NO: 360
CSRC	5′-CTGTTCGGAGGCTTCAACTC-3′;	5′-AGGGATCTCCCAGGCATC-3′;
	SEQ ID NO: 361	SEQ ID NO: 362
LAMA3	5′-TACCTGGGATCACCTCCATC-3′;	5′-ACAGGGATCCTCAGTGTCGT-3′;
	SEQ ID NO: 363	SEQ ID NO: 364
CDKN1A	5′-CGGGATGAGTTGGGAGGAG-3′;	5′-TTAGGGCTTCCTCTTGGAGA-3′;
	SEQ ID NO: 365	SEQ ID NO: 366
CDKN2A-004	5′-ATGGTGCGCAGGTTCTTG-3′;	5′-ACCAGCGTGTCCAGGAAG-3′;
2A-201	SEQ ID NO: 367	SEQ ID NO: 368
CDKN2A-001	5′-GAGCAGCATGGAGCCTTC-3′;	5′-GCATGGTTACTGCCTCTGGT-3′;
2A-202	SEQ ID NO: 369	SEQ ID NO: 370
ITGA2	5′-CAAACAGACAAGGCTGGTGA-3′;	5′-TCAATCTCATCTGGATTTTTGG-3′;
	SEQ ID NO: 371	SEQ ID NO: 372
LAMC2	5′-CTGCAGGTGGACAACAGAAA-3′;	5′-CATCAGCCAGAATCCCATCT-3′;
	SEQ ID NO: 373	SEQ ID NO: 374
PCOLCE2	5′-GTCCCCAGAGAGACCTGTTT-3′;	5′-AGACACAATTGGCGCAGGT-3′;
	SEQ ID NO: 375	SEQ ID NO: 376
LOXL4	5′-AAGACTGGACGCGATAGCTG-3′;	5′-GGTTGTTCCTGAGACGCTGT-3′;
	SEQ ID NO: 377	SEQ ID NO: 378
PCOLCE	5′-TACACCAGACCCGTGTTCCT-3′;	5′-TCCAGGTCAAACTTCTCGAAGG-3′;
	SEQ ID NO: 379	SEQ ID NO: 380
LAMB3	5′-CTTCAATGCCCAGCTCCA-3′;	5′-TTCCCAACCACATCTTCCAC-3′;
	SEQ ID NO: 381	SEQ ID NO: 382
CSF2	5′-CTGCTGCTCTTGGGCACT-3′;	5′-CAGCAGTCAAAGGGGATGAC-3′;
	SEQ ID NO: 383	SEQ ID NO: 384
ACTB	5′-AGGATTCCTATGTGGGCGACG-3′;	5′-TCAGGCAGCTCGTAGCTCTTC-3′;
	SEQ ID NO: 385	SEQ ID NO: 386
RPLP0	5′-GGAATGTGGGCTTTGTGTTCACC-3′;	5′-AGGCCAGGACTCGTTTGTACC-3′;
	SEQ ID NO: 387	SEQ ID NO: 388
RLP8	5′-ACATCAAGGGCATCGTCAAGG-3′;	5′-TCTCTTTCTCCTGCACAGTCTTGG-3′;
	SEQ ID NO: 389	SEQ ID NO: 390
B2M	5′-TGCTCGCGCTACTCTCTCTTTC-3′;	5′-TCACATGGTTCACACGGCAG-3′;
	SEQ ID NO: 391	SEQ ID NO: 392
K10	5′-TGGCCTTCTCTCTGGAAATG-3′;	5′-TCATTTCCTCCTCGTGGTTC-3′;
	SEQ ID NO: 393	SEQ ID NO: 394
K14	5′-AGGTGACCATGCAGAACCTC-3′;	5′-CCTCGTGGTTCTTCTTCAGG-3′;
	SEQ ID NO: 395	SEQ ID NO: 396
MITF	5′-GAAATCTTGGGCTTGATGGA-3′;	5′-CCGAGGTTGTTGTTGAAGGT-3′;
	SEQ ID NO: 397	SEQ ID NO: 398
TYR	5′-CCATGGATAAAGCTGCCAAT-3′;	5′-GACACAGCAAGCTCACAAGC-3′;
	SEQ ID NO: 399	SEQ ID NO: 400
MLANA	5′-CACTCTTACACCACGGCTGA-3′;	5′-CATAAGCAGGTGGAGCATTG-3′;
	SEQ ID NO: 401	SEQ ID NO: 402
PMEL	5′-TTGTCCAGGGTATTGAAAGTGC-3′;	5′-GACAAGAGCAGAAGATGCGGG-3′;
	SEQ ID NO: 403	SEQ ID NO: 404
NES	5′-GCGTTGGAACAGAGGTTGGAG-3′;	5′-CAGGTGTCTCAAGGGTAGCAGG-3′;
	SEQ ID NO: 405	SEQ ID NO: 406
L1CAM	5′-CTTCCCTTTCGCCACAGTATG-3′;	5′-CCTCCTTCTCCTTCTTGCCACT-3′;
	SEQ ID NO: 407	SEQ ID NO: 408
GDF15	5′-AATGGCTCTCAGATGCTCCTGG-3′;	5′-GATTCTGCCAGCAGTTGGTCC-3′;
	SEQ ID NO: 409	SEQ ID NO: 410
ARPC1B	5′-ACCACAGCTTCCTGGTGGAG-3′;	5′-GAGCGGATGGGCTTCTTGATG-3′;
	SEQ ID NO: 411	SEQ ID NO: 412
FARP1	5′-AACGTGACCTTGTCTCCCAAC-3′;	5′-GCATGACATCGCCGATTCTT-3′;
	SEQ ID NO: 413	SEQ ID NO: 414
NTRK3	5′-TTCAACAAGCCCACCCACTAC-3′;	5′-GTTCTCAATGACAGGGATGCG-3′;
	SEQ ID NO: 415	SEQ ID NO: 416
CSK	5′-CATGGAATACCTGGAGGGCAAC-3′;	5′-CAGGTGCCAGCAGTTCTTCAT-3′;
	SEQ ID NO: 417	SEQ ID NO: 418
CD44	5′-TCTCAGAGCTTCTCTACATCAC-3′;	5′-CTGACGACTCCTTGTTCACCA-3′;
	SEQ ID NO: 419	SEQ ID NO: 420
SNX17	5′-TCACCTCCTCTGTACCATTGC-3′;	5′-CTCATCTCCAATGCCCTCGA-3′;
	SEQ ID NO: 421	SEQ ID NO: 422
PLAT	5′-TGCAATGAAGAGAGGGCTCTG-3′;	5′-CGTGGCCCTGGTATCTATTTCA-3′;
	SEQ ID NO: 432	SEQ ID NO: 424

The PCR reactions were performed using a high-fidelity polymerase (product name: “Phusion,” obtained from New England Biolabs). PCR amplification products were checked for correct size and subsequently gel purified using the Qiagen Gel Extraction kit. Purified PCR fragments were subcloned into the bacterial expression vector pJET1.2 using a commercially available kit (Fermentas). The subcloned fragments were subsequently checked by restriction digest and DNA sequencing. Bacterial clones harboring the pJET1.2 expression vector with the correct PCR insert (containing the desired amplicon for real time PCR primer pairs) were frozen and stored at −80° C. This was done to regenerate the same real time PCR standards over time.

Bacteria harboring the pJET1.2 expression vector with PCR inserts were cultured to generate sufficient amounts of vector. A small aliquot of the total retrieved expression vector with insert was linearized using the PvuI-HF restriction enzyme (from New England Biolabs). The digest was then purified using the Qiagen PCR purification kit. Linearized cDNA was diluted to a concentration of 20 ng/μL. One μL of each of a total of 71 linearized cDNA fragments (each at a 20 ng/μL concentration) were mixed and brought to a final volume of 1 mL to obtain standard S7.

Standard S7 was then diluted six times at a 1:10 ratio to obtained standards S1 to S6. Dilution was performed using ultrapure water obtained from Promega (Cat. No. P1193).

The following was performed to generate cDNA from FFPE samples. FFPE blocks were cut at 20 μm sections using a standard Leica microtome. For large pieces of tissue, 2×20 μm full sections were used for RNA retrieval. For smaller tissues, up to 5×20 μm sections were combined for RNA retrieval. RNA extraction was performed using the Qiagen RNA FFPE retrieval kit and a Qiagen QiaCube extraction robot. 0.5 to 1 μg of RNA with a 260/280 ratio of greater than 1.8 were transcribed into cDNA using the BioRad iScript cDNA Synthesis kit. All biospecimens were annotated with clinical data from Mayo Clinic databases. H&E stained sections were obtained for each block analyzed and digitalized using a high-resolution slide scanner.

Fluidigm RT-PCR was performed using a 96×96 format for high throughput analysis (i.e., 96 cDNAs were analyzed for 96 markers; 9216 data points). The primer pairs and cDNAs were prepared in a 96 well format. Standard curves were calculated for each primer pair. Copy numbers per 100,000 housekeeping genes were calculated for each primer pair and averaged per gene. This was initially done for cDNAs derived from FFPE-embedded skin. To correct for epidermal cell-derived cross-contamination, background signal per one copy of K14 (a basal keratinocyte marker) was calculated from FFPE-embedded normal skin samples for each primer pair and averaged. Experimental samples were then normalized first to 100,000 housekeeping genes and then background-corrected for epidermal cross-contamination based on K14 copy number. In particular, the keratinocyte correction factor used for each gene is set forth in Table E under the column titled “AVG per copy K14.”

The study design (Example 1) involved a comparison of the expression profile of “true” benign pigmented skin lesions (nevi, n=73) with “true” malignant melanomas of the skin. The latter comprised i) primary skin melanomas that were documented to metastasize, either to regional lymph nodes, to other areas of skin (in-transit), or to other organs; and ii) in-transit or comparison of nevi to in-transit melanoma metastases (n=54).

Tables C and D summarize the comparisons of the gene expressions between the 73 benign and 54 metastatic. Table A compares the ranked values using the Wilcoxon rank sum test, and Table E compares the dichotomized values (zero vs. >0) using the chi-square test.

A recursive partitioning approach was used to identify cut-points for the genes that would discriminate between these two groups. After partitioning the data at a cut-point of 45 for FN1, no further additional splits in the data based on the other genes were identified by this method.

Using a cutoff of 45 for FN1, the sensitivity was 92.6%, and the specificity was 98.6%. These results are provided in Tables 4 and 5 along with the next possible cutoff for FN1 at 124.

TABLE 4
	Frequency
	Percent
	Row Pct
	Col Pct	Malignant	Benign	Total
	FN1 < 45	4	72	76
		3.15	56.69	59.84
		5.26	94.74
		7.41	98.63
	FN1 ≥ 45	50	1	51
		39.37	0.79	40.16
		98.04	1.96
		92.59	1.37
	Total	54	73	127
		42.52	57.48	100.00

TABLE 5
	Frequency
	Percent
	Row Pct
	Col Pct	Malignant	Benign	Total
	FN1 < 124	8	73	81
		6.30	57.48	63.78
		9.88	90.12
		14.81	100.00
	FN1 ≥ 124	46	0	46
		36.22	0.00	36.22
		100.00	0.00
		85.19	0.00
	Total	54	73	127
		42.52	57.48	100.00

The ability to further discriminate between the groups was assessed by considering SPP1 or ITGB3 in addition to FN1.

Benign Vs. Malignant—Option 1 Using FN1 and SPP1 (FIG. 5)

The results are set forth in Table 6.

TABLE 6
	RULE for FIG. 5	Malignant	Benign
	FN1 < 45 and SPP1 = 0	2	72
	FN1 ≥ 45	52	1
	or
	(FN1 < 45 and SPP1 > 0)
	Total	54	73

Benign Vs. Malignant—Option 2 Using FN1 and ITGB3 (FIG. 6)

The results are set forth in Table 7.

TABLE 7
	RULE for FIG. 6	Malignant	Benign
	FN1 < 45 and ITGB3 = 0	3	72
	FN1 ≥ 45	51	1
	or
	(FN1 < 45 and ITGB3 > 0)
	Total	54	73

If all three genes are included, the rule was as follows:

• • FN1<45 and SPP1=0 and ITGB3=0 denotes a negative test
    • vs.
  • all other combinations denotes a positive test.

This rule resulted in a specificity of 72/73 (98.6%), and a sensitivity of 53/54 (98.2%) (Table 8). Compared to a rule using FN1 alone, the specificity stayed the same but the sensitivity increased from 92.6% to 98.2% using this new rule.

TABLE 8
FN1	SPP1	ITGB3	malignant	Frequency
<45	Zero	Zero	No	72
<45	Zero	Zero	Yes	1	False Neg
					ID MM150
					(case added from
					the Breslow file)
≥45	Zero	Zero	No	1	False Pos
					ID N29
≥45	Zero	Zero	Yes	9
≥45	Zero	>0	Yes	1
≥45	>0	Zero	Yes	18
≥45	>0	>0	Yes	22
<45	Zero	>0	Yes	1
<45	>0	Zero	Yes	2

The rule was evaluated using 25 additional malignant patients who did not have mets (from the “Breslow” file). For 19 of these 25 patients, the rule was “negative” (Table 9).

TABLE 9
	FN1	SPP1	ITGB3	Frequency
	<45	Zero	Zero	19
	<45	>0	Zero	1
	≥45	Zero	Zero	2
	≥45	>0	Zero	3
	<45			1

The rule also was evaluated using 33 thin melanomas (Table 10). For 25 of these 33 patients, the rule was “negative.”

TABLE 10
	FN1	SPP1	ITGB3	Frequency
	<45	Zero	Zero	25
	<45	Zero	>0	1
	≥45	Zero	Zero	5
	≥45	>0	Zero	2

TABLE C
Comparison of gene expression between benign and malignant
	Benign (N = 73)	Malignant (N = 54)	p value
CXCL1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	4.8 (18.4)	20.0 (26.1)
Median	0.0	10.3
Q1, Q3	0.0, 0.0	0.3, 31.1
Range	(0.0-141.7)	(0.0-120.4)
CSF2_AVG_NORM			0.0482
N	73	54
Mean (SD)	10.5 (44.1)	4.3 (8.4)
Median	2.5	1.0
Q1, Q3	0.6, 7.0	0.0, 4.0
Range	(0.0-375.0)	(0.0-41.0)
CCL2_AVG_NORM			<0.0001
N	73	54
Mean (SD)	37.0 (99.4)	244.2 (360.9)
Median	0.0	112.8
Q1, Q3	0.0, 9.1	7.2, 342.2
Range	(0.0-572.0)	(0.0-1777.1)
IL8_AVG_NORM			<0.0001
N	73	54
Mean (SD)	125.5 (671.3)	53.2 (160.8)
Median	0.0	13.0
Q1, Q3	0.0, 0.0	2.1, 52.5
Range	(0.0-5058.7)	(0.0-1171.7)
IL6_AVG_NORM			<0.0001
N	73	54
Mean (SD)	9.9 (69.1)	21.6 (35.0)
Median	0.0	8.8
Q1, Q3	0.0, 0.0	0.3, 25.2
Range	(0.0-589.1)	(0.0-152.3)
ITGA5_AVG_NORM			<0.0001
N	73	54
Mean (SD)	0.0 (0.0)	9.8 (26.8)
Median	0.0	0.0
Q1, Q3	0.0, 0.0	0.0, 7.0
Range	(0.0-0.0)	(0.0-168.0)
ITGA3_AVG_NORM			<0.0001
N	73	54
Mean (SD)	3.2 (27.5)	168.2 (313.4)
Median	0.0	50.2
Q1, Q3	0.0, 0.0	2.0, 160.5
Range	(0.0-235.4)	(0.0-1506.0)
ITGA2_AVG_NORM			0.0007
N	73	54
Mean (SD)	0.0 (0.0)	2.6 (10.0)
Median	0.0	0.0
Q1, Q3	0.0, 0.0	0.0, 0.0
Range	(0.0-0.0)	(0.0-69.7)
ITGAV_AVG_NORM			<0.0001
N	73	54
Mean (SD)	3.3 (23.9)	22.0 (32.9)
Median	0.0	8.0
Q1, Q3	0.0, 0.0	0.0, 31.0
Range	(0.0-199.9)	(0.0-176.8)
ITGB3_AVG_NORM			<0.0001
N	73	54
Mean (SD)	0.0 (0.0)	43.6 (90.3)
Median	0.0	0.0
Q1, Q3	0.0, 0.0	0.0, 52.5
Range	(0.0-0.0)	(0.0-495.3)
ITGB1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	29.9 (95.1)	616.2 (742.2)
Median	0.0	400.2
Q1, Q3	0.0, 0.0	84.7, 869.0
Range	(0.0-487.9)	(0.0-3877.9)
FN1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	2.9 (15.6)	1570.9 (1949.8)
Median	0.0	898.4
Q1, Q3	0.0, 0.0	299.5, 2186.1
Range	(0.0-123.2)	(0.0-11073.5)
THBS1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	0.0 (0.0)	85.1 (136.1)
Median	0.0	16.8
Q1, Q3	0.0, 0.0	0.0, 153.8
Range	(0.0-0.0)	(0.0-786.2)
THBS2_AVG_NORM			<0.0001
N	73	54
Mean (SD)	25.9 (113.4)	280.0 (513.5)
Median	0.0	44.1
Q1, Q3	0.0, 0.0	0.0, 340.1
Range	(0.0-729.2)	(0.0-3030.5)
THBS4_AVG_NORM			<0.0001
N	73	54
Mean (SD)	38.5 (151.2)	228.2 (663.7)
Median	0.0	22.5
Q1, Q3	0.0, 0.0	0.0, 97.9
Range	(0.0-1130.3)	(0.0-3977.7)
VCAN_AVG_NORM			<0.0001
N	73	54
Mean (SD)	3.0 (21.7)	202.4 (262.8)
Median	0.0	103.4
Q1, Q3	0.0, 0.0	0.0, 283.5
Range	(0.0-181.3)	(0.0-1113.2)
BGAN_AVG_NORM			<0.0001
N	73	54
Mean (SD)	69.3 (121.0)	422.4 (573.1)
Median	0.0	248.5
Q1, Q3	0.0, 97.9	113.5, 462.9
Range	(0.0-496.3)	(0.0-3348.1)
SPP1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	0.0 (0.0)	1490.2 (3397.4)
Median	0.0	338.1
Q1, Q3	0.0, 0.0	4.9, 1577.7
Range	(0.0-0.0)	(0.0-22427.0)
TNC_AVG_NORM			<0.0001
N	73	54
Mean (SD)	66.4 (240.1)	800.1 (808.7)
Median	0.0	495.8
Q1, Q3	0.0, 0.0	174.5, 1322.9
Range	(0.0-1393.3)	(0.0-3162.2)
SPARC_AVG_NORM			<0.0001
N	73	54
Mean (SD)	843.7 (2222.8)	3208.4 (3182.6)
Median	0.0	2895.8
Q1, Q3	0.0, 0.0	407.2, 5216.3
Range	(0.0-11175.6)	(0.0-13631.9)
AGRN_AVG_NORM			<0.0001
N	73	54
Mean (SD)	4.7 (18.1)	51.2 (53.8)
Median	0.0	42.1
Q1, Q3	0.0, 0.0	10.7, 69.7
Range	(0.0-121.7)	(0.0-242.0)
CTGF_AVG_NORM			<0.0001
N	73	54
Mean (SD)	0.4 (3.6)	90.9 (231.6)
Median	0.0	22.1
Q1, Q3	0.0, 0.0	0.0, 125.9
Range	(0.0-30.6)	(0.0-1631.4)
CYR61_AVG_NORM			<0.0001
N	73	54
Mean (SD)	4.8 (13.0)	27.2 (39.2)
Median	0.0	18.7
Q1, Q3	0.0, 0.0	4.9, 32.2
Range	(0.0-70.4)	(0.0-267.2)
LAMA3_AVG_NORM			0.0004
N	73	54
Mean (SD)	1.1 (9.0)	1.2 (2.9)
Median	0.0	0.0
Q1, Q3	0.0, 0.0	0.0, 0.0
Range	(0.0-76.8)	(0.0-11.3)
LAMC1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	0.0 (0.0)	70.6 (159.4)
Median	0.0	28.4
Q1, Q3	0.0, 0.0	0.0, 99.3
Range	(0.0-0.0)	(0.0-1136.2)
LAMB1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	9.2 (38.4)	221.1 (354.3)
Median	0.0	73.1
Q1, Q3	0.0, 0.0	0.0, 339.8
Range	(0.0-248.8)	(0.0-1877.6)
LAMA1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	5.7 (14.5)	65.4 (149.0)
Median	<0.0	10.6
Q1, Q3	0.0, 0.0	0.0, 49.0
Range	(0.0-76.5)	(0.0-754.3)
LAMC2_AVG_NORM			0.0003
N	73	54
Mean (SD)	0.0 (0.0)	4.0 (15.3)
Median	0.0	0.0
Q1, Q3	0.0, 0.0	0.0, 0.0
Range	(0.0-0.0)	(0.0-91.1)
LAMB3_AVG_NORM			0.1473
N	73	54
Mean (SD)	33.5 (60.3)	32.2 (54.5)
Median	0.0	12.1
Q1, Q3	0.0, 44.6	0.0, 37.0
Range	(0.0-323.9)	(0.0-246.0)
COL1A1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	1534.4 (4365.3)	4191.6 (5865.9)
Median	0.0	1704.4
Q1, Q3	0.0, 0.0	0.0, 6850.9
Range	(0.0-22510.2)	(0.0-31867.0)
COL4A1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	0.0 (0.0)	211.8 (344.1)
Median	0.0	118.4
Q1, Q3	0.0, 0.0	2.3, 261.2
Range	(0.0-0.0)	(0.0-1774.4)
COL18A1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	94.2 (783.4)	22.8 (38.8)
Median	0.0	4.1
Q1, Q3	0.0, 0.0	0.0, 34.4
Range	(0.0-6695.7)	(0.0-208.8)
LOX_AVG_NORM			0.0003
N	73	54
Mean (SD)	37.7 (132.8)	65.0 (113.9)
Median	0.0	3.5
Q1, Q3	0.0, 0.0	0.0, 58.0
Range	(0.0-991.2)	(0.0-443.3)
LOXL1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	0.8 (7.1)	39.6 (60.3)
Median	0.0	18.5
Q1, Q3	0.0, 0.0	0.0, 65.0
Range	(0.0-60.4)	(0.0-349.0)
LOXL2_AVG_NORM			<0.0001
N	73	54
Mean (SD)	43.3 (356.8)	68.5 (129.9)
Median	0.0	22.1
Q1, Q3	0.0, 0.0	0.0, 89.1
Range	(0.0-3048.4)	(0.0-821.4)
LOXL3_AVG_NORM			<0.0001
N	73	54
Mean (SD)	2.2 (12.3)	28.4 (71.1)
Median	0.0	9.2
Q1, Q3	0.0, 0.0	2.5, 29.4
Range	(0.0-89.7)	(0.0-507.5)
LOXL4_AVG_NORM			0.0010
N	73	54
Mean (SD)	33.8 (91.0)	129.1 (300.4)
Median	0.0	9.1
Q1, Q3	0.0, 10.2	0.0, 67.0
Range	(0.0-529.2)	(0.0-1230.0)
PLOD1_AVG_NORM			<0.0001
N	73	54
Mean (SD)	33.7 (116.5)	420.3 (532.2)
Median	0.0	242.3
Q1, Q3	0.0, 0.0	90.2, 659.3
Range	(0.0-878.2)	(0.0-3336.8)
PLOD2_AVG_NORM			<0.0001
N	73	54
Mean (SD)	44.5 (151.7)	314.8 (1284.4)
Median	0.0	53.7
Q1, Q3	0.0, 0.0	2.3, 103.3
Range	(0.0-1124.0)	(0.0-9110.5)
PLOD3_AVG_NORM			<0.0001
N	73	54
Mean (SD)	2.7 (11.9)	68.0 (81.2)
Median	0.0	38.3
Q1, Q3	0.0, 0.0	4.2, 101.9
Range	(0.0-87.4)	(0.0-330.2)
PCOLCE2_AVG_NORM			0.0010
N	73	54
Mean (SD)	7.7 (25.8)	6.4 (14.9)
Median	0.0	0.0
Q1, Q3	0.0, 0.0	0.0, 3.1
Range	(0.0-104.8)	(0.0-68.4)
PCOLCE_AVG_NORM			0.0232
N	73	54
Mean (SD)	92.1 (159.7)	170.4 (339.4)
Median	0.0	40.9
Q1, Q3	0.0, 122.2	0.0, 175.1
Range	(0.0-699.2)	(0.0-1945.2)
PTK2_AVG_NORM			<0.0001
N	73	54
Mean (SD)	2.8 (14.4)	76.6 (81.8)
Median	0.0	70.0
Q1, Q3	0.0, 0.0	0.0, 127.7
Range	(0.0-116.5)	(0.0-323.3)
CSRC_AVG_NORM			0.0001
N	73	54
Mean (SD)	19.0 (40.9)	45.1 (65.9)
Median	0.3	19.6
Q1, Q3	0.0, 24.8	4.2, 46.6
Range	(0.0-266.6)	(0.0-290.2)
CDKN1A_AVG_NORM			0.0005
N	73	54
Mean (SD)	78.5 (150.9)	181.0 (271.7)
Median	0.0	84.2
Q1, Q3	0.0, 118.9	0.0, 253.3
Range	(0.0-788.2)	(0.0-1083.2)
CDKN2A_AVG_NORM			0.0002
N	73	54
Mean (SD)	6.1 (19.6)	9.7 (25.8)
Median	0.0	1.0
Q1, Q3	0.0, 0.0	0.0, 6.9
Range	(0.0-113.2)	(0.0-175.1)
TP53_AVG_NORM			<0.0001
N	73	54
Mean (SD)	40.6 (98.6)	231.2 (289.8)
Median	0.0	166.9
Q1, Q3	0.0, 0.0	0.0, 359.9
Range	(0.0-410.8)	(0.0-1722.4)
YAP_AVG_NORM			<0.0001
N	73	54
Mean (SD)	7.8 (36.6)	112.4 (161.4)
Median	0.0	63.1
Q1, Q3	0.0, 0.0	0.0, 173.5
Range	(0.0-246.3)	(0.0-769.0)
TAZ_AVG_NORM			<0.0001
N	73	54
Mean (SD)	12.2 (27.9)	32.8 (44.3)
Median	0.0	15.0
Q1, Q3	0.0, 0.7	0.0, 49.0
Range	(0.0-122.7)	(0.0-186.4)
MITF_AVG_NORM			<0.0001
N	73	54
Mean (SD)	251.0 (399.5)	569.8 (494.8)
Median	45.5	467.3
Q1, Q3	0.0, 331.5	184.9, 777.8
Range	(0.0-2143.3)	(0.0-2200.0)
MLANA_AVG_NORM			0.1823
N	73	54
Mean (SD)	3596.0 (3671.3)	4865.4 (4966.1)
Median	2446.8	2803.5
Q1, Q3	950.9, 5019.4	1210.7, 6773.0
Range	(14.0-17180.3)	(62.8-19672.1)
TYR_AVG_NORM			0.0040
N	73	54
Mean (SD)	349.7 (301.8)	839.8 (996.3)
Median	254.3	515.1
Q1, Q3	119.5, 527.5	161.0, 1244.9
Range	(0.0-1169.8)	(2.0-5500.0)
POSTN_AVG_NORM			0.0001
N	73	54
Mean (SD)	1138.7 (2155.7)	1933.9 (2318.1)
Median	191.6	1252.0
Q1, Q3	0.0, 1449.9	397.4, 2457.4
Range	(0.0-11078.1)	(0.0-11193.2)
FBLN2_AVG_NORM			<0.0001
N	73	54
Mean (SD)	2.1 (17.3)	26.5 (42.2)
Median	0.0	0.0
Q1, Q3	0.0, 0.0	0.0, 48.8
Range	(0.0-148.2)	(0.0-150.9)

TABLE D
Comparison of gene expression between benign and malignant
	Benign	Malignant
	(N = 73)	(N = 54)	p value
CXCL1_AVG_NORM01					<0.0001
Zero	58	(79.5%)	12	(22.2%)
>0	15	(20.5%)	42	(77.8%)
CSF2_AVG_NORM01					0.0398
Zero	15	(20.5%)	20	(37.0%)
>0	58	(79.5%)	34	(63.0%)
CCL2_AVG_NORM01					<0.0001
Zero	53	(72.6%)	12	(22.2%)
>0	20	(27.4%)	42	(77.8%)
IL8_AVG_NORM01					<0.0001
Zero	63	(86.3%)	10	(18.5%)
>0	10	(13.7%)	44	(81.5%)
IL6_AVG_NORM01					<0.0001
Zero	65	(89.0%)	13	(24.1%)
>0	8	(11.0%)	41	(75.9%)
ITGA5_AVG_NORM01					<0.0001
Zero	73	(100.0%)	38	(70.4%)
>0	0	(0.0%)	16	(29.6%)
ITGA3_AVG_NORM01					<0.0001
Zero	72	(98.6%)	13	(24.1%)
>0	1	(1.4%)	41	(75.9%)
ITGA2_AVG_NORM01					0.0007
Zero	73	(100.0%)	46	(85.2%)
>0	0	(0.0%)	8	(14.8%)
ITGAV_AVG_NORM01					<0.0001
Zero	71	(97.3%)	24	(44.4%)
>0	2	(2.7%)	30	(55.6%)
ITGB3_AVG_NORM01					<0.0001
Zero	73	(100.0%)	30	(55.6%)
>0	0	(0.0%)	24	(44.4%)
ITGB1_AVG_NORM01					<0.0001
Zero	64	(87.7%)	11	(20.4%)
>0	9	(12.3%)	43	(79.6%)
FN1_AVG_NORM01					<0.0001
Zero	69	(94.5%)	2	(3.7%)
>0	4	(5.5%)	52	(96.3%)
THBS1_AVG_NORM01					<0.0001
Zero	73	(100.0%)	24	(44.4%)
>0	0	(0.0%)	30	(55.6%)
THBS2_AVG_NORM01					<0.0001
Zero	67	(91.8%)	23	(42.6%)
>0	6	(8.2%)	31	(57.4%)
THBS4_AVG_NORM01					<0.0001
Zero	58	(79.5%)	15	(27.8%)
>0	15	(20.5%)	39	(72.2%)
VCAN_AVG_NORM01					<0.0001
Zero	71	(97.3%)	16	(29.6%)
>0	2	(2.7%)	38	(70.4%)
BGAN_AVG_NORM01					<0.0001
Zero	42	(57.5%)	7	(13.0%)
>0	31	(42.5%)	47	(87.0%)
SPP1_AVG_NORM01					<0.0001
Zero	73	(100.0%)	12	(22.2%)
>0	0	(0.0%)	42	(77.8%)
TNC_AVG_NORM01					<0.0001
Zero	60	(82.2%)	3	(5.6%)
>0	13	(17.8%)	51	(94.4%)
SPARC_AVG_NORM01					<0.0001
Zero	57	(78.1%)	13	(24.1%)
>0	16	(21.9%)	41	(75.9%)
AGRN_AVG_NORM01					<0.0001
Zero	59	(80.8%)	5	(9.3%)
>0	14	(19.2%)	49	(90.7%)
CTGF_AVG_NORM01					<0.0001
Zero	72	(98.6%)	21	(38.9%)
>0	1	(1.4%)	33	(61.1%)
CYR61_AVG_NORM01					<0.0001
Zero	56	(76.7%)	9	(16.7%)
>0	17	(23.3%)	45	(83.3%)
LAMA3_AVG_NORM01					0.0003
Zero	72	(98.6%)	43	(79.6%)
>0	1	(1.4%)	11	(20.4%)
LAMC1_AVG_NORM01					<0.0001
Zero	73	(100.0%)	24	(44.4%)
>0	0	(0.0%)	30	(55.6%)
LAMB1_AVG_NORM01					<0.0001
Zero	66	(90.4%)	22	(40.7%)
>0	7	(9.6%)	32	(59.3%)
LAMA1_AVG_NORM01					<0.0001
Zero	57	(78.1%)	16	(29.6%)
>0	16	(21.9%)	38	(70.4%)
LAMC2_AVG_NORM01					0.0003
Zero	73	(100.0%)	45	(83.3%)
>0	0	(0.0%)	9	(16.7%)
LAMB3_AVG_NORM01					0.0061
Zero	45	(61.6%)	20	(37.0%)
>0	28	(38.4%)	34	(63.0%)
COL1A1_AVG_NORM01					<0.0001
Zero	60	(82.2%)	17	(31.5%)
>0	13	(17.8%)	37	(68.5%)
COL4A1_AVG_NORM01					<0.0001
Zero	73	(100.0%)	13	(24.1%)
>0	0	(0.0%)	41	(75.9%)
COL18A1_AVG_NORM01					<0.0001
Zero	64	(87.7%)	18	(33.3%)
>0	9	(12.3%)	36	(66.7%)
LOX_AVG_NORM01					<0.0001
Zero	60	(82.2%)	26	(48.1%)
>0	13	(17.8%)	28	(51.9%)
LOXL1_AVG_NORM01					<0.0001
Zero	72	(98.6%)	23	(42.6%)
>0	1	(1.4%)	31	(57.4%)
LOXL2_AVG_NORM01					<0.0001
Zero	70	(95.9%)	19	(35.2%)
>0	3	(4.1%)	35	(64.8%)
LOXL3_AVG_NORM01					<0.0001
Zero	69	(94.5%)	10	(18.5%)
>0	4	(5.5%)	44	(81.5%)
LOXL4_AVG_NORM01					0.0006
Zero	53	(72.6%)	23	(42.6%)
>0	20	(27.4%)	31	(57.4%)
PLOD1_AVG_NORM01					<0.0001
Zero	59	(80.8%)	12	(22.2%)
>0	14	(19.2%)	42	(77.8%)
PLOD2_AVG_NORM01					<0.0001
Zero	59	(80.8%)	10	(18.5%)
>0	14	(19.2%)	44	(81.5%)
PLOD3_AVG_NORM01					<0.0001
Zero	66	(90.4%)	11	(20.4%)
>0	7	(9.6%)	43	(79.6%)
PCOLCE2_AVG_NORM01					0.0002
Zero	66	(90.4%)	34	(63.0%)
>0	7	(9.6%)	20	(37.0%)
PCOLCE_AVG_NORM01					0.0036
Zero	42	(57.5%)	17	(31.5%)
>0	31	(42.5%)	37	(68.5%)
PTK2_AVG_NORM01					<0.0001
Zero	67	(91.8%)	16	(29.6%)
>0	6	(8.2%)	38	(70.4%)
CSRC_AVG_NORM01					0.0001
Zero	36	(49.3%)	9	(16.7%)
>0	37	(50.7%)	45	(83.3%)
CDKN1A_AVG_NORM01					0.0001
Zero	48	(65.8%)	16	(29.6%)
>0	25	(34.2%)	38	(70.4%)
CDKN2A_AVG_NORM01					<0.0001
Zero	57	(78.1%)	23	(42.6%)
>0	16	(21.9%)	31	(57.4%)
TP53_AVG_NORM01					<0.0001
Zero	59	(80.8%)	16	(29.6%)
>0	14	(19.2%)	38	(70.4%)
YAP_AVG_NORM01					<0.0001
Zero	68	(93.2%)	22	(40.7%)
>0	5	(6.8%)	32	(59.3%)
TAZ_AVG_NORM01					<0.0001
Zero	54	(74.0%)	19	(35.2%)
>0	19	(26.0%)	35	(64.8%)
MITF_AVG_NORM01					<0.0001
Zero	26	(35.6%)	2	(3.7%)
>0	47	(64.4%)	52	(96.3%)
MLANA_AVG_NORM01
>0	73	(100.0%)	54	(100.0%)
TYR_AVG_NORM01					0.2202
Zero	2	(2.7%)	0	(0.0%)
>0	71	(97.3%)	54	(100.0%)
POSTN_AVG_NORM01					<0.0001
Zero	32	(43.8%)	4	(7.4%)
>0	41	(56.2%)	50	(92.6%)
FBLN2_AVG_NORM01					<0.0001
Zero	71	(97.3%)	31	(57.4%)
>0	2	(2.7%)	23	(42.6%)

	TABLE E
	MM79_CN	MM80_CN	MM81_CN	MM82_CN	AVG
	AVG	AVG	AVG	AVG	per
	per copy	per copy	per copy	per copy	copy
	K14	K14	K14	K14	K14	STDEV	% STDEV
KRT14_AVG_NORM	1	1	1	1	1	0.000
KRT10_AVG_NORM	2.209	2.229	2.92	3.015	2.593	0.434	17%
MITF_AVG_NORM	0.021	0.018	0.016	0.015	0.018	0.003	15%
MLANA_AVG_NORM	0.021	0.018	0.016	0.015	0.018	0.003	15%
TYR_AVG_NORM	0.004	0.002	0.002	0.001	0.002	0.001	56%
PMEL_AVG_NORM	0.025	0.027	0.03	0.018	0.025	0.005	20%
FN1_AVG_NORM	0.077	0.065	0.035	0.042	0.055	0.020	36%
SPARC_AVG_NORM	1.294	1.143	0.568	1.707	1.178	0.471	40%
AGRN_AVG_NORM	0.004	0.006	0.003	0.002	0.004	0.002	46%
THBS1_AVG_NORM	0.064	0.015	0.018	0.005	0.026	0.026	103%
THBS2_AVG_NORM	0.366	0.061	0.104	0.057	0.147	0.148	100%
THBS4_AVG_NORM	0.018	0.006	0.005	0.001	0.008	0.007	98%
VCAN_AVG_NORM	0.095	0.034	0.04	0.027	0.049	0.031	64%
BGAN_AVG_NORM	0.015	0.027	0.014	0.015	0.018	0.006	35%
COL1A1_AVG_NORM	1.695	3.44	0.689	6.695	3.130	2.635	84%
COL4A1_AVG_NORM	0.069	0.026	0.03	0.016	0.035	0.023	66%
COL4A2_AVG_NORM	0.115	0.042	0.041	0.004	0.051	0.046	92%
COL18A1_AVG_NORM	0.015	0.009	0.005	0.002	0.008	0.006	73%
CTGF_AVG_NORM	0.012	0.008	0.016	0.004	0.010	0.005	52%
LOX_AVG_NORM	0.029	0.021	0.028	0.021	0.025	0.004	18%
LOXL1_AVG_NORM	0.015	0.009	0.016	0.015	0.014	0.003	23%
LOXL2_AVG_NORM	0.016	0.011	0.008	0.006	0.010	0.004	42%
LOXL3_AVG_NORM	0.003	0.002	0.002	0.001	0.002	0.001	41%
LOXL4_AVG_NORM	0.02	0.004	0.003	0.001	0.007	0.009	125%
PLOD2_AVG_NORM	0.018	0.014	0.007	0.001	0.010	0.008	75%
PLOD1_AVG_NORM	0.069	0.053	0.026	0.017	0.041	0.024	58%
SPP1_AVG_NORM	0.092	0.002	0.007	0	0.025	0.045	177%
TNC_AVG_NORM	0.025	0.02	0.027	0.013	0.021	0.006	29%
PCOLCE2_AVG_NORM	0.011	0.001	0.006	0	0.005	0.005	113%
PCOLCE_AVG_NORM	0.028	0.049	0.032	0.04	0.037	0.009	25%
PLOD3_AVG_NORM	0.03	0.006	0.007	0.002	0.011	0.013	113%
ITGB3_AVG_NORM	0.03	0.006	0.007	0.002	0.011	0.013	113%
ITGB1_AVG_NORM	0.164	0.054	0.074	0.038	0.083	0.056	68%
FBLN2_AVG_NORM	0.049	0.022	0.02	0.016	0.027	0.015	56%
CYR61_AVG_NORM	0.006	0.002	0.003	0	0.003	0.003	91%
ITGA5_AVG_NORM	0.011	0.005	0.007	0.003	0.007	0.003	53%
ITGA3_AVG_NORM	0.016	0.008	0.006	0.008	0.010	0.004	47%
ITGA2_AVG_NORM	0.08	0.034	0.019	0.084	0.054	0.033	60%
ITGAV_AVG_NORM	0.013	0.005	0.003	0.003	0.006	0.005	79%
CSRC_AVG_NORM	0.006	0.003	0.005	0.001	0.004	0.002	59%
PTK2_AVG_NORM	0.035	0.02	0.011	0.009	0.019	0.012	63%
POSTN_AVG_NORM	0.077	0.092	0.117	0.193	0.120	0.052	43%
YAP_AVG_NORM	0.079	0.029	0.033	0.031	0.043	0.024	56%
CXCL1_AVG_NORM	0.002	0	0	0	0.001	0.001	200%
CSF2_AVG_NORM	0.002	0	0	0	0.001	0.001	200%
CCL2_AVG_NORM	0.039	0.018	0.013	0.008	0.020	0.014	70%
IL8_AVG_NORM	0.003	0	0.001	0	0.001	0.001	141%
IL6_AVG_NORM	0.001	0	0	0	0.000	0.001	200%
LAMA3_AVG_NORM	0.038	0.012	0.021	0.011	0.021	0.013	61%
TP53_AVG_NORM	0.08	0.04	0.039	0.052	0.053	0.019	36%
CDKN1A_AVG_NORM	0.057	0.029	0.037	0.014	0.034	0.018	52%
CDKN2A_AVG_NORM	0.003	0.001	0.001	0	0.001	0.001	101%
TAZ_AVG_NORM	0.026	0.008	0.008	0.003	0.011	0.010	90%
LAMC1_AVG_NORM	0.062	0.013	0.016	0.008	0.025	0.025	101%
LAMB1_AVG_NORM	0.046	0.019	0.026	0.008	0.025	0.016	65%
LAMA1_AVG_NORM	0.007	0	0.001	0	0.002	0.003	168%
LAMC2_AVG_NORM	0.034	0.009	0.012	0.016	0.018	0.011	63%
LAMB3_AVG_NORM	0.042	0.016	0.026	0.017	0.025	0.012	48%
PLAT_AVG_NORM	0.032	0.02	0.034	0.04	0.032	0.001	27%
CSK_AVG_NORM	0.027	0.034	0.021	0.041	0.031	0.001	28%
GDF15_AVG_NORM	0.029	0.019	0.033	0.019	0.025	0.001	28%
FARP1_AVG_NORM	0.019	0.029	0.022	0.031	0.025	0.001	22%
ARPC1B_AVG_NORM	0.015	0.03	0.042	0.018	0.026	0.012	47%
NES_AVG_NORM	0.114	0.125	0.112	0.084	0.109	0.017	16%
NTRK3_AVG_NORM	0.021	0.025	0.022	0.033	0.025	0.001	25%
SNX17_AVG_NORM	0.112	0.099	0.089	0.123	0.106	0.015	14%
L1CAM_AVG_NORM	0.017	0.04	0.01	0.024	0.023	0.013	56%
CD44_AVG_NORM	0.112	0.089	0.09	0.123	0.104	0.017	16%

The results provided herein demonstrate the development of a method for determining absolute levels (copy numbers) of genes of interest (e.g., FN-associated genes) from paraffin-embedded tissue by generating a highly defined internal standard that can be regenerated indefinitely. This standardization approach can allow for the comparison of results from independent experiments and thus, allows for extensive validation. The RT-PCR not only produced strong signals from highly degraded RNA due to FFPE embedding, but also was amendable to high-throughput analysis and was highly cost effective. While the methods provided herein were validated for melanoma, these methods are likely applicable to other human cancers. The results provided herein also demonstrate the discrimination between benign and malignant pigmented lesions based on multiple markers.

Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Claims

1. A set of kit components within a kit for identifying a malignant skin lesion in a subject when used together with a set of reagents comprising: (a) primer pairs for determining, within a test sample taken from the subject, the expression level of marker genes PLAT, ITGB3, and IL8 to obtain a measured expression level of the marker genes for the test sample, and(b) a primer pair for determining, within the test sample, the expression level of marker gene GDF15, to obtain a measured expression level of the marker gene GDF15 for the test sample,wherein the set of kit components comprises:a control nucleic acid for each of the primer pairs,wherein each control nucleic acid comprises a target nucleic acid for one of the primer pairs configured to obtain a standard curve for the primer pair, andwherein each of the control nucleic acids is complementary DNA (cDNA) specific for cDNA and not specific for genomic DNA.

2. A set of kit components within a kit comprising: (i) a first composition comprising a control nucleic acid for a primer pair for determining, within a test sample, the expression level of marker gene GDF15, said control nucleic acid comprising a target nucleic acid for the primer pair configured to obtain a standard curve for the primer pair;(ii) a second composition comprising a control nucleic acid for a primer pair for determining, within the test sample, the expression level of marker gene PLAT, said control nucleic acid comprising a target nucleic acid for the primer pair configured to obtain a standard curve for the primer pair;(iii) a third composition comprising a control nucleic acid for a primer pair for determining, within the test sample, the expression level of marker gene ITGB3, said control nucleic acid comprising a target nucleic acid for the primer pair configured to obtain a standard curve for the primer pair; and(iv) a fourth composition comprising a control nucleic acid for a primer pair for determining, within the test sample, the expression level of marker gene IL8, said control nucleic acid comprising a target nucleic acid for the primer pair configured to obtain a standard curve for the primer pair,wherein each of the control nucleic acids is complementary DNA (cDNA) specific for cDNA and not specific for genomic DNA.