Molecular malignancy in melanocytic lesions

A method of determining gene expression in a sample, comprising:

• obtaining from a subject a melanocyte-containing sample;
• determining in the sample the expression levels of a plurality of genes comprising at least two of the biomarkers selected from MAGEA2, PRAME, PDIA4, NR4A1, PDLIM7, B4GALT1, SAT1, RUNX1, SOCS3, and those in Table 13;
• and
• providing a report of the plurality of genes expression levels in the sample or a characterization of the sample as a nevus or melanoma based on the expression levels of the plurality of genes.

A method of determining malignancy in a melanocyte-containing sample, comprising:

• determining, in a melanocyte-containing sample obtained from a subject, an expression level of at least two biomarkers selected from:
• B4GALT1, BAX, MAGEA2, NR4A1, PDIA4, PRAME, RUNX1, SOCS3, SAT1, PDLIM7, BIRC5, MET, MAGEC2, POLR2J3, ZFYVE16, and BEST1;
• calculating an output from an algorithm that uses the expression levels of the at least two biomarkers as an input;
• and
• determining from the algorithm output that the sample is or is not malignant by comparing the output to a reference standard from known malignant melanocyte-containing samples.

An array, comprising:

• at least three addressable locations, each location comprising immobilized capture probes having the same specificity, and each location comprising capture probes having specificity different than capture probes at each other location,
• wherein the capture probes at two of the at least three locations are capable of directly or indirectly specifically hybridizing a biomarker that includes two or more of MAGEA2, PRAME, PDIA4, NR4A1, PDLIM7, B4GALT1, SAT1, RUNX1, SOCS3 and those in Table 13, and the capture probes at one of the at least three locations is capable of directly or indirectly specifically hybridizing a normalization biomarker listed in Table 3;
• and
• wherein the specificity of each capture probe is identifiable by the addressable location the array.