Patent Publication Number: US-2020291480-A1

Title: Methods and materials for identifying metastatic malignant skin lesions and treating skin cancer

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation of U.S. patent application Ser. No. 15/503,973, filed Feb. 24, 2017, pending, which is a national stage entry under 35 U.S.C. § 371 of International Application No. PCT/US2015/045065, having an International Filing Date of Aug. 13, 2015, which claims the benefit of U.S. Provisional Ser. No. 62/037,325, filed Aug. 14, 2014, and U.S. Provisional Ser. No. 62/142,831, filed Apr. 3, 2015, the disclosure of each of which is incorporated herein in its entirety by this reference. 
    
    
     TECHNICAL FIELD 
     This application relates to methods and materials for identifying metastatic malignant skin lesions (e.g., metastatic 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 metastatic malignant skin lesions. This document also relates to methods and materials for treating skin cancer. For example, this document relates to methods and materials for identifying a mammal (e.g., a human) having a pre-metastatic skin lesion (e.g., pre-metastatic melanoma) and treating that mammal with pentamidine (4,4′-[pentane-1,5-diylbis(oxy)]dibenzenecarboximidamide). 
     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 Ser. No. 15/503,973, filed Feb. 24, 2017, the contents of which are incorporated herein by this reference. 
     BACKGROUND 
     Malignant skin lesions are typically identified by obtaining a skin biopsy and morphologically assessing the biopsy&#39;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 metastatic malignant skin lesions (e.g., metastatic 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 metastatic 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 or metastatic biological behavior of the tested skin lesion. 
     Also provided are methods and materials for treating skin cancer. For example, this document provides methods and materials for identifying a mammal (e.g., a human) having a pre-metastatic skin lesion (e.g., pre-metastatic melanoma) and treating that mammal with pentamidine. 
     As described herein, aggressive cancer cells (e.g., melanoma cells) can remodel their cell adhesion structures (e.g., osteopontin (SPP1) polypeptides) to invade tissues and metastasize. Screening over 1,200 compounds for the ability to reduce expression of SPP1 polypeptides resulted in the identification of pentamidine as an effective agent for disrupting integrin adhesion remodeling, thereby demonstrating that pentamidine can be used to reduce or inhibit cancer progression at an early stage (e.g., prior to metastatic cancer). In some cases, a mammal (e.g., a human) identified as having skin cancer cells that express an elevated level of PLAT, ITGB3, LAMB1, and/or TP53 can be administered pentamidine to reduce or inhibit cancer progression. For example, pentamidine can be administered to a mammal (e.g., a human) having pre-metastatic melanoma cells that were determined to have an elevated level of PLAT, ITGB3, LAMB1, and/or TP53 expression. In such cases, the mammal being treated with pentamidine may not experience cancer progression from the pre-metastatic melanoma state to a metastatic melanoma state. 
     In general, one aspect hereof features a method for identifying a metastatic 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, ITGB3, LAMB1, and TP53 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 metastatic 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 PLAT or ITGB3. 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. The method can comprise determining, within the test sample, the expression level of at least two marker genes selected from the group consisting of PLAT, ITGB3, LAMB1, and TP53 to obtain measured expression levels of the at least two marker genes for the test sample. The method can comprise determining, within the test sample, the expression level of at least three marker genes selected from the group consisting of PLAT, ITGB3, LAMB1, and TP53 to obtain measured expression levels of the at least three marker genes for the test sample. The method can comprise determining, within the test sample, the expression level of PLAT, ITGB3, LAMB1, and TP53 to obtain measured expression levels of the PLAT, ITGB3, LAMB1, and TP53 for the test sample. 
     In another aspect, this document features a kit for identifying a metastatic malignant skin lesion. The kit comprises, or consists essentially of, (a) a primer pair for determining, within a test sample, the expression level of a marker gene selected from the group consisting of LAMB1 and TP53 to obtain a measured expression level of the marker gene for the test sample, and (b) a primer pair for 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. The keratinocyte marker gene can be K14. The marker gene can be LAMB1. The marker gene can be TP53. The kit can comprise primer pairs for determining, within the test sample, the expression level of LAMB1 and TP53 to obtain measured expression levels of the LAMB1 and TP53 for the test sample. The kit can comprise primer pairs for determining, within the test sample, the expression level of PLAT to obtain measured expression levels of the PLAT for the test sample. The kit can comprise primer pairs for determining, within the test sample, the expression level of ITGB3 to obtain measured expression levels of the ITGB3 for the test sample. The kit can comprise primer pairs for determining, within the test sample, the expression level of PLAT and ITGB3 to obtain measured expression levels of the ITGB3 and PLAT for the test sample. 
     In another aspect, this document features a method for identifying a metastatic 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, ITGB3, LAMB1, and TP53 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 metastatic 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 LAMB1 or TP53. 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. 
     In another aspect, this document features a method for identifying a pre-metastatic skin lesion having an increased likelihood of metastasizing. The method comprises, or consists essentially of, (a) detecting the presence of an elevated level of PLAT, ITGB3, LAMB1, and TP53 expression in cells of the pre-metastatic skin lesion, and (d) classifying the pre-metastatic skin lesion as having an increased likelihood of metastasizing based, at least in part, on the presence. The method can comprise measuring the levels of PLAT, ITGB3, LAMB1, and TP53 expression in cells of the pre-metastatic skin lesion and performing an analysis using a two trees, two leaves model. The pre-metastatic skin lesion can be a human pre-metastatic skin lesion. 
     In another aspect, this document features a method for treating skin cancer, wherein the method comprises, or consists essentially of, (a) detecting the presence of an elevated level of PLAT, ITGB3, LAMB1, and TP53 expression in skin cancer cells of a mammal, and (d) administering pentamidine to the mammal. The mammal can be a human. The skin cancer can be pre-metastatic skin cancer. The skin cancer can be pre-metastatic melanoma. Administration of the pentamidine can reduce the progression of the pre-metastatic melanoma to metastatic melanoma. The pre-metastatic melanoma can fail to progress to metastatic melanoma following administration of the pentamidine. The method can comprise measuring the levels of PLAT, ITGB3, LAMB1, and TP53 expression in cells of the skin cancer cells and performing an analysis using a two trees, two leaves model. 
     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 disclosure pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the disclosure, 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. 
     Other features and advantages of the disclosure will be apparent from the following detailed description, and from the claims. 
    
    
     
       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. 
         FIGS. 8A-8D  depict logic regression.  FIG. 8A , is a graph depicting a null model randomization test suggesting a relationship exists between SLN positivity and the gene expression variables. The “best model” and “null model” reference lines mark the deviance scores for the best model fit to outcomes and the null model. The histogram shows the distribution of deviance scores for models fit against randomize outcomes. Since the best model outperforms the randomized outcome models there was a relationship between SLN positivity and gene expression.  FIG. 8B  illustrates the results from ten-fold cross validation results for models using 1, 2, and 3 trees with at most six binary variables or leaves. The label in each square denotes the number of trees used in the model. The scores on the y-axis are the deviance scores using the test data and the x-axis denotes the number of binary variables (leaves) used in each model. Notice that model the using two trees and four leaves had the best test score.  FIG. 8C  is a summary of the permutation test results for two trees using two to five leaves. The two solid reference lines indicate the best deviance score and the null model deviance score. The dashed reference line represents the deviance score using a one tree model. The histogram summarizes the deviance scores using permuted outcomes. There were 1,000 model fits for each model size. Scores above the best model reference line indicate there were models that fit the permuted data better than the actual data. For the model with two tree and five leaves about 10% deviance scores for models fit using permuted data have a lower score than using the best model for the observed original data indicated by the left most vertical reference line.  FIG. 8D  are the formulas for the best fitting models involved two trees with a model size of 4 or 5. 
         FIG. 9  depicts differential expression analysis by next-generation sequencing reveals that integrin adhesion genes are up-regulated in benign nevi vs. invasive melanoma. 160 of 15,413 genes were significantly regulated in benign nevi vs. invasive melanoma (FDR&lt;0.01) as determined by next-generation sequencing (NGS). Functional relationships between these genes were mapped by the STRING database. Two main functional clusters emerged; the largest was related to integrin-linked cell adhesion. The particularly indicated circles indicate gene up-regulation; other circles indicate down-regulation. Numbers indicate fold-change, malignant over benign. 
         FIG. 10  illustrates that integrin adhesion genes are over-expressed in invasive melanoma vs. non-invasive precursor lesions. Confirmation of NGS results by quantitative PCR. Genes with significant regulation (p&lt;0.001, Mann-Whitney U Test) are bolded and marked with an asterisk. FC, fold change; S, severe atypia. 
         FIGS. 11A-11C  illustrate that integrin adhesion genes predict SLN metastasis.  FIG. 11A  is a graph depicting receiver operating characteristic curves for the three models in Table 16 using the model development cohort.  FIG. 11B  is a graph summarizing the sensitivity and specificity according to the predicted probability of a positive SLNB estimated from model C.  FIG. 11C  is a nomogram for the predicting positive SLNB based on model C. 
         FIGS. 12A-12D  illustrate that IPTG-inducible shRNA effectively knocks down FAK in a B-rafV600E melanoma cell line.  FIG. 12A  is a chart illustrating that IPTG reduces FAK mRNA through shRNA 841 and 102 but not control shRNA (NC) in WM858 cells (mean.+−.s.d.; n=4; *, p&lt;0.05; **, p&lt;0.005; ***, p&lt;0.001). p values, Student&#39;s t-test; ns, not significant.  FIG. 12B  illustrates that FAK shRNA 102 but not control shRNA (NC) reduces FAK protein levels in WM858 cells. IPTG treatment of shRNA-free normal WM858 cells (no shRNA) was without effect on FAK protein levels.  FIGS. 12C and 12D  depict that FAK could be visualized in focal adhesions in WM858 NC but not shRNA 102 cells after 0.05 mM IPTG for 5 days.  FIG. 12C  depicts triple staining DAPI; FAK; Paxillin (PAX) as a focal adhesion marker.  FIG. 12D  depicts DAPI/FAK staining only. Bar, 
         FIGS. 13A-13P  illustrate B-raf V 600E inhibits FAK to promote integrin surface expression.  FIG. 13A : shRNAs 841, 102 and NC were induced in WM858 cells by IPTG for 5 days (n=4) followed by RNA quantitation. Genes regulated at 0 vs. 0.05 mM IPTG in 841 and 102 but not NC cells are shown. These were: ITGB3 (orange), FAK (blue). Light orange, light blue: up- or down-regulation, respectively, by either 841 or 102 shRNA.  FIG. 13B : WM858 cells were transfected with FAK or EGFP cDNA. Regulated genes, FAK over EGFP cells, are shown in orange (up) or blue (down) (n=4).  FIG. 13C : Flow cytometry of NC, 841 and 102 cells (un-induced vs. 0.05 mM IPTG for 5 days).  FIG. 13D : Integrin cell surface mean intensities; mean.+−.s.d.; n=3; *, p&lt;0.05; p values, Student&#39;s t-test; ns, not significant.  FIG. 13E : Visualization of focal adhesions by paxillin staining on micropatterned fibronectin disks.  FIGS. 13F and 13G : Proliferation speed in the absence ( FIG. 13F ) or presence ( FIG. 13G ) of FAK shRNAs; mean.+−.s.d.; n=8; *, p&lt;0.05; p values, Student&#39;s t-test; ns, not significant.  FIGS. 13H and 13I : Scratch wound healing in IPTG-induced cells; representative experiment (n=3).  FIGS. 13J and 13K : Effect of IPTG-induced FAK knock-down on total (t) and phospho (p)-ERK; mean.+−.s.d.; n=4; *, p&lt;0.05; p values, Student&#39;s t-test.  FIG. 13L : Cell surface β1 and β3 integrin expression (flow cytometry) in B-raf V 600E and wild-type cells after overnight drug incubation; % expression relative to DMSO is shown.  FIGS. 13M-13O : FAK/ERK levels in NHM and WM858 after overnight drug incubation ( FIG. 13M ); quantification of FAK ( FIG. 13N ) and ERK phosphorylation ( FIG. 13O ); mean.+−.s.d.; n=4; *, p&lt;0.05; p values, Student&#39;s t-test.  FIG. 13P : ERK activity in NC, 841 and 102 cells (0.05 mM IPTG for 5 days) after overnight drug incubation. 
         FIG. 14  depict the luciferase construct for high-throughput screening. Genomic structure of the SPP1 gene is shown as well as a targeting approach. A DNA double-strand break was induced in exon (E) 2 of SPP1, 3′ of the ATG start codon by a custom-made zinc finger nuclease (ZFN), arrow. A targeting vector with 500 bp homology arms (HA, middle), Hygromycin resistance (HYGRO), a target promoter-driven firefly luciferase (LUC2P), and a CMV-pomoter driven renilla luciferase (HRLUC) was offered for repair at the time of the double-strand break. PA, PA terminator signal. Blue boxes, untranslated region; black boxes, translated region. 
         FIGS. 15A-15J  illustrate that pentamidine inhibits SPP1 expression, proliferation, and invasion of melanoma cells.  FIG. 15A  shows WM858 cells with a luciferase-tagged SPP1 promoter were screened against a LOPAC.  FIGS. 15B-15D  illustrate that pentamidine inhibits SPP1 promoter activity in the DUAL-GLO® assay ( FIG. 15B ), but also by quantitative PCR in normal WM858 ( FIG. 15C ) and M12 cells ( FIG. 15D ).  FIG. 15E  illustrates that pentamidine inhibits the expression of other adhesion molecules, i.e., (33 integrin (ITGB3) and t-PA (PLAT).  FIGS. 15F and 15G  illustrate that pentamidine effectively inhibits M12 invasion into 2 mg/mL of MATRIGEL®.  FIG. 15F  depicts that a visible reduction in Matrigel invasion is observed that exceeds the effects of B-raf inhibition ( FIG. 15G ); blue, area of scratch wound at time zero; yellow line, invasion front; red, RFP-labeled M12 nuclei on phase contrast background.  FIG. 15H  is an image of a female nude mouse harboring an intradermal M12 PDX.  FIG. 15I  is an H&amp;E stained cryosection of an untreated M12 PDX.  FIG. 15I  is a chart illustrating that pentamidine injections reduce SPP1, (33 integrin, and t-PA (PLAT) mRNA expression in M12 PDX. Average of three mice is shown. PENTA, Pentamidine; DABRA, Dabrafenib. WM858 and M12 are B-rafV600E metastatic melanoma cells. 
         FIG. 16  illustrates differential gene expression by NGS in a cohort of four patients with primary skin melanoma that had not metastasized (median Breslow depth: 2.6 mm) and three patients that had metastasized regionally (median Breslow depth: 2.3 mm). Out of a total of 15,196 genes, 208 genes were identified with a FDR&lt;0.01. ITGB3 as well as SRC, a downstream effector of β3 integrin, one formed the center of a functional network deregulated in regionally metastatic vs. non-metastatic melanoma. Genes (nodes) functionally disconnected to any of the other genes were hidden. Functional relationships between genes are indicated by lines and were plotted using the STRING database. 
         FIG. 17  shows integrin cell adhesion is a cellular system differentially expressed in metastatic melanoma vs. non-metastatic pigmented lesions. 164 of 16,029 genes were significantly regulated in benign nevi vs. regionally metastatic melanoma (FDR&lt;0.01) as determined by next-generation sequencing (NGS). Functional relationships between these genes were mapped by the STRING database. Genes without known functional relationships to other genes (i.e., disconnected nodes) or networks with &lt;3 genes were hidden. A large cluster emerged that was functionally related to integrin cell adhesion and the extracellular space (ECM). Additional NGS-based comparison of samples from patients with regional metastasis vs. non-metastatic melanoma revealed the deregulation of an ITGB3/protein kinase C/SRC network in regionally metastatic melanoma. The particularly indicated circles indicate gene up-regulation, regionally metastatic melanoma vs. nevi; blue circles indicate down-regulation, regionally metastatic melanoma vs. nevi. The particularly indicated rings indicate up-regulation, regionally metastatic vs. non-metastatic melanoma. 
     
    
    
     DETAILED DESCRIPTION 
     Provided are methods and materials for identifying metastatic malignant skin lesions (e.g., metastatic 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 metastatic 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  114 ). 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, GAPDH, PGK1, PPIA, RPL13A, YWHAZ, SDHA, TFRC, ALAS1, GUSB, HMBS, HPRT1, TBP, CLTC, MRFAP1, PPP2CA, PSMA1, RPL13A, RPS29, SLC25A3, TXNL1, 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, box  118 . 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 , which is a flow chart of an exemplary process  300 , once a keratinocyte correction factor is 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 disclosures 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 controller  1412  connecting to low-speed expansion port  1414  and storage device  1406 . Each of the components  1402 ,  1404 ,  1406 ,  1408 ,  1410 , and  1412 , are interconnected using various buses, 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 interface  1408  manages bandwidth-intensive operations for the computing device  1400 , while the low-speed controller  1412  manages lower bandwidth-intensive operations. Such allocation of functions is exemplary only. In one implementation, the high-speed interface  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  1412  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 the figure. 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 the figure. 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. 
     This document also provides methods and materials involved in treating mammals having skin cancer (e.g., melanoma such as pre-metastatic melanoma) by administering pentamidine to the mammal. Any appropriate mammal having skin cancer can be treated as described herein. For example, humans and other primates such as monkeys having skin cancer can be treated with pentamidine. In some cases, dogs, cats, horses, bovine species, porcine species, mice, or rats can be treated with pentamidine as described herein. In addition, a mammal having any particular type of skin cancer can be treated as described herein. For example, a mammal having melanoma, pre-metastatic melanoma, locally metastatic melanoma (i.e., skin in close proximity to primary melanoma), regionally metastatic melanoma (e.g., metastases to regional sentinel lymph nodes), or distant metastases (e.g., metastases to internal organs) can be treated with pentamidine as described herein. In some cases, a mammal determined to have skin cancer cells that express an elevated level of one or more marker genes described herein (e.g., PLAT, ITGB3, LAMB1, and/or TP53) can be treated with pentamidine. In some cases, a mammal (e.g., a human) determined to have skin cancer cells that express an elevated level of one or more marker genes (e.g., PLAT, ITGB3, LAMB1, and/or TP53) using the methods or materials provided herein can be treated with pentamidine. 
     Any appropriate method can be used to identify a mammal having skin cancer (e.g., pre-metastatic melanoma) that can be treated using pentamidine. For example, imaging, biopsy, pathology, PCR, and sequencing techniques can be used to identify a human having skin cancer cells that express an elevated level of PLAT, ITGB3, LAMB1, and/or TP53. 
     Once identified as having skin cancer or skin cancer that expresses an elevated level of PLAT, ITGB3, LAMB1, and/or TP53, the mammal can be administered pentamidine. In some cases, pentamidine can be administered in combination with a chemotherapeutic agent to treat skin cancer (e.g., pre-metastatic melanoma). Examples of chemotherapeutic agents that can be used in combination with pentamidine include, without limitation, taxane therapies, anthracycline therapies, and gemcitabine therapies. Examples of taxane therapies include, without limitation, cancer treatments that involve administering taxane agents such as paclitaxel, docetacel, or other microtubule disrupting agents such as vinblastine, vincristine, or vinorelbine. In some cases, drugs used to treat gout or chochicine can be used as described herein to treat a mammal having skin cancer. Examples of anthracycline therapies include, without limitation, cancer treatments that involve administering anthracycline agents such as doxorubicine, daunorubicin, epirubicin, idarubicin, valrubicin, or mitoxantrone. 
     In some cases, pentamidine can be formulated into a pharmaceutically acceptable composition for administration to a mammal having skin cancer (e.g., pre-metastatic melanoma). For example, a therapeutically effective amount of pentamidine can be formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents. A pharmaceutical composition can be formulated for administration in solid or liquid form including, without limitation, sterile solutions, suspensions, sustained-release formulations, tablets, capsules, pills, powders, and granules. 
     Pharmaceutically acceptable carriers, fillers, and vehicles that may be used in a pharmaceutical composition described herein include, without limitation, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, polyethylene glycol and wool fat. 
     A pharmaceutical composition containing pentamidine can be designed for oral or parenteral (including subcutaneous, intramuscular, intravenous, and intradermal) administration. When being administered orally, a pharmaceutical composition containing pentamidine can be in the form of a pill, tablet, or capsule. Compositions suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions that can contain anti-oxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions that may include suspending agents and thickening agents. The formulations can be presented in unit-dose or multi-dose containers, for example, sealed ampules and vials, and may be stored in a freeze dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, water for injections, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules, and tablets. 
     Such injection solutions can be in the form, for example, of a sterile injectable aqueous or oleaginous suspension. This suspension may be formulated using, for example, suitable dispersing or wetting agents (such as, for example, TWEEN® 80) and suspending agents. The sterile injectable preparation can be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Examples of acceptable vehicles and solvents that can be used include, without limitation, mannitol, Ringer&#39;s solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils can be used as a solvent or suspending medium. In some cases, a bland fixed oil can be used such as synthetic mono- or di-glycerides. Fatty acids, such as oleic acid and its glyceride derivatives can be used in the preparation of injectables, as can natural pharmaceutically-acceptable oils, such as olive oil or castor oil, including those in their polyoxyethylated versions. In some cases, these oil solutions or suspensions can contain a long-chain alcohol diluent or dispersant. 
     In some cases, a pharmaceutically acceptable composition including pentamidine can be administered locally or systemically. For example, a composition containing pentamidine can be administered locally by injection into lesions at surgery or by subcutaneous administration of a sustained release formulation. In some cases, a composition containing pentamidine can be administered systemically orally or by injection to a mammal (e.g., a human). 
     Effective doses can vary depending on the severity of the cancer, the route of administration, the age and general health condition of the subject, excipient usage, the possibility of co-usage with other therapeutic treatments such as use of chemotherapeutic agents, and the judgment of the treating physician. 
     An effective amount of a composition containing pentamidine can be any amount that reduces skin cancer progression without producing significant toxicity to the mammal. For example, an effective amount of pentamidine can be from about 0.01 mg/kg to about 4 mg/kg. In some cases, between about 10 mg and about 1500 mg of pentamidine can be administered to an average sized human (e.g., about 70-75 kg human) daily for about one week to about one year (e.g., about two weeks to about four months). If a particular mammal fails to respond to a particular amount, then the amount of pentamidine can be increased by, for example, two fold. After receiving this higher amount, the mammal can be monitored for both responsiveness to the treatment and toxicity symptoms, and adjustments made accordingly. The effective amount can remain constant or can be adjusted as a sliding scale or variable dose depending on the mammal&#39;s response to treatment. Various factors can influence the actual effective amount used for a particular application. For example, the frequency of administration, duration of treatment, use of multiple treatment agents, route of administration, and severity of the cancer may require an increase or decrease in the actual effective amount administered. 
     The frequency of administration can be any frequency that reduces skin cancer progression without producing significant toxicity to the mammal. For example, the frequency of administration can be from about once a week to about once every two to three weeks. The frequency of administration can remain constant or can be variable during the duration of treatment. A course of treatment with a composition containing pentamidine can include rest periods. For example, a composition containing pentamidine can be administered daily over a two week period followed by a two week rest period, and such a regimen can be repeated multiple times. As with the effective amount, various factors can influence the actual frequency of administration used for a particular application. For example, the effective amount, duration of treatment, use of multiple treatment agents, route of administration, and severity of the cancer may require an increase or decrease in administration frequency. 
     An effective duration for administering a composition containing pentamidine can be any duration that reduces skin cancer progression without producing significant toxicity to the mammal. Thus, the effective duration can vary from several days to several weeks, months, or years. In general, the effective duration for the treatment with pentamidine to reduce skin cancer progression can range in duration from six months to one year. Multiple factors can influence the actual effective duration used for a particular treatment. For example, an effective duration can vary with the frequency of administration, effective amount, use of multiple treatment agents, route of administration, and severity of the condition being treated. 
     In certain instances, a course of treatment and the severity of one or more symptoms related to the skin cancer being treated (e.g., pre-metastatic melanoma) can be monitored. Any appropriate method can be used to determine whether or not cancer progression is reduced. For example, the severity of a symptom of skin cancer can be assessed using imagine and pathology assessment of biopsy samples or surgical samples. 
     This disclosure will be further described in the following examples, which do not limit the scope of the disclosure 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. &gt;zero versions of each variable were included. The top five discriminatory genes based on each statistical test were highlighted in bold. 
     
       
         
           
               
               
               
             
               
                   
                 TABLE A 
               
             
            
               
                   
                   
               
               
                   
                   
                 Test statistic value 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 Wilcoxon 
                 Winsorized 
                   
               
               
                   
                   
                 rank sum 
                 two-sample 
                 Chi-square 
               
               
                   
                 gene 
                 test 
                 t-test 
                 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, LAMAS, CDKN1A, CDKN2A, LAMC2, PCOLCE2, LOXL4, PCOLCE, LAMBS, 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 five genes were highlighted. 
     
       
         
           
               
               
             
               
                 TABLE B 
               
             
            
               
                   
               
               
                   
                 Test statistic value 
               
            
           
           
               
               
               
               
            
               
                   
                 Wilcoxon 
                 Winsorized 
                   
               
               
                   
                 rank sum 
                 two-sample 
                 Chi-square 
               
               
                 gene 
                 test 
                 t-test 
                 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 &gt; 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 &gt; 0 
               
               
                 CD44 
                 
                   5.23089 
                 
                 
                   7.17590 
                 
                 All but 1 value &gt; 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. 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 GENBANK ® 
                 GENBANK ® 
               
               
                   
                 Gene Name 
                 Accession No. 
                 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 
                 067782348 
               
               
                   
                 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′-CCAGAGCTGTGCAGATGAGT-3′; 
                 5′-TGCATCTAGATTCTTTGCCTTT-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: 431 
                 SEQ ID NO: 432 
               
               
                   
                 5′-GGTGGTATGTGACCTTGGAAA-3′; 
                 5′-GCACACTGAAACGAAGACCA-3′; 
               
               
                   
                 SEQ ID NO: 439 
                 SEQ ID NO: 440 
               
               
                   
               
               
                 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 
               
               
                   
               
               
                 ITGB3 
                 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′-CTGCCATGACCTGTTTCCT-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′-CGGCTTTCTCATCAGGI1TTC-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: 443 
                 SEQ ID NO: 444 
               
               
                   
               
               
                 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′-GCTGACCTCCTGGATAGTGG-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′-GAGACCTTCGGCGAGTACAG-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′-ATTCTTTCGGTCGTGGATG-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′-GCTTGAGCTGAGCTTTTCC-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- 
                 5′-ATGGTGCGCAGGTTCTTG-3′; 
                 5′-ACCAGCGTGTCCAGGAAG-3′; 
               
               
                 004 2A-201 
                 SEQ ID NO: 367 
                 SEQ ID NO: 368 
               
               
                   
               
               
                 CDKN2A- 
                 5′-GAGCAGCATGGAGCCTTC-3′; 
                 5′-GCATGGTTACTGCCTCTGGT-3′; 
               
               
                 001 2A-202 
                 SEQ ID NO: 369 
                 SEQ ID NO: 370 
               
               
                   
               
               
                 ITGA2 
                 5′-CAAACAGACAAGGCTGGTGA-3′; 
                 5′-TCAATCTCATCTGGATTTTGG-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 
               
               
                   
               
               
                 RPL8 
                 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: 423 
                 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 51 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&amp;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. &gt;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 &lt; 
                 4 
                 72 
                 76 
               
               
                   
                 45 
                 3.15 
                 56.69 
                 59.84 
               
               
                   
                   
                 5.26 
                 94.74 
                   
               
               
                   
                   
                 7.41 
                 98.63 
                   
               
               
                   
                 FN1 ≥ 
                 50 
                 1 
                 51 
               
               
                   
                 45 
                 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 &lt; 
                 8 
                 73 
                 81 
               
               
                   
                 124 
                 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 &lt; 45 and SPP1 = 0   2   72           FN1 ≥ 45   52   1           or                   (FN1 &lt; 45 and SPP1 &gt; 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 &lt; 45 and ITGB3 = 0 
                 3 
                 72 
               
               
                   
                 FN1 ≥ 45 
                 51 
                 1 
               
               
                   
                 or 
                   
                   
               
               
                   
                 (FN1 &lt; 45 and ITGB3 &gt; 0) 
                   
                   
               
               
                   
                 Total 
                 54 
                 73 
               
               
                   
                   
               
            
           
         
       
     
     If all three genes are included, the rule was as follows: 
     FN1&lt;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 
                   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 &lt;45 
                 Zero 
                 Zero 
                 No 
                 72 
                   
               
               
                 &lt;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 
                 &gt;0 
                 Yes 
                 1 
                   
               
               
                 ≥45 
                 &gt;0 
                 Zero 
                 Yes 
                 18 
                   
               
               
                 ≥45 
                 &gt;0 
                 &gt;0 
                 Yes 
                 22 
                   
               
               
                 &lt;45 
                 Zero 
                 &gt;0 
                 Yes 
                 1 
                   
               
               
                 &lt;45 
                 &gt;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 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 &lt;45 
                 Zero 
                 Zero 
                 19 
               
               
                   
                 &lt;45 
                 &gt;0 
                 Zero 
                 1 
               
               
                   
                 ≥45 
                 Zero 
                 Zero 
                 2 
               
               
                   
                 ≥45 
                 &gt;0 
                 Zero 
                 3 
               
               
                   
                 &lt;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 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 &lt;45 
                 Zero 
                 Zero 
                 25 
               
               
                   
                 &lt;45 
                 Zero 
                 &gt;0 
                 1 
               
               
                   
                 ≥45 
                 Zero 
                 Zero 
                 5 
               
               
                   
                 ≥45 
                 &gt;0 
                 Zero 
                 2 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE C 
               
             
            
               
                   
               
               
                 Comparison of gene expression between benign and malignant 
               
            
           
           
               
               
               
               
            
               
                   
                 Benign 
                 Malignant 
                   
               
               
                   
                 (N = 73) 
                 (N = 54) 
                 p value 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 CXCL1_AVG_NORM 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;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 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 58 (79.5%) 
                 12 (22.2%) 
                   
               
               
                   
                 &gt;0 
                 15 (20.5%) 
                 42 (77.8%) 
                   
               
               
                   
                 CSF2_AVG_NORM01 
                   
                   
                 0.0398 
               
               
                   
                 Zero 
                 15 (20.5%) 
                 20 (37.0%) 
                   
               
               
                   
                 &gt;0 
                 58 (79.5%) 
                 34 (63.0%) 
                   
               
               
                   
                 CCL2_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 53 (72.6%) 
                 12 (22.2%) 
                   
               
               
                   
                 &gt;0 
                 20 (27.4%) 
                 42 (77.8%) 
                   
               
               
                   
                 IL8_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 63 (86.3%) 
                 10 (18.5%) 
                   
               
               
                   
                 &gt;0 
                 10 (13.7%) 
                 44 (81.5%) 
                   
               
               
                   
                 IL6_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 65 (89.0%) 
                 13 (24.1%) 
                   
               
               
                   
                 &gt;0 
                  8 (11.0%) 
                 41 (75.9%) 
                   
               
               
                   
                 ITGA5_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                  73 (100.0%) 
                 38 (70.4%) 
                   
               
               
                   
                 &gt;0 
                 0 (0.0%) 
                 16 (29.6%) 
                   
               
               
                   
                 ITGA3_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 72 (98.6%) 
                 13 (24.1%) 
                   
               
               
                   
                 &gt;0 
                 1 (1.4%) 
                 41 (75.9%) 
                   
               
               
                   
                 ITGA2_AVG_NORM01 
                   
                   
                 0.0007 
               
               
                   
                 Zero 
                  73 (100.0%) 
                 46 (85.2%) 
                   
               
               
                   
                 &gt;0 
                 0 (0.0%) 
                  8 (14.8%) 
                   
               
               
                   
                 ITGAV_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 71 (97.3%) 
                 24 (44.4%) 
                   
               
               
                   
                 &gt;0 
                 2 (2.7%) 
                 30 (55.6%) 
                   
               
               
                   
                 ITGB3_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                  73 (100.0%) 
                 30 (55.6%) 
                   
               
               
                   
                 &gt;0 
                 0 (0.0%) 
                 24 (44.4%) 
                   
               
               
                   
                 ITGB1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 64 (87.7%) 
                 11 (20.4%) 
                   
               
               
                   
                 &gt;0 
                  9 (12.3%) 
                 43 (79.6%) 
                   
               
               
                   
                 FN1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 69 (94.5%) 
                 2 (3.7%) 
                   
               
               
                   
                 &gt;0 
                 4 (5.5%) 
                 52 (96.3%) 
                   
               
               
                   
                 THBS1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                  73 (100.0%) 
                 24 (44.4%) 
                   
               
               
                   
                 &gt;0 
                 0 (0.0%) 
                 30 (55.6%) 
                   
               
               
                   
                 THBS2_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 67 (91.8%) 
                 23 (42.6%) 
                   
               
               
                   
                 &gt;0 
                 6 (8.2%) 
                 31 (57.4%) 
                   
               
               
                   
                 THBS4_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 58 (79.5%) 
                 15 (27.8%) 
                   
               
               
                   
                 &gt;0 
                 15 (20.5%) 
                 39 (72.2%) 
                   
               
               
                   
                 VCAN_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 71 (97.3%) 
                 16 (29.6%) 
                   
               
               
                   
                 &gt;0 
                 2 (2.7%) 
                 38 (70.4%) 
                   
               
               
                   
                 BGAN_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 42 (57.5%) 
                  7 (13.0%) 
                   
               
               
                   
                 &gt;0 
                 31 (42.5%) 
                 47 (87.0%) 
                   
               
               
                   
                 SPP1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                  73 (100.0%) 
                 12 (22.2%) 
                   
               
               
                   
                 &gt;0 
                 0 (0.0%) 
                 42 (77.8%) 
                   
               
               
                   
                 TNC_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 60 (82.2%) 
                 3 (5.6%) 
                   
               
               
                   
                 &gt;0 
                 13 (17.8%) 
                 51 (94.4%) 
                   
               
               
                   
                 SPARC_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 57 (78.1%) 
                 13 (24.1%) 
                   
               
               
                   
                 &gt;0 
                 16 (21.9%) 
                 41 (75.9%) 
                   
               
               
                   
                 AGRN_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 59 (80.8%) 
                 5 (9.3%) 
                   
               
               
                   
                 &gt;0 
                 14 (19.2%) 
                 49 (90.7%) 
                   
               
               
                   
                 CTGF_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 72 (98.6%) 
                 21 (38.9%) 
                   
               
               
                   
                 &gt;0 
                 1 (1.4%) 
                 33 (61.1%) 
                   
               
               
                   
                 CYR61_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 56 (76.7%) 
                  9 (16.7%) 
                   
               
               
                   
                 &gt;0 
                 17 (23.3%) 
                 45 (83.3%) 
                   
               
               
                   
                 LAMA3_AVG_NORM01 
                   
                   
                 0.0003 
               
               
                   
                 Zero 
                 72 (98.6%) 
                 43 (79.6%) 
                   
               
               
                   
                 &gt;0 
                 1 (1.4%) 
                 11 (20.4%) 
                   
               
               
                   
                 LAMC1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                  73 (100.0%) 
                 24 (44.4%) 
                   
               
               
                   
                 &gt;0 
                 0 (0.0%) 
                 30 (55.6%) 
                   
               
               
                   
                 LAMB1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 66 (90.4%) 
                 22 (40.7%) 
                   
               
               
                   
                 &gt;0 
                 7 (9.6%) 
                 32 (59.3%) 
                   
               
               
                   
                 LAMA1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 57 (78.1%) 
                 16 (29.6%) 
                   
               
               
                   
                 &gt;0 
                 16 (21.9%) 
                 38 (70.4%) 
                   
               
               
                   
                 LAMC2_AVG_NORM01 
                   
                   
                 0.0003 
               
               
                   
                 Zero 
                  73 (100.0%) 
                 45 (83.3%) 
                   
               
               
                   
                 &gt;0 
                 0 (0.0%) 
                  9 (16.7%) 
                   
               
               
                   
                 LAMB3_AVG_NORM01 
                   
                   
                 0.0061 
               
               
                   
                 Zero 
                 45 (61.6%) 
                 20 (37.0%) 
                   
               
               
                   
                 &gt;0 
                 28 (38.4%) 
                 34 (63.0%) 
                   
               
               
                   
                 COL1A1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 60 (82.2%) 
                 17 (31.5%) 
                   
               
               
                   
                 &gt;0 
                 13 (17.8%) 
                 37 (68.5%) 
                   
               
               
                   
                 COL4A1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                  73 (100.0%) 
                 13 (24.1%) 
                   
               
               
                   
                 &gt;0 
                 0 (0.0%) 
                 41 (75.9%) 
                   
               
               
                   
                 COL18A1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 64 (87.7%) 
                 18 (33.3%) 
                   
               
               
                   
                 &gt;0 
                 9 (12.3%) 
                 36 (66.7%) 
                   
               
               
                   
                 LOX_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 60 (82.2%) 
                 26 (48.1%) 
                   
               
               
                   
                 &gt;0 
                 13 (17.8%) 
                 28 (51.9%) 
                   
               
               
                   
                 LOXL1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 72 (98.6%) 
                 23 (42.6%) 
                   
               
               
                   
                 &gt;0 
                 1 (1.4%) 
                 31 (57.4%) 
                   
               
               
                   
                 LOXL2_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 70 (95.9%) 
                 19 (35.2%) 
                   
               
               
                   
                 &gt;0 
                 3 (4.1%) 
                 35 (64.8%) 
                   
               
               
                   
                 LOXL3_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 69 (94.5%) 
                 10 (18.5%) 
                   
               
               
                   
                 &gt;0 
                 4 (5.5%) 
                 44 (81.5%) 
                   
               
               
                   
                 LOXL4_AVG_NORM01 
                   
                   
                 0.0006 
               
               
                   
                 Zero 
                 53 (72.6%) 
                 23 (42.6%) 
                   
               
               
                   
                 &gt;0 
                 20 (27.4%) 
                 31 (57.4%) 
                   
               
               
                   
                 PLOD1_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 59 (80.8%) 
                 12 (22.2%) 
                   
               
               
                   
                 &gt;0 
                 14 (19.2%) 
                 42 (77.8%) 
                   
               
               
                   
                 PLOD2_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 59 (80.8%) 
                 10 (18.5%) 
                   
               
               
                   
                 &gt;0 
                 14 (19.2%) 
                 44 (81.5%) 
                   
               
               
                   
                 PLOD3_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 66 (90.4%) 
                 11 (20.4%) 
                   
               
               
                   
                 &gt;0 
                 7 (9.6%) 
                 43 (79.6%) 
                   
               
               
                   
                 PCOLCE2_AVG_NORM01 
                   
                   
                 0.0002 
               
               
                   
                 Zero 
                 66 (90.4%) 
                 34 (63.0%) 
                   
               
               
                   
                 &gt;0 
                 7 (9.6%) 
                 20 (37.0%) 
                   
               
               
                   
                 PCOLCE_AVG_NORM01 
                   
                   
                 0.0036 
               
               
                   
                 Zero 
                 42 (57.5%) 
                 17 (31.5%) 
                   
               
               
                   
                 &gt;0 
                 31 (42.5%) 
                 37 (68.5%) 
                   
               
               
                   
                 PTK2_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 67 (91.8%) 
                 16 (29.6%) 
                   
               
               
                   
                 &gt;0 
                 6 (8.2%) 
                 38 (70.4%) 
                   
               
               
                   
                 CSRC_AVG_NORM01 
                   
                   
                 0.0001 
               
               
                   
                 Zero 
                 36 (49.3%) 
                  9 (16.7%) 
                   
               
               
                   
                 &gt;0 
                 37 (50.7%) 
                 45 (83.3%) 
                   
               
               
                   
                 CDKN1A_AVG_NORM01 
                   
                   
                 0.0001 
               
               
                   
                 Zero 
                 48 (65.8%) 
                 16 (29.6%) 
                   
               
               
                   
                 &gt;0 
                 25 (34.2%) 
                 38 (70.4%) 
                   
               
               
                   
                 CDKN2A_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 57 (78.1%) 
                 23 (42.6%) 
                   
               
               
                   
                 &gt;0 
                 16 (21.9%) 
                 31 (57.4%) 
                   
               
               
                   
                 TP53_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 59 (80.8%) 
                 16 (29.6%) 
                   
               
               
                   
                 &gt;0 
                 14 (19.2%) 
                 38 (70.4%) 
                   
               
               
                   
                 YAP_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 68 (93.2%) 
                 22 (40.7%) 
                   
               
               
                   
                 &gt;0 
                 5 (6.8%) 
                 32 (59.3%) 
                   
               
               
                   
                 TAZ_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 54 (74.0%) 
                 19 (35.2%) 
                   
               
               
                   
                 &gt;0 
                 19 (26.0%) 
                 35 (64.8%) 
                   
               
               
                   
                 MITF_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 26 (35.6%) 
                 2 (3.7%) 
                   
               
               
                   
                 &gt;0 
                 47 (64.4%) 
                 52 (96.3%) 
                   
               
               
                   
                 MLANA_AVG_NORM01 
                   
                   
                   
               
               
                   
                 &gt;0 
                  73 (100.0%) 
                  54 (100.0%) 
                   
               
               
                   
                 TYR_AVG_NORM01 
                   
                   
                 0.2202 
               
               
                   
                 Zero 
                 2 (2.7%) 
                 0 (0.0%) 
                   
               
               
                   
                 &gt;0 
                 71 (97.3%) 
                  54 (100.0%) 
                   
               
               
                   
                 POSTN_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 32 (43.8%) 
                 4 (7.4%) 
                   
               
               
                   
                 &gt;0 
                 41 (56.2%) 
                 50 (92.6%) 
                   
               
               
                   
                 FBLN2_AVG_NORM01 
                   
                   
                 &lt;0.0001 
               
               
                   
                 Zero 
                 71 (97.3%) 
                 31 (57.4%) 
                   
               
               
                   
                 &gt;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. 
     Example 3—Additional Marker Panel 
     A test kit panel was designed to include primers for assessing expression levels of eight marker genes (ITGB3, TNC, SPP1, SPARC, PLAT, COL4A1, PLOD3, and PTK2) as well as three housekeeping genes (ACTB, RPLP0, and RPL8), one keratinocyte markers (K14) to assess keratinocyte contamination, and two melanocyte markers (MLANA and MITF) to assess melanocyte content in the skin sections. The primers designed for this collection are set forth in Table 11. 
     
       
         
           
               
             
               
                 TABLE 11 
               
             
            
               
                   
               
               
                 Primers for marker panel kit. 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Primer 
                   
                   
                 SEQ 
               
               
                   
                 pair 
                 Direc- 
                   
                 ID 
               
               
                 Gene 
                 name 
                 tion 
                 Sequence 
                 NO: 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 ACTB 
                 ACTB-G 
                 -F 
                 TGCTATCCCTGTACGCCTCT 
                 433 
               
               
                   
                 ACTB-G 
                 -R 
                 GAGTCCATCACGATGCCAGT 
                 434 
               
               
                   
               
               
                 ACTB 
                 ACTB-H 
                 -F 
                 GGACTTCGAGCAAGAGATGG 
                 435 
               
               
                   
                 ACTB-H 
                 -R 
                 CTTCTCCAGGGAGGAGCTG 
                 436 
               
               
                   
               
               
                 ACTB 
                 ACTB-I 
                 -F 
                 GGCTACAGCTTCACCACCAC 
                 425 
               
               
                   
                 ACTB-I 
                 -R 
                 TAATGTCACGCACGATTTCC 
                 426 
               
               
                   
               
               
                 RPLP0 
                 RPLP0-B 
                 -F 
                 AACTCTGCATTCTCGCTTCC 
                 9 
               
               
                   
                 RPLP0-B 
                 -R 
                 GCAGACAGACACTGGCAACA 
                 10 
               
               
                   
               
               
                 RPLP0 
                 RPLP0-C 
                 -F 
                 GCACCATTGAAATCCTGAGTG 
                 11 
               
               
                   
                 RPLP0-C 
                 -R 
                 GCTCCCACTTTGTCTCCAGT 
                 12 
               
               
                   
               
               
                 RPL8 
                 RPL8-B 
                 -F 
                 ACAGAGCTGTGGTTGGTGTG 
                 19 
               
               
                   
                 RPL8-B 
                 -R 
                 TTGTCAATTCGGCCACCT 
                 20 
               
               
                   
               
               
                 RPL8 
                 RPL8-E 
                 -F 
                 ACTGCTGGCCACGAGTACG 
                 17 
               
               
                   
                 RPL8-E 
                 -R 
                 ATGCTCCACAGGATTCATGG 
                 18 
               
               
                   
               
               
                 KRT14 
                 KRT14-D 
                 -F 
                 TCCGCACCAAGTATGAGACA 
                 39 
               
               
                   
                 KRT14-D 
                 -R 
                 ACTCATGCGCAGGTTCAACT 
                 40 
               
               
                   
               
               
                 KRT14 
                 KRT14-F 
                 -F 
                 GATGCAGATTGAGAGCCTGA 
                 437 
               
               
                   
                 KRT14-F 
                 -R 
                 TTCTTCAGGTAGGCCAGCTC 
                 438 
               
               
                   
               
               
                 MLANA 
                 MLANA-C 
                 -F 
                 GAGAAAAACTGTGAACCTGTGG 
                 53 
               
               
                   
                 MLANA-C 
                 -R 
                 ATAAGCAGGTGGAGCATTGG 
                 54 
               
               
                   
               
               
                 MITF 
                 MITF-B 
                 -F 
                 CGGCATTTGTTGCTCAGAAT 
                 47 
               
               
                   
                 MITF-B 
                 -R 
                 GAGCCTGCATTTCAAGTTCC 
                 48 
               
               
                   
               
               
                 ITGB3 
                 ITGB3-A 
                 -F 
                 AAGAGCCAGAGTGTCCCAAG 
                 159 
               
               
                   
                 ITGB3-A 
                 -R 
                 ACTGAGAGCAGGACCACCA 
                 160 
               
               
                   
               
               
                 ITGB3 
                 ITGB3-B 
                 -F 
                 CTTCTCCTGTGTCCGCTACAA 
                 161 
               
               
                   
                 ITGB3-B 
                 -R 
                 CATGGCCTGAGCACATCTC 
                 162 
               
               
                   
               
               
                 PLAT 
                 PLAT-C 
                 -F 
                 CCCAGCCAGGAAATCCAT 
                 427 
               
               
                   
                 PLAT-C 
                 -R 
                 CTGGCTCCTCTTCTGAATCG 
                 428 
               
               
                   
               
               
                 PLAT 
                 PLAT-D 
                 -F 
                 CAGTGCCTGTCAAAAGTTGC 
                 429 
               
               
                   
                 PLAT-D 
                 -R 
                 CCCCGTTGAAACACCTTG 
                 430 
               
               
                   
               
               
                 PLAT 
                 PLAT-E 
                 -F 
                 GAAGGATTTGCTGGGAAGTG 
                 441 
               
               
                   
                 PLAT-E 
                 -R 
                 CGTGGCCCTGGTATCTATTT 
                 442 
               
               
                   
               
               
                 PLOD3 
                 PLOD3-D 
                 -F 
                 GGAAGGAATCGTGGAGCAG 
                 111 
               
               
                   
                 PLOD3-D 
                 -R 
                 CAGCAGTGGGAACCAGTACA 
                 112 
               
               
                   
               
               
                 PTK2 
                 PTK2-D 
                 -F 
                 GAGACCATTCCCCTCCTACC 
                 119 
               
               
                   
                 PTK2-D 
                 -R 
                 GCTTCTGTGCCATCTCAATCT 
                 120 
               
               
                   
               
               
                 CDKN2A 
                 CDKN2A1-C 
                 -F 
                 AGGAGCCAGCGTCTAGGG 
                 219 
               
               
                   
                 CDKN2A1-C 
                 -R 
                 CTGCCCATCATCATGACCT 
                 220 
               
               
                   
               
               
                 CDKN2A 
                 CDKN2A2-C 
                 -F 
                 AACGCACCGAATAGTTACGG 
                 221 
               
               
                   
                 CDKN2A2-C 
                 -R 
                 CATCATCATGACCTGGATCG 
                 222 
               
               
                   
               
            
           
         
       
     
     One purpose of the kit was to differentiate between melanoma with high and low risk of regional metastasis, and to appropriately select patients for surgical procedures such as sentinel lymph node biopsy (SLNB) or total lymphadenectomy. Another purpose of this kit was to estimate disease-free survival, disease relapse, or likelihood of death from melanoma. To study the ability of these methods to discriminate between melanoma with high and low risk of metastasis and to establish superiority to established methods, a cohort of 158 patients between October 1998 and June 2013 were identified as having been diagnosed with high-risk melanoma and as having underwent SLNB with the intention to assess metastatic potential of the tumor. Of note, high-risk melanoma by current criteria are defined as melanoma with an invasion depth (Breslow depth) of ≥1 mm; or melanoma with an invasion depth of 0.75 to 0.99 mm plus the presence of either one of the following three risk factors: &gt;0 mitotic figures/mm 2 ; tumor ulceration present; patient age&lt;40 years. 
     All 158 patients met the criteria for high risk. 136 patients had a Breslow Depth≥1 mm. 22 patients had a Breslow Depth between 0.75 and 0.99 and had at least one of the aforementioned three risk factors (ulceration, mitotic rate&gt;0, age&lt;40). Of the 158 patients, 36 (22.8%) had a melanoma-positive SLNB. 
     To select genes for a test kit from a pool of genes, the expression level of 52 genes (variables) was initially determined and dichotomized as zero vs. &gt;zero and evaluated for an association with positive SLNB using the chi-square test for a 2×2 contingency level. The genes are ordered based on the value of the chi-square test statistic (Table 12). 
     
       
         
           
               
               
               
             
               
                   
                 TABLE 12 
               
               
                   
                   
               
               
                   
                 Value of the chi-square  
                   
               
               
                   
                 test statistic 
                 variable 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                   
                 ITGB3 
                 68.3522 
               
               
                   
                 SPP1 
                 25.8460 
               
               
                   
                 LOXL3 
                 16.7683 
               
               
                   
                 PLAT 
                 16.5721 
               
               
                   
                 LAMB1 
                 15.7544 
               
               
                   
                 YAP 
                 13.4049 
               
               
                   
                 PLOD3 
                 12.6062 
               
               
                   
                 TP53 
                 12.3662 
               
               
                   
                 COL4A1 
                 11.8336 
               
               
                   
                 TNC 
                 11.3862 
               
               
                   
                 IL8 
                 10.4697 
               
               
                   
                 ITGA5 
                 10.3561 
               
               
                   
                 COL1A1 
                 10.0006 
               
               
                   
                 VCAN 
                 9.3250 
               
               
                   
                 PLOD1 
                 8.6959 
               
               
                   
                 FN1 
                 8.4857 
               
               
                   
                 PTK2 
                 7.9874 
               
               
                   
                 ITGAV 
                 7.7181 
               
               
                   
                 LOXL1 
                 7.2109 
               
               
                   
                 LOXL2 
                 6.6348 
               
               
                   
                 ITGB1 
                 6.3556 
               
               
                   
                 CDKN1A 
                 6.3117 
               
               
                   
                 CTGF 
                 6.2588 
               
               
                   
                 GDF15 
                 5.96939 
               
               
                   
                 CSRC 
                 5.4435 
               
               
                   
                 ITGA2 
                 5.0326 
               
               
                   
                 ITGA3 
                 4.0603 
               
               
                   
                 LOX 
                 3.8697 
               
               
                   
                 COL18A1 
                 3.3392 
               
               
                   
                 IL6 
                 3.0435 
               
               
                   
                 DSPP 
                 2.7822 
               
               
                   
                 NTRK3 
                 2.7822 
               
               
                   
                 LOXL4 
                 2.7279 
               
               
                   
                 THBS2 
                 2.5110 
               
               
                   
                 SPARC 
                 1.9884 
               
               
                   
                 PCOLCE2 
                 1.6499 
               
               
                   
                 AGRN 
                 1.6118 
               
               
                   
                 CXCL1 
                 1.3483 
               
               
                   
                 TAZ 
                 1.3458 
               
               
                   
                 THBS4 
                 1.1281 
               
               
                   
                 PCOLCE 
                 0.9198 
               
               
                   
                 FBLN2 
                 0.9198 
               
               
                   
                 LAMC2 
                 0.9157 
               
               
                   
                 CCL2 
                 0.8701 
               
               
                   
                 CDKN2A 
                 0.6047 
               
               
                   
                 CSF2 
                 0.5408 
               
               
                   
                 CYR61 
                 0.4713 
               
               
                   
                 BGAN 
                 0.4364 
               
               
                   
                 LAMA3 
                 0.3455 
               
               
                   
                 POSTN 
                 0.1902 
               
               
                   
                 LAMB3 
                 0.1058 
               
               
                   
                 PLOD2 
                 0.0152 
               
               
                   
                   
               
            
           
         
       
     
     As can be deduced from the chi-square test statistic, ITGB3 was highly discriminatory between melanoma with and without regional lymph node metastasis. The n (%) with a positive SLNB for those with no expression vs. expression level&gt;0 was summarized (Table 13). 
     
       
         
           
               
               
               
               
               
             
               
                   
                 TABLE 13 
               
               
                   
                   
               
               
                   
                   
                   
                 Overall 
                 Positive 
               
               
                   
                   
                   
                 No. (% of 158) 
                 No. (% of each row) 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 FN1_01 
                   
                   
               
               
                   
                   
                 Zero 
                 110 (69.6%) 
                 18 (16.4%) 
               
               
                   
                   
                 &gt;0 
                  48 (30.4%) 
                 18 (37.5%) 
               
               
                   
                   
                 SPP1_01 
                   
                   
               
               
                   
                   
                 Zero 
                  93 (58.9%) 
                 8 (8.6%) 
               
               
                   
                   
                 &gt;0 
                  65 (41.1%) 
                 28 (43.1%) 
               
               
                   
                   
                 ITGB3_01 
                   
                   
               
               
                   
                   
                 Zero 
                 107 (67.7%) 
                 4 (3.7%) 
               
               
                   
                   
                 &gt;0 
                  51 (32.3%) 
                 32 (62.7%) 
               
               
                   
                   
                 TNC_01 
                   
                   
               
               
                   
                   
                 Zero 
                 114 (72.2%) 
                 18 (15.8%) 
               
               
                   
                   
                 &gt;0 
                  44 (27.8%) 
                 18 (40.9%) 
               
               
                   
                   
                 PLAT_01 
                   
                   
               
               
                   
                   
                 Missing 
                  18 
                 0 
               
               
                   
                   
                 Zero 
                  83 (59.3%) 
                 11 (13.3%) 
               
               
                   
                   
                 &gt;0 
                  57 (40.7%) 
                 25 (43.9%) 
               
               
                   
                   
                 COL4A1_01 
                   
                   
               
               
                   
                   
                 Zero 
                 111 (70.3%) 
                 17 (15.3%) 
               
               
                   
                   
                 &gt;0 
                  47 (29.7%) 
                 19 (40.4%) 
               
               
                   
                   
                 SPARC_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 138 (89.6%) 
                 30 (21.7%) 
               
               
                   
                   
                 &gt;0 
                  16 (10.4%) 
                  6 (37.5%) 
               
               
                   
                   
                 AGRN_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  23 (14.9%) 
                  3 (13.0%) 
               
               
                   
                   
                 &gt;0 
                 131 (85.1%) 
                 33 (25.2%) 
               
               
                   
                   
                 THBS1_01 
                   
                   
               
               
                   
                   
                 Missing 
                 135 
                 33  
               
               
                   
                   
                 Zero 
                  18 (78.3%) 
                 0 (0.0%) 
               
               
                   
                   
                 &gt;0 
                  5 (21.7%) 
                  3 (60.0%) 
               
               
                   
                   
                 THBS2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 114 (74.0%) 
                 23 (20.2%) 
               
               
                   
                   
                 &gt;0 
                  40 (26.0%) 
                 13 (32.5%) 
               
               
                   
                   
                 THBS4_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 136 (88.3%) 
                 30 (22.1%) 
               
               
                   
                   
                 &gt;0 
                  18 (11.7%) 
                  6 (33.3%) 
               
               
                   
                   
                 VCAN_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 137 (89.0%) 
                 27 (19.7%) 
               
               
                   
                   
                 &gt;0 
                  17 (11.0%) 
                  9 (52.9%) 
               
               
                   
                   
                 BGAN_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  97 (63.0%) 
                 21 (21.6%) 
               
               
                   
                   
                 &gt;0 
                  57 (37.0%) 
                 15 (26.3%) 
               
               
                   
                   
                 COL1A1_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 145 (94.2%) 
                 30 (20.7%) 
               
               
                   
                   
                 &gt;0 
                  9 (5.8%) 
                  6 (66.7%) 
               
               
                   
                   
                 COL18A1_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 146 (94.8%) 
                 32 (21.9%) 
               
               
                   
                   
                 &gt;0 
                  8 (5.2%) 
                  4 (50.0%) 
               
               
                   
                   
                 CTGF_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 128 (83.1%) 
                 25 (19.5%) 
               
               
                   
                   
                 &gt;0 
                  26 (16.9%) 
                 11 (42.3%) 
               
               
                   
                   
                 LOX_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 149 (96.8%) 
                 33 (22.1%) 
               
               
                   
                   
                 &gt;0 
                  5 (3.2%) 
                  3 (60.0%) 
               
               
                   
                   
                 LOXL1_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 146 (94.8%) 
                 31 (21.2%) 
               
               
                   
                   
                 &gt;0 
                  8 (5.2%) 
                  5 (62.5%) 
               
               
                   
                   
                 LOXL2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 115 (74.7%) 
                 21 (18.3%) 
               
               
                   
                   
                 &gt;0 
                  39 (25.3%) 
                 15 (38.5%) 
               
               
                   
                   
                 LOXL3_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  67 (43.5%) 
                 5 (7.5%) 
               
               
                   
                   
                 &gt;0 
                  87 (56.5%) 
                 31 (35.6%) 
               
               
                   
                   
                 LOXL4_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 122 (79.2%) 
                 25 (20.5%) 
               
               
                   
                   
                 &gt;0 
                  32 (20.8%) 
                 11 (34.4%) 
               
               
                   
                   
                 PLOD2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 136 (88.3%) 
                 32 (23.5%) 
               
               
                   
                   
                 &gt;0 
                  18 (11.7%) 
                  4 (22.2%) 
               
               
                   
                   
                 PLOD1_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 111 (72.1%) 
                 19 (17.1%) 
               
               
                   
                   
                 &gt;0 
                  43 (27.9%) 
                 17 (39.5%) 
               
               
                   
                   
                 PCOLCE2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 144 (93.5%) 
                 32 (22.2%) 
               
               
                   
                   
                 &gt;0 
                  10 (6.5%) 
                  4 (40.0%) 
               
               
                   
                   
                 PCOLCE_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 139 (90.3%) 
                 31 (22.3%) 
               
               
                   
                   
                 &gt;0 
                  15 (9.7%) 
                  5 (33.3%) 
               
               
                   
                   
                 PLOD3_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 109 (70.8%) 
                 17 (15.6%) 
               
               
                   
                   
                 &gt;0 
                  45 (29.2%) 
                 19 (42.2%) 
               
               
                   
                   
                 ITGB1_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  62 (40.3%) 
                  8 (12.9%) 
               
               
                   
                   
                 &gt;0 
                  92 (59.7%) 
                 28 (30.4%) 
               
               
                   
                   
                 FBLN2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 139 (90.3%) 
                 31 (22.3%) 
               
               
                   
                   
                 &gt;0 
                  15 (9.7%) 
                  5 (33.3%) 
               
               
                   
                   
                 CYR61_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  50 (32.5%) 
                 10 (20.0%) 
               
               
                   
                   
                 &gt;0 
                 104 (67.5%) 
                 26 (25.0%) 
               
               
                   
                   
                 ITGA5_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 135 (87.7%) 
                 26 (19.3%) 
               
               
                   
                   
                 &gt;0 
                  19 (12.3%) 
                 10 (52.6%) 
               
               
                   
                   
                 ITGA3_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  56 (36.4%) 
                  8 (14.3%) 
               
               
                   
                   
                 &gt;0 
                  98 (63.6%) 
                 28 (28.6%) 
               
               
                   
                   
                 ITGA2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 139 (90.3%) 
                 29 (20.9%) 
               
               
                   
                   
                 &gt;0 
                  15 (9.7%) 
                  7 (46.7%) 
               
               
                   
                   
                 ITGAV_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 120 (77.9%) 
                 22 (18.3%) 
               
               
                   
                   
                 &gt;0 
                  34 (22.1%) 
                 14 (41.2%) 
               
               
                   
                   
                 CSRC_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  90 (58.4%) 
                 15 (16.7%) 
               
               
                   
                   
                 &gt;0 
                  64 (41.6%) 
                 21 (32.8%) 
               
               
                   
                   
                 PTK2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  61 (39.6%) 
                  7 (11.5%) 
               
               
                   
                   
                 &gt;0 
                  93 (60.4%) 
                 29 (31.2%) 
               
               
                   
                   
                 POSTN_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 103 (66.9%) 
                 23 (22.3%) 
               
               
                   
                   
                 &gt;0 
                  51 (33.1%) 
                 13 (25.5%) 
               
               
                   
                   
                 YAP_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 137 (89.0%) 
                 26 (19.0%) 
               
               
                   
                   
                 &gt;0 
                  17 (11.0%) 
                 10 (58.8%) 
               
               
                   
                   
                 CXCL1_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  94 (61.0%) 
                 19 (20.2%) 
               
               
                   
                   
                 &gt;0 
                  60 (39.0%) 
                 17 (28.3%) 
               
               
                   
                   
                 CSF2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 131 (85.1%) 
                 32 (24.4%) 
               
               
                   
                   
                 &gt;0 
                  23 (14.9%) 
                  4 (17.4%) 
               
               
                   
                   
                 CCL2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 112 (72.7%) 
                 24 (21.4%) 
               
               
                   
                   
                 &gt;0 
                  42 (27.3%) 
                 12 (28.6%) 
               
               
                   
                   
                 IL8_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  99 (64.3%) 
                 15 (15.2%) 
               
               
                   
                   
                 &gt;0 
                  55 (35.7%) 
                 21 (38.2%) 
               
               
                   
                   
                 IL6_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                  62 (40.3%) 
                 10 (16.1%) 
               
               
                   
                   
                 &gt;0 
                  92 (59.7%) 
                 26 (28.3%) 
               
               
                   
                   
                 LAMA3_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 148 (96.1%) 
                 34 (23.0%) 
               
               
                   
                   
                 &gt;0 
                  6 (3.9%) 
                  2 (33.3%) 
               
               
                   
                   
                 TP53_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 125 (81.2%) 
                 22 (17.6%) 
               
               
                   
                   
                 &gt;0 
                  29 (18.8%) 
                 14 (48.3%) 
               
               
                   
                   
                 CDKN1A_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 118 (76.6%) 
                 22 (18.6%) 
               
               
                   
                   
                 &gt;0 
                  36 (23.4%) 
                 14 (38.9%) 
               
               
                   
                   
                 CDKN2A_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 103 (66.9%) 
                 26 (25.2%) 
               
               
                   
                   
                 &gt;0 
                  51 (33.1%) 
                 10 (19.6%) 
               
               
                   
                   
                 TAZ_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 133 (86.4%) 
                 29 (21.8%) 
               
               
                   
                   
                 &gt;0 
                  21 (13.6%) 
                  7 (33.3%) 
               
               
                   
                   
                 LAMC1_01 
                   
                   
               
               
                   
                   
                 Missing 
                 136 
                 33  
               
               
                   
                   
                 Zero 
                  19 (86.4%) 
                 0 (0.0%) 
               
               
                   
                   
                 &gt;0 
                  3 (13.6%) 
                  3 (100.0%) 
               
               
                   
                   
                 LAMB1_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 109 (70.8%) 
                 16 (14.7%) 
               
               
                   
                   
                 &gt;0 
                  45 (29.2%) 
                 20 (44.4%) 
               
               
                   
                   
                 LAMA1_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 128 (83.1%) 
                 30 (23.4%) 
               
               
                   
                   
                 &gt;0 
                  26 (16.9%) 
                  6 (23.1%) 
               
               
                   
                   
                 LAMC2_01 
                   
                   
               
               
                   
                   
                 Missing 
                  5 
                 0 
               
               
                   
                   
                 Zero 
                 145 (94.8%) 
                 33 (22.8%) 
               
               
                   
                   
                 &gt;0 
                  8 (5.2%) 
                  3 (37.5%) 
               
               
                   
                   
                 LAMM_01 
                   
                   
               
               
                   
                   
                 Missing 
                  4 
                 0 
               
               
                   
                   
                 Zero 
                 139 (90.3%) 
                 33 (23.7%) 
               
               
                   
                   
                 &gt;0 
                  15 (9.7%) 
                  3 (20.0%) 
               
               
                   
                   
                 GDF15_01 
                   
                   
               
               
                   
                   
                 Missing 
                  28 
                 4 
               
               
                   
                   
                 Zero 
                  65 (50.0%) 
                 10 (15.4%) 
               
               
                   
                   
                 &gt;0 
                  65 (50.0%) 
                 22 (33.8%) 
               
               
                   
                   
                 DSPP_01 
                   
                   
               
               
                   
                   
                 Missing 
                  73 
                 13  
               
               
                   
                   
                 Zero 
                  16 (18.8%) 
                  7 (43.8%) 
               
               
                   
                   
                 &gt;0 
                  69 (81.2%) 
                 16 (23.2%) 
               
               
                   
                   
                 NTRK3_01 
                   
                   
               
               
                   
                   
                 Missing 
                  28 
                 4 
               
               
                   
                   
                 Zero 
                 130 (100.0%) 
                 32 (24.6%) 
               
               
                   
                   
               
            
           
         
       
     
     To formulate a model that distinguishes melanoma that presents with regional metastasis at the time of diagnosis vs. no metastasis, logic regression was used. Logic regression is a machine learning technique that uses Boolean explanatory variables. There was not a typical technique to create good cut points for logic regression. To assign cut points in the variables, recursive partitioning followed by standardization of cut point levels was used. These were arbitrarily set at 0, 50, 250, and 500. Cut points derived by logic regression were adjusted to the next highest standard level. The cut point for ITGB3 was maintained at 0. The selected model for predicting metastasis was the following:
         IF(OR(ITGB3&gt;0,(AND(OR(PTK2&gt;250,PLAT&gt;500,PLOD3&gt;250),CDKN2A&lt;-;50)))=TRUE then predict metastasis   Cut point ITGB3=0   Cut point PLAT=500   Cut point PTK2=250   Cut point PLOD3=250   Cut point CDKN2A=50       

     As can be seen from the formula, the risk of melanoma metastasis was high if ITGB3, PLAT, PTK2 or PLOD3 levels are increased and CDKN2A is low. 
     This model predicted regional metastasis (defined as a positive SLN biopsy at the time of primary cancer diagnosis) with a specificity of 80.3% and sensitivity of 97.3%. 
     Example 4—Use of Integrin Adhesions as a Biomarker of Melanoma Sentinel Lymph Node Metastasis 
     Patient Sample 
     Model Development Cohort 
     All patients with a diagnosis of malignant primary skin melanoma who had a SLN biopsy performed within 90 days of their diagnosis at Mayo Clinic Rochester, Mayo Clinic Arizona, or Mayo Clinic Florida were identified. The diagnosis of melanoma and all related histopathology data were established by ≥2 board-certified Mayo Clinic dermatopathologists. Patients evaluated at Mayo Clinic Rochester were excluded if they had denied access to their medical records for research purposes. The medical records were reviewed, and patients were excluded if they had a “thick” melanoma (Breslow depth&gt;4 mm; T classification T4). The following four variables were used to identify lesions of sufficient risk for inclusion: Breslow depth, presence of ulceration, mitotic rate&gt;0 and age&lt;40 years. A patient was included if i) Breslow depth&gt;1 to &lt;4 mm, or ii) Breslow depth between 0.75 and &lt;1 mm with one or more of the other three risk factors, or iii) Breslow depth between 0.50 and &lt;0.75 mm with two or more of the other three risk factors. Patients with ambiguous pathology or SLN biopsy findings were also excluded. The tissue blocks were reviewed, and patients were excluded if i) the blocks were not retrievable, or ii) sufficient material was not dispensable for research, or iii) only partial primary biopsy samples were available (i.e., biopsies with &lt;80% of total Breslow depth), or iv) available tissue was limited to re-excision specimens in lieu of the original biopsy, or v) the quality of retrievable RNA was poor. 
     Model Validation Cohort 
     The model validation cohort consisted of patients who met the same criteria as described for the model development cohort. These patients had a SLN biopsy performed within 90 days of their diagnosis at either Mayo Clinic Rochester or Mayo Clinic Florida. 
     Data Collection 
     The following demographic, diagnosis, and pathologic information was abstracted from the medical record: gender, date of birth, date of malignant melanoma diagnosis, date of SLN biopsy, SLN biopsy finding, Breslow depth, mitotic rate (absent, 1-6, &gt;6) presence of ulceration, presence of tumor invading lymphocytes, and presence of angiolymphatic invasion. For analysis purposes, Breslow depth was categorized using recent AJCC guidelines (Balch et al.,  J. Clin. Oncol.,  27:6199 (2009)). 
     Block Processing 
     All tissue used was routinely processed, formalin-fixed and paraffin-embedded (FFPE). Preferred starting material for RNA purification was from freshly cut sections of FFPE tissue, each with a thickness of 20 μm. If a tissue was available only as unstained sections mounted on glass slides, RNA retrieval was attempted but typically yielded lower concentrations and poorer quality. 
     Microfluidic RT-PCR 
     The Fluidigm BioMark HD System was used for quantitative RT-PCR using EvaGreen DNA binding dye (Biotium) and 96.96 dynamic array integrated fluid circuits (Fluidigm). 77 specific targets in 62 genes (54 experimental and 8 control genes) were amplified per cDNA (standards, controls and experimental samples). Genes included: house-keeping (ACTB, RPLP0, RPL8), melanocyte lineage (MLANA, MITF, TYR, PMEL), basal keratinocyte lineage (KRT14), integrin cell adhesion receptors (ITGB1, ITGB3, ITGA2, ITGA3, ITGA5, ITGAV), integrin trafficking (SNX17, SNX31), fibronectin-related (FN1, THBS1, THBS2, THBS4, SPP1, PLAT, TNC, SPARC, POSTN, FBLN2, DSPP1), collagen-related (COL1A1, COL4A1, COL18A1, PLOD1, PLOD2, PLOD3, LOX, LOXL1, LOXL3, PCOLCE, PCOLCE2), laminins (LAMA1, LAMB1, LAMC1, LAMA3, LAMB3, LAMC2), other extracellular matrix (AGRN, VCAN, GDF15, BGAN, CTGF, CYR61, CSF2, CXCL1, CCL2, IL8, IL6), adhesion signaling (PTK2, CSRC), and cell cycle (CDKN1A, CDKN2A, TP53, YAP, TAZ). The following cDNA were run per array: standards, i.e., linearized cDNA mixes of targets ranging from 5 to 500,000 in copy number and prepared as 1:10 dilutions (a total of six standards), run in triplicates; control cDNA (nevi and melanoma metastases); experimental cDNA; the latter two were in duplicates. All cDNA was pre-amplified in a 14 cycle reaction (TAQMAN® Preamp Master Mix, Applied Biosystems). Array-based quantitative PCR was with the help of the TAQMAN® Gene Expression Master Mix (Applied Biosystems). After thermal cycling, raw Ct data was exported for further analysis. Standards were checked for linear amplification, i.e., a drop in Ct value by approximately log 2  10 per 1:10 dilution. Copy numbers for negative and positive controls were normalized to 25,000 copies of total housekeeping genes. Averaged, normalized gene copy numbers were compared to an internal standard for inter-experiment variation. Data from arrays that did not pass both linear amplification and reproducibility checks were discarded. 
     To account for sample contamination from keratinocyte-derived RNA, the gene copy number of KRT14, a basal keratinocyte marker, was determined. This number was multiplied with a gene-specific contamination factor, i.e., a value of gene copy number contamination per copy of KRT14. Expression profiling of normal skin devoid of melanocyte nests was performed to establish a contamination factor. The calculated number of keratinocyte-derived RNA contamination was then deducted from the averaged, normalized gene copy number. The final averaged, normalized and background-corrected gene copy number was used for further analysis. 
     To assess for melanocyte content, at least two melanocyte lineage markers were amplified: MLANA and MITF. Sufficient melanocyte content was assumed if the sum of their averaged, normalized and background-corrected copy numbers was 1,000. If this was not the case, presence of melanocytic tumor had to be confirmed on tissue recuts followed by histologic review. Samples from tissue blocks exhausted of tumor were discarded. Expression data from samples that passed all quality controls were combined with pathology and clinical data and used for statistical modeling. 
     Chemicals, Antibodies and cDNA 
     Isopropyl β-D-1-thiogalactopyranoside (IPTG), 4′,6-Diamidino-2-phenylindole dihydrochloridemitomycin (DAPI), blebbistatin and PF-573228 were purchased from Sigma-Aldrich. Dabrafenib (GSK2118436) was purchased from Selleckchem. FAK antibody (06-543) was from EMD MILLIPORE®. FAK pY397 (44624G) antibody was from Life Technologies. Total ERK (9102) and phospho-ERK (4370) antibodies were from Cell Signaling. Paxillin (610051), ITGB3 (555754), ITGB1 (555443) and mouse IgG 1  kappa (555749) antibodies were from BD Transduction Labs. Drugs were used at 5 μM final concentration. EGFP control cDNA was from (Lonza). FAK cDNA was obtained from A. Huttenlocher, Addgene plasmid number 35039 (Chan et al.,  J. Biol. Chem.,  285:11418-26 (2010)). 
     Cell Lines 
     WM858 were purchased from the Meenhard Herlyn lab (Wistar Institute). WM278 and WM1617 lines were purchased from Coriell Cell Repositories. KN lines were isolated from lymph node metastases using a gentle MACS dissociator and tumor dissociation kit (Miltenyi Biotec). WM and KN lines were propagated exclusively in vitro. M lines were isolated from melanoma brain metastases using previously described methods (Carlson et al.,  Curr. Prot. Pharmacology,  14.6.1-14.6, 23 (2011)). Some M lines were propagated in mice. Cells were cultured in vitro using DermaLife M Medium (Lifeline Cell Technology). 
     Generation of IPTG-Inducible FAK shRNA Cells 
     Five TRC clones were cloned into the pLKO-puro-IPTG-1XLacO vector. The same vector format was used for the non-target negative control (NC) shRNA SHC312V (Sigma-Aldrich). TRC identifiers were as follows: TRCN0000121207, TRCN0000121318, TRCN0000121129, TRCN0000194984, and TRCN0000196310. Lentivirus was produced for each TRC clone and multiple pools of WM858 cells were transduced per clone. The first three TRC sequences did not induce significant FAK knockdown in WM858 cells. The latter two (abbreviated as shRNA 841 and 102) were effective and used for experiments. Selection of successfully transduced cells was with puromycin (Sigma-Aldrich). 
     Focal Adhesion Visualization on Fibronectin Micropatterns 
     Cells were plated on micropatterned disks of fluorescent fibronectin surrounded by a cytophobic surface (CYTOO). Cells were allowed to adhere for 1 hour in serum-free medium, and then were fixed and incubated with anti-paxillin antibody followed by a fluorescent secondary antibody and DAPI. Images of fluorescent cells were obtained with a laser scanning confocal microscope (Zeiss LSM780). Max intensity overlays of 15 representative cells per cell type were generated using a plug-in ImageJ macro from CYTOO. 
     Cell Proliferation 
     Automated quantification of cell proliferation was by the I NCU C YTE ™ kinetic imaging system (Essen Bioscience). Approximately 2,000 cells were seeded into a 96-well cell culture dish, eight replicates per condition over the indicated time. Data analysis was with the I NCU C YTE  ZOOM software package. 
     Western Blotting by Protein Simple 
     Western blotting was by standard techniques or automated with a Wes device from ProteinSimple. The automated work-flow was according to the manufacturer&#39;s instructions. Image analysis was with the ProteinSimple Compass software. 
     Gene Expression by Next-Generation Sequencing 
     Sequencing of FFPE-derived RNA was performed using standard methods. Briefly, RNA-derived cDNA libraries were prepared using the NuGen OVATION® RNAseq FFPE library system. Concentration and size distribution of the resulting libraries were determined on an AGILENT BIOANALYZER® DNA 1000 chip and confirmed by QUBIT® fluorometry (Life Technologies, Grand Island, N.Y.). Unique indexes were incorporated at the adaptor ligation phase for 3-plex sample loading. Libraries were loaded onto paired end flow cells to generate cluster densities of 700,000/mm 2  following Illumina&#39;s standard protocol. The flow cells were sequenced as 51×2 paired end reads on an ILLUMINA® HISEQ® 2000. For differential gene expression analysis, the edgeR bioconductor software package was used. Because scaling by total lane counts (e.g., by the “reads per kilobase of exon model per million mapped reads” (RPKM) method) can bias estimates of differential expression, quantile-based normalization was used on read counts to determine if genes are differentially expressed (Bullard et al.,  BMC bioinformatics,  11:94 (2010)) using the negative binomial method (Anders and Huber,  Genome Biol.,  11:R106 (2010)) requiring an adjusted p-value of &lt;0.01 controlled for multiple testing using the Benjamini and Hochberg correction. 
     Statistical Methods 
     Model Development 
     The primary outcome measure for this study is a positive SLN within 90 days of the primary melanoma diagnosis. Clinical and pathologic characteristics were evaluated univariately for an association with SLN positivity using the chi-square test for categorical variables and the two-sample t-test for continuous variables. A prediction model was constructed from these characteristics using multivariable logistic regression. Associations were summarized using the odds ratio (OR) and corresponding 95% confidence intervals (CI) derived from the model estimates. 
     When evaluating gene expression data as potential predictors of outcomes, it is useful to model interactions between the genes. Logic regression can be used to discover and model interactions of binary explanatory variables, and combinations are created using Boolean operators (“and,” “or” and “not”) (Ruczinski et al.,  J. Comput. Graph. Stat.,  12:475-511 (2003)). Since logic regression is limited to using binary explanatory variables, reasonable cutoff values needed to be established for each of the 54 experimental genes. For each gene, a separate Classification and Regression Tree (CART) model was fit to identify the best gene expression cutoffs to differentiate between patients with positive and negative SLN using the Gini rule for splitting, prior probabilities proportional to the observed data frequencies, and 0/1 losses. The AUC for these models ranged from 0.50 to 0.781. A total of 147 binary variables were created using all the breakpoints generated by the CART models and these breakpoints were then used to fit the logic regression. 
     Receiver operating characteristic (ROC) curves were constructed for the final prediction models. The predictive ability of each model was summarized by the area under curve (AUC), and the AUC estimates were compared between models using the DeLong, DeLong, and Clarke-Pearson non-parametric method for comparing the AUC for correlated ROC curves. 
     Model Validation 
     The performance of the prognostic model developed using the development cohort was validated in a new cohort by assessing the discrimination and calibration. Discrimination was assessed by quantifying the model&#39;s ability to discriminate between patients in the new cohort who do and do not have a positive SLNB using the area under the ROC curve. Calibration was assessed by grouping patients into 5 quintiles based on their predicted probabilities estimated by the model and comparing the median predicted probability in each quintile with the observed proportion of patients with a positive SNLB in that quintile. 
     The statistical analysis was performed SAS version 9.2 and R version 3.0.1. The CART analysis was performed using the rpart package (rpart: Recursive Partitioning, Version 4.1-1; Therneau and Atkinson). An introduction to recursive partitioning using the RPART routines: Technical Report 61, Section of Biostatistics, Mayo Clinic, Rochester). The logic regression used LogicReg package (LogicReg: Logic Regression, Version 1.5.5; Ruczinski et al., J. Comput. Graph. Stat., 12:475-511 (2003)). 
     Logic Regression 
     Logic regression fits regression models using one to five trees, and the trees can be composed of many leaves. Simulated annealing was used to explore possible logic regression models to find a good model. The technique starts by fitting a model built randomly using a specified number of leaves and trees. A new model is created by randomly permuting the current model by changing a leaf or Boolean operator. The performance of the current model is then compared to the new model. If the new model performs better, then it becomes the current model, and the process is repeated. Simulated annealing avoids local optima by controlling when inferior models were chosen. The null model randomization test was used to determine if there was a relationship between the 147 binary gene expression variables and SLN positivity. The optimal number of leafs and trees was determined using cross validation and permutation techniques. 
     The null model randomization test was used to determine if there was a relationship between the 147 binary gene expression variables and SLN positivity. First, the best model was fit for all biopsy samples using logic regression. Next, the SLN positivity outcome for all the patients was randomly reassigned and fit another model. The process of randomly reassigning the SLN positivity outcome and fitting a model was performed 25 times.  FIG. 8A  shows the histogram of the deviance scores from the models built using the randomized outcomes. The null model randomization test demonstrated there was a relationship between SLN positivity and gene expression since the deviance scores were all worse than the best model deviance scores. 
     The optimal number of leafs and trees in the logic regression model was determined using cross validation and permutation techniques. Ten-fold cross validation was used to help determine the ideal model size given the data.  FIG. 8B  shows the deviance score for the test samples for different model configurations. The label in the square represents the number of trees used in the model. The x-axis indicates the number of binary variables or leaves used in the model. The best deviance score was obtained using a two-tree model using four binary explanatory variables. When more than four explanatory variables were used in the model, there may be an over-fitting issue since the test data deviance scores degrade when there are more than four explanatory variables. The permutation test was also used to confirm ideal model size given the data. The permutation test fits the best model given the model size. In each tree the binary variables are put together using “and,” “or” and “not.” It follows that each logic tree has a binary outcome. For a model having n trees the sample could be partitioned into 2n groups. With two trees, the sample was partitioned into four groups. The SLN outcomes were permuted by randomly reassigning the outcome within each of the four groups. The model was refit based on permuted data. Notice that the exact same model can be found within the permuted data. Models scoring better than the best model were likely because of fitting on noise. Models scores worse than the best model were likely caused by the model being too small.  FIG. 8C  shows this process repeated 1,000 times for each model size. Most of the permuted models with two leaves performed worse than the best model, indicating a larger model would be optimal. About 10% of the models using five leaves fit using permuted data outperformed the best model. It was recommended to choose the model size where the permuted outcome variables outperform the best model 5% to 20% of the time (Ruczinski et al., J. Comput. Graph. Stat., 12:475-511 (2003)). The cross validation test and the permutation test indicate that the optimum model size was two trees using four or five binary variables. The formulas for the best fitting models involved two trees with a model size of 4 or 5 ( FIG. 8D ). The best four-leaf model considered (33 integrin (ITGB3), cellular tumor antigen p53 (TP53), the laminin B1 chain (LAMB1), and tissue-type plasminogen activator (PLAT). The best five-leaf model considered the same four genes plus agrin (AGRN). Notice that the composition for one tree was exactly the same for both models ((LAMB1&gt;250) or (PLAT&gt;427)). 
     Results 
     This investigation started by identifying functional networks of differentially expressed genes in benign melanocytic lesions vs. invasive melanoma. In a pilot study, three patients with benign nevi were age and gender-matched one-to-one to a patient with a primary skin melanoma that had metastasized regionally. A total of 15,413 genes were identified and measured by next-generation sequencing (NGS) of patient biopsy-derived RNA. Differential gene expression analysis yielded 160 genes with a false-discovery rate (FDR)&lt;0.01. These were entered into the STRING database to identify functional gene networks. Genes that were without known functional relationships to other genes were hidden. Two clusters with more than two nodes emerged; the largest was linked to integrin cell adhesion ( FIG. 9 ). Within that cluster, (33 integrin (ITGB3) had the lowest FDR and the highest connectivity. 
     Next, the objective was to confirm that genes involved in integrin cell adhesion are up-regulated in invasive melanoma. A test set of 73 benign nevi (53 were without histological atypia, 7 were with mild, 11 with moderate and two with severe atypia), 38 primary skin melanoma that had metastasized regionally (median Breslow depth of 3 mm; IQR, 2 to 4 mm), and 11 in-transit regional melanoma metastases was assembled. A method for determining copy number of 77 specific targets in 62 genes (54 experimental and 8 control genes) by quantitative PCR was established as described herein. Genes were categorized as follows: i) integrin adhesion receptor subunits; ii) FN1 and related extracellular matrix (ECM) components; iii) collagen genes and enzymes that facilitate the cross-linking of collagens; iv) laminin subunits; v) other ECM components including those of a pro-inflammatory DNA damage response (Coppe et al.,  PLoS biology,  6:e301 (2008)); vi) integrin-activated kinases, and vii) cell cycle related. Genes with significant regulation between benign and malignant were mainly in the categories of integrins and FN1 and related ECM components, thus confirming NGS results ( FIG. 10 ). (33 integrin was with the highest fold change of all tested integrin subunits. 
     The following was performed to assess whether adhesion gene expression in tissue sections predicted metastasis to SLN and to determine whether the method outperformed the current clinical gold standard for predicting metastasis risk, i.e., Breslow invasion depth (Breslow,  Annals of Surg.,  172:902 (1970)). The model development cohort consisted of a total of 360 thin and intermediate thickness primary melanoma (Breslow depth≤4 mm) of all histologic types with a SLN biopsy within 90 days of their diagnosis (Table 14). To exclude minimal risk lesions, thin melanoma (Breslow depth≤1 mm; T classification 1) without additional risk factors (ulceration, mitoses, patient age&lt;40) were not considered. Thick melanoma (Breslow depth&gt;4 mm; T classification 4) were excluded because they frequently metastasize to SLN and the clinical utility of a molecular test is low. 
     
       
         
           
               
             
               
                 TABLE 14 
               
             
            
               
                   
               
               
                 Summary of histologic types of melanoma that  
               
               
                 triggered a SLN biopsy. 
               
            
           
           
               
               
               
            
               
                   
                 Histologic Type 
                 No. (%) 
               
               
                   
                   
               
               
                   
                 Superficial Spreading 
                 180 (50.0%) 
               
               
                   
                 Nodular 
                  70 (19.4%) 
               
               
                   
                 Unclassifiable 
                 30 (8.3%) 
               
               
                   
                 Desmoplastic 
                 16 (4.4%) 
               
               
                   
                 Lentigo Maligna 
                 15 (4.2%) 
               
               
                   
                 Spindled 
                 13 (3.6%) 
               
               
                   
                 Acral Lentiginous 
                  9 (2.5%) 
               
               
                   
                 Spitzoid 
                  4 (1.1%) 
               
               
                   
                 Nevoid 
                  3 (0.8%) 
               
               
                   
                 Dermal 
                  1 (0.3%) 
               
               
                   
                 Not documented 
                 19 (5.3%) 
               
               
                   
                   
               
            
           
         
       
     
     Table 15 summarizes the clinical and pathologic factors that were evaluated univariately for an association with SLN positivity. Ulceration, Breslow depth, and age were identified as independently associated with SLN positivity (Table 16, Model A). Logic regression models were fit utilizing 147 binary variables derived from 54 experimental genes and evaluated using the breakpoints generated by the CART models for the 54 genes. The best four-leaf model considered 3 integrin (ITGB3), cellular tumor antigen p53 (TP53), the laminin B1 chain (LAMB1), and tissue-type plasminogen activator (PLAT). SLN positivity within each of these four categories is summarized at the bottom of Table 15. The model results for a combined model including both the clinical/pathologic factors and the gene expression parameters are presented as model B in Table 16. 
     
       
         
           
               
             
               
                 TABLE 15 
               
             
            
               
                   
               
               
                 Summary of the association of clinical and pathologic factors with SLN 
               
               
                 positivity based on 360 SLN biopsies. 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 Positive SLNB 
                 Chi-square test 
               
               
                   
                 Factor 
                 N (%) 
                 p value 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                   
                 Gender 
                   
                 0.84 
               
               
                   
                 Male (N = 225) 
                 47 (20.9%) 
                   
               
               
                   
                 Female (N = 135) 
                 27 (20.0%) 
                   
               
               
                   
                 Age (years) 
                   
                 &lt;0.001 
               
               
                   
                 16- &lt;40 (N = 55) 
                 16 (29.1%) 
                   
               
               
                   
                 40- &lt;59 (N = 112) 
                 33 (29.5%) 
                   
               
               
                   
                 60+ (N = 193) 
                 25 (13.0%) 
                   
               
               
                   
                 Ulceration 
                   
                 &lt;0.001 
               
               
                   
                 No (N = 295) 
                 50 (16.9%) 
                   
               
               
                   
                 Yes (N = 65) 
                 24 (36.9%) 
                   
               
               
                   
                 Breslow depth (mm) 
                   
                 &lt;0.001 
               
               
                   
                 0.50-1 (N = 93) 
                 6 (6.4%) 
                   
               
               
                   
                 1.01-2 (N = 177) 
                 31 (17.5%) 
                   
               
               
                   
                 2.01-4 (N = 90) 
                 37 (41.1%) 
                   
               
               
                   
                 Mitotic rate 
                   
                 0.12 † 
               
               
                   
                 Missing (N = 14) 
                  4 
                   
               
               
                   
                 Absent (N = 42) 
                 4 (9.5%) 
                   
               
               
                   
                 1-6 (N = 246) 
                 51 (20.7%) 
                   
               
               
                   
                 &gt;6 (N = 58) 
                 15 (25.9%) 
                   
               
               
                   
                 Tumor invading lymphocytes 
                   
                 0.37 † 
               
               
                   
                 Missing (N = 31) 
                 12 
                   
               
               
                   
                 No (N = 86) 
                 19 (22.1%) 
                   
               
               
                   
                 Yes (N = 243) 
                 43 (17.7%) 
                   
               
               
                   
                 Angiolymphatic invasion 
                   
                 0.28 
               
               
                   
                 No (N = 344) 
                 69 (20.1%) 
                   
               
               
                   
                 Yes (N = 16) 
                  5 (31.3%) 
                   
               
               
                   
                 4-level gene score 
                   
                 &lt;0.001 
               
               
                   
                 A: NOT (lamb1 &gt;250 or plat &gt;427) 
                 10 (4.2%)  
                   
               
               
                   
                 and NOT (itgb3 &gt;10 and tp53 ≤50)  
                   
                   
               
               
                   
                 (N = 237) 
                   
                   
               
               
                   
                 B: (lamb1 &gt;250 or plat &gt;427) 
                 26 (38.2%) 
                   
               
               
                   
                 but NOT (itgb3 &gt;10 and tp53 ≤50)  
                   
                   
               
               
                   
                 (N = 68) 
                   
                   
               
               
                   
                 C: (itgb3 &gt;10 and tp53 ≤50) 
                 18 (52.9%) 
                   
               
               
                   
                 but NOT (lamb1 &gt;250 or plat &gt;427)  
                   
                   
               
               
                   
                 (N = 34) 
                   
                   
               
               
                   
                 D: (lamb1 &gt;250 or plat &gt;427)  AND   
                 20 (95.2%) 
                   
               
               
                   
                 (itgb3 &gt;10 and tp53 ≤50) (N = 21) 
               
               
                   
               
               
                 † P-values were calculated based on the subset of patients with non-missing values. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 16 
               
             
            
               
                   
               
               
                 Multivariable logistic regression analyses of characteristics associated with SLN positivity. 
               
            
           
           
               
               
               
               
            
               
                   
                 Model A 
                 Model B 
                 Model C 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                 Adjusted OR 
                   
                 Adjusted OR 
                   
                   
                 Adjusted OR 
                   
               
               
                 Factor 
                 (95% CI) 
                 p-value 
                 (95% CI) 
                 p-value 
                   
                 (95% CI) 
                 p-value 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Ulceration 
                   
                 0.026 
                   
                 0.25 
                   
                   
                 0.39 
               
               
                 No 
                 Referent 
                   
                 Referent 
                   
                   
                 Referent 
                   
               
               
                 Yes 
                 2.11 (1.10, 4.06) 
                   
                 1.58 (0.73, 3.44) 
                   
                   
                 1.38 (0.66, 2.88) 
                   
               
               
                 Breslow depth (mm) 
                   
                 &lt;0.001 
                   
                 0.13 
                   
                   
                 0.036 
               
               
                 0.50-1 
                 Referent 
                   
                 Referent 
                   
                   
                 Referent 
                   
               
               
                 1.01-2 
                 3.33 (1.31, 8.44) 
                   
                 1.28 (0.46, 3.59) 
                   
                   
                 1.50 (0.54, 4.21) 
                   
               
               
                 2.01-4 
                 11.46 (4.34, 30.27) 
                   
                 2.52 (0.84, 7.58) 
                   
                   
                 3.30 (1.11, 9.77) 
                   
               
               
                 Patient age (years) 
                   
                 &lt;0.001 
                   
                 0.001 
                   
                   
                 0.001 
               
               
                 16-&lt;40 
                 3.85 (1.75, 8.50) 
                   
                  6.18 (2.24, 17.06) 
                   
                   
                  5.14 (1.99, 13.25) 
                   
               
               
                 40-&lt;59 
                 3.47 (1.83, 6.59) 
                   
                 2.92 (1.31, 6.52) 
                   
                   
                 2.91 (1.41, 6.00) 
                   
               
               
                 60+ 
                 Referent 
                   
                 Referent 
                   
                   
                 Referent 
                   
               
               
                 Gene score 
                   
                   
                   
                 &lt;0.001 
                   
                   
                 &lt;0.001 
               
               
                 A 
                 — 
                   
                 Referent 
                   
                   
                 Referent 
                   
               
               
                 B 
                 — 
                   
                 13.17 (5.53, 31.39) 
                   
                   
                   
                   
               
               
                 C 
                 — 
                   
                 12.27 (4.52, 33.33) 
                   
                  {close oversize brace}  
                 17.32 (8.02, 37.41) 
                   
               
               
                 D 
                 — 
                   
                 236.60 (36.95, &gt;999)  
               
               
                   
               
            
           
         
       
     
     It was subsequently decided to collapse the four categories in the gene model into two categories, which yielded a simpler model without loss of overall predictive ability (Table 16, model C). The receiver operating characteristic (ROC) curves for the three models are displayed in  FIG. 11A . The overall predictive ability of the combined model as measured by the area under the curve (AUC) or c-index was significantly greater for model C compared to model A (0.89 vs. 0.77, p&lt;0.001).  FIG. 11B  depicts the sensitivity and specificity of model C as the level of the predicted probability of a positive SLNB used to define a positive test was varied. A predicted probability of 0.255 corresponds to a sensitivity and specificity of 82%. A nomogram constructed from model C is presented in  FIG. 11C . For a given patient, points were assigned to each of the variables, and a total score was derived. The total points score corresponded to a predicted probability of positive SLN biopsy. 
     The model validation cohort included 104 patients. Table 17 summarizes the association of the clinical and pathologic factors with SLN positivity, separately for the two cohorts. The discriminative ability of the predictive model was excellent when applied to the validation cohort (AUC 0.92, 95% CI 0.87-0.97). Table 18 compares the predicted and observed rate of positive SLNB for the 5 quintiles defined by the distribution of the predicted probabilities. The two rates track consistently across the 5 quintiles suggesting reasonable calibration. 
     
       
         
           
               
             
               
                 TABLE 17 
               
             
            
               
                   
               
               
                 Summary of the association of clinical and pathologic factors with SLN 
               
               
                 positivity, separately for the model development and model validation cohorts. 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 Model development cohort 
                 Model validation cohort 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                 Positive 
                   
                 Positive 
                   
               
               
                   
                   
                 SLNB 
                   
                 SLNB 
                   
               
               
                   
                 Factor 
                 N (%) 
                 p value† 
                 N (%) 
                 p value† 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Gender 
                   
                 0.84 
                   
                 0.54 
               
               
                   
                 Male 
                 47/225 (20.9) 
                   
                 22/78 (28.2) 
                   
               
               
                   
                 Female 
                 27/135 (20.0) 
                   
                  9/26 (34.6) 
                   
               
               
                   
                 Age (years) 
                   
                 &lt;0.001 
                   
                 0.17 
               
               
                   
                 16- &lt;40 
                  16/55 (29.1) 
                   
                  3/5 (60.0) 
                   
               
               
                   
                 40- &lt;59 
                 33/112 (29.5) 
                   
                 12/34 (35.3) 
                   
               
               
                   
                 60+ 
                 25/193 (13.0) 
                   
                 16/65 (24.6) 
                   
               
               
                   
                 Ulceration 
                   
                 &lt;0.001 
                   
                 0.35 
               
               
                   
                 No 
                 50/295 (16.9) 
                   
                 23/83 (27.7) 
                   
               
               
                   
                 Yes 
                  24/65 (36.9) 
                   
                  8/21 (38.1) 
                   
               
               
                   
                 Breslow depth (mm) 
                   
                 &lt;0.001 
                   
                 0.035 
               
               
                   
                 0.50-1 
                  6/93 (6.4) 
                   
                  5/28 (17.9) 
                   
               
               
                   
                 1.01-2 
                 31/177 (17.5) 
                   
                 10/41 (24.4) 
                   
               
               
                   
                 2.01-4 
                  37/90 (41.1) 
                   
                 16/35 (45.7) 
                   
               
               
                   
                 Mitotic rate 
                   
                 0.12 
                   
                 0.21 
               
               
                   
                 Missing 
                  4/14 
                   
                 5/14 
                   
               
               
                   
                 Absent 
                  4/42 (9.5) 
                   
                  0/7 (0.0) 
                   
               
               
                   
                 1-6 
                 51/246 (20.7) 
                   
                 21/68 (30.9) 
                   
               
               
                   
                 &gt;6 
                  15/58 (25.9) 
                   
                  5/15 (33.3) 
                   
               
               
                   
                 Tumor invading lymphocytes 
                   
                 0.37 
                   
                 0.011 
               
               
                   
                 Missing 
                 12/31 
                   
                 8/26 
                   
               
               
                   
                 No 
                  19/86 (22.1) 
                   
                 10/19 (52.6) 
                   
               
               
                   
                 Yes 
                 43/243 (17.7) 
                   
                 13/59 (22.0) 
                   
               
               
                   
                 Angiolymphatic invasion 
                   
                 0.28 
                   
                 0.89 
               
               
                   
                 No 
                 69/344 (20.1) 
                   
                 30/101 (29.7)  
                   
               
               
                   
                 Yes 
                  5/16 (31.3) 
                   
                  1/3 (33.3) 
                   
               
               
                   
                 4-level gene score 
                   
                 &lt;0.001 
                   
                 &lt;0.001 
               
               
                   
                 A: NOT (lamb1 &gt;250 or plat &gt;427) 
                  10/237 (4.2%) 
                   
                 1/63 (1.6) 
                   
               
               
                   
                 and NOT (itgb3 &gt;10 and tp53 ≤50) 
                   
                   
                   
                   
               
               
                   
                 B: (lamb1 &gt;250 or plat &gt;427) 
                   26/68 (38.2%) 
                   
                 18/25 (72.0) 
                   
               
               
                   
                 but NOT (itgb3 &gt;10 and tp53 ≤50) 
                   
                   
                   
                   
               
               
                   
                 C: (itgb3 &gt;10 and tp53 ≤50) 
                   18/34 (52.9%) 
                   
                  3/4 (75.0) 
                   
               
               
                   
                 but NOT (lamb1 &gt;250 or plat &gt;427) 
                   
                   
                   
                   
               
               
                   
                 D: (lamb1 &gt;250 or plat &gt;427)  AND   
                   20/21 (95.2%) 
                   
                  9/12 (75.0) 
                   
               
               
                   
                 (itgb3 &gt;10 and tp53 ≤50) 
               
               
                   
               
               
                 †P-values were calculated using the chi-square rest based on the subset of patients with non-missing values. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 18 
               
             
            
               
                   
               
               
                 Summary of the predicted and observed rate of positive SLNB for the  
               
               
                 5 quintiles defined by the distribution of the predicted probabilities. 
               
            
           
           
               
               
               
            
               
                 Quintile defined based on 
                 Predicted rate of 
                 Observed rate 
               
               
                 the predicted probability 
                 positive SLNB† 
                 of positive SLNB 
               
               
                   
               
               
                 ≤0.02 
                  1.4% 
                 0/15 (0%) 
               
               
                 &gt;0.02-0.04 
                  2.1% 
                 0/23 (0%) 
               
               
                 &gt;0.04-0.16 
                  5.9% 
                 0/24 (0%) 
               
               
                 &gt;0.16-0.45 
                 30.7% 
                   17/22 (77.3%) 
               
               
                 &gt;0.45 
                 65.4% 
                   14/20 (70.0%) 
               
               
                   
               
               
                 †Median predicted probability in each quintile 
               
            
           
         
       
     
     The following was performed to determine whether the expression of (33 integrin and other adhesion-related genes in melanoma is influenced by focal adhesion kinase (FAK), a key transducer of integrin signals and novel cancer therapy target (Infante et al.,  J. Clin. Oncol.  30:1527-33 (2012)). To test whether FAK controls adhesion gene expression, B-rafV600E WM858 cells were engineered to contain IPTG-inducible short hairpin RNA (shRNA) against FAK. FAK knock-down was highly effective at the RNA and protein level at concentrations equal to or exceeding 0.025 mM IPTG (Figure S3A-B). FAK could not be visualized in focal adhesions after 0.05 mM IPTG for 5 days ( FIGS. 12C and 12D ). PYK2, a FAK-like tyrosine kinase, could not be detected in WM858 cells, irrespective of endogenous FAK levels. WM858 cells carrying control (NC) or FAK-specific shRNAs (841 and 102) were then exposed to IPTG for 5 days, and changes in adhesion gene expression were subsequently quantified by PCR. FAK-specific shRNA increased (33 integrin expression 2-fold ( FIG. 13A ). Vice versa, over-expression of a FAK cDNA led to a 2-fold down-regulation of (33 integrin and other integrin subunits ( FIG. 13B ). At the protein level, FAK knock-down led to an increase in cell surface (33 integrin ( FIGS. 13C and 13D ), which was accompanied by a noticeable increase in focal adhesion size and number ( FIG. 13E ). An increase in proliferation was observed when FAK levels were reduced ( FIGS. 13F and 13G ) as was a faster scratch wound healing ( FIGS. 13H and 13I ). In line with these data, FAK knock-down was found to induce extracellular regulated kinases (ERK) activity ( FIGS. 13J and 13K ). FAK inhibition by the small molecule FAK kinase inhibitor PF-573228 or blebbistatin, a drug that inhibits FAK by blocking myosin II-dependent contractile forces (Seo et al.,  Biomaterials  32:9568-75 (2011)), induced (33 and also (31 integrin surface levels in B-rafV600E, but not B-raf wild-type melanoma cells ( FIG. 13L ). In contrast, Dabrafenib, a B-raf inhibitor and established single agent therapeutic of metastatic melanoma, reduced integrin levels in most melanoma cells but not in NHM ( FIG. 13L ). While FAK inhibitors effectively suppressed FAK tyrosine (Y) 397 auto-phosphorylation in melanoma cells, Dabrafenib increased FAK phosphorylation ( FIG. 13M ), suggesting that in melanoma B-raf promotes integrin expression by inhibiting FAK, which in turn provides a scaffold for active ERK. In line with this hypothesis, PF-573228 was found to induce ERK activity ( FIGS. 13M-13O ). Moreover, Dabrafenib-induced blockage of ERK activity could be partially reversed by a complete FAK knock-down in 102 cells ( FIG. 13P ). 
     As described herein, a completely customizable high-density microfluidic PCR platform was used to allow for the quantification of multiple genes by repeat measurements. For example, at least 26 individual PCR reactions were performed per patient sample to measure house-keeping genes. To account for RNA contamination by basal keratinocytes—a cell type with stem cell-like features and high levels of adhesion gene expression—keratin 14 (KRT14), a basal keratinocyte marker, was quantified. KRT14 copy number was multiplied with a gene specific, per-copy-of-KRT14 contamination factor that was pre-determined by analyzing normal skin; and the product of this calculation was used to correct for keratinocyte background. In addition, melanocyte markers were routinely assayed to quantify melanocyte content in processed tissue. Aside from throughput, the methods provided herein have several other advantages. First, they are quantitative. This is an advantage over IHC or fluorescent in-situ hybridization (FISH), where the signal intensity is difficult to normalize and/or image analysis is subjective and time consuming. Second, they are based on the quantitation of RNA, which in contrast to DNA carries epigenetic information. Third, they are devoid of array-based hybridization steps, which can lead to hybridization errors and noise. Fourth, they are easily adjusted to include additional genes of interest. 
     The results provided herein demonstrate that the best four-leaf molecular model for predicting SLN metastasis considered (33 integrin, the laminin B1 chain, tissue-type plasminogen activator and tumor antigen p53. The overall predictive ability of a combined model that included molecular parameters was significantly greater than a model that only included clinical/pathologic factors (0.89 vs. 0.77, p&lt;0.001). 
     The results provided herein also demonstrate that FAK inhibition induces the expression of integrins, induces the size of focal adhesions, and stimulates proliferation and mitogen activated kinases. These effects were strongest in B-raf V 600E cells, likely because mutant B-raf inhibits FAK to trigger integrin expression. 
     The two-tree two-leaf model was generated using logic regression and slow cooling on simulated annealing parameters. 
     Additional analysis of samples by next generation sequencing using a cohort of four patients with primary skin melanoma that had not metastasized (median Breslow depth: 2.6 mm) and three patients that had metastasized regionally (median Breslow depth: 2.3 mm) yielded a total of 208 differentially regulated genes out of a total of 15,196 measured genes. ITGB3 as well as SRC, a key downstream effector of (33 integrin, formed the center of a functional network deregulated in regionally metastatic vs. non-metastatic melanoma ( FIGS. 16 and 17 ). 
     Expanding the sample size of the model validation cohort from 104 to 146 resulted in excellent discriminative ability of the clinicopathologic+molecular model with an AUC of 0.93, 95% CI 0.87-0.97 ( FIG. 17 ). Using the suggested cutoff of 10% (Balch et al.,  J Am. Acad. Dermatol.,  60:872-875 (2009)), the false positive rate was 22%, and the false negative rate was 0%. These results demonstrate that data obtained by gene expressing profiling can be combined with Breslow depth, tumor ulceration, and patient age to calculate the predicted probability of SLN positivity at the time of primary diagnosis. These results also can be used to improve patient care by avoiding unnecessary SLN procedures. 
     Example 5—Identifying Inhibitors of Integrin Cell Adhesion Remodeling 
     Osteopontin (SPP1) is a proto-typical cancer-associated extracellular matrix gene and ligand of αv and α5β1 integrins. SPP1 is highly overexpressed in melanoma (Talantov et al.,  Clin. Cancer Res.  11:7234-42 (2005)) and its upregulation correlates with metastasis risk (Conway et al.,  Clin. Cancer Res.  15:6939-6946 (2009) and Mitra et al.,  Br. J. Cancer  103:1229-1236 (2010)). To rapidly screen chemical compounds for their ability to inhibit SPP1 expression in vitro, the endogenous SPP1 promoter of WM858 melanoma cells was tagged with a dual luciferase system using zinc finger nucleases. The SPP1-promoter drives firefly luciferase tagged with a protein degradation sequence (hPEST). A CMV-promoter driven renilla luciferase was used as a loading control ( FIG. 14 ). Assaying both luciferase signals was fast and amendable to high-throughput screening. 
     The investigation was started by screening a 1280 compound library of pharmaceutically active compounds (LOPAC; Sigma-Aldrich). The firefly signal was first normalized to the renilla signal, then to DMSO-treated control wells ( FIG. 15A ). Normalized ratios&lt;0.25 were observed for a handful of compounds, including Pentamidine ( FIG. 15B ). Pentamidine is an FDA approved antimicrobial drug that is used in the prevention and treatment of Pneumocystis pneumonia. It appears to possess other activities as well. See, e.g., Pathak et al., Molecular Cancer Therapeutics, 1:1255-1264 (2002); Smith et al., Anti-Cancer Drugs, 21:181 (2010); and Sun and Zhang, Nucleic Acids Res., 36:1654-1664 (2008). 
     Pentamidine exhibited little cytotoxicity in WM858 and M12 cells with ED 50&#39;s &gt;100 μM (M12 cells are metastatic B-raf V 600E melanoma cells that were recently established from a patient). Pentamidine inhibited SPP1 mRNA in both WM858 ( FIG. 15C ) and M12 cells ( FIG. 15D ). Pentamidine also reduced expression of β integrin and t-PA (PLAT) ( FIG. 15E ). Next, a red-fluorescent nuclear protein was stably expressed in M12 cells to automatically count nuclei over time (using the IncuCyte ZOOM system, Essen Bioscience), a surrogate measure of cell proliferation. Pentamidine reduced M12 proliferation with an ED 50  of 40 μM. When M12 cells were allowed to migrate into Matriger-embedded scratch wounds, Pentamidine inhibited Matrigel® invasion more effectively than Dabrafenib ( FIGS. 15F and 15G ). 
     To determine whether Pentamidine reduces SPP1 expression in vivo, M12 cells were injected intradermally into female nude mice and left to grow until xenograft tumors formed ( FIGS. 15H and 15I ). Then, four different doses of Pentamidine were injected intramuscularly (i.m.) into groups of three mice for six consecutive days. It was previously shown that serum concentration in patients injected with 4 mg/kg Pentamidine i.m. daily (FDA labeling) range from 0.2-1.4 μg/mL (0.3-2.4 μM). In rats, slightly lower levels can be achieved using 10 mg/kg i.m. daily (0.1-0.4 μg/mL) (Bernard et al.,  J. Inf. Dis.  152:750-754 (1985) and Waalkes et al.,  Clin. Pharma. Therap.  11:505-512 (1969)). In the current study, at the highest Pentamidine dose (80 mg/kg/daily), all mice died. Mice survived at 40 mg/kg/day, but appeared sick. The other two doses, specifically the 8 mg/kg/day dose, were well tolerated. Tumors were subsequently harvested, lysed, and analyzed by quantitative PCR. All doses of Pentamidine led to a reduction of SPP1, β3 integrin, and t-PA (PLAT) mRNA expression in tumor tissue ( FIG. 15J ). 
     These results demonstrate that pentamidine can be used to reduce the expression of ITGB3, PLAT, and SPP1. 
     Other Embodiments 
     It is to be understood that while the disclosure has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the disclosure, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.