Test Overview
Test Methodology

SNP microarray analysis is performed using the Affymetrix OncoScan (TM) FFPE Assay Kit. The assay utilizes Molecular Inversion Probe (MIP) technology, which is optimized for highly degraded FFPE samples (probe interrogation site of just 40 base pairs). For copy number analysis the assay has a resolution of 50-100 kb in genomic regions spanning selected 900 cancer genes and of 300 kb outside of these regions. Isolated patient DNA is annealed to the MIP probe panel. Annealed MIPs are circularized, followed by enzymatic removal of any un-ligated probe and template DNA. Remaining MIPs are linearized, amplified, enzymatically fragmented, and hybridized to oligonucleotide microarrays. The arrays are washed, scanned, and the results are analyzed and interpreted using OncoScan Console and Nexus Express for OncoScan 3 software.

Test Usage

This SNP microarray assay detects DNA copy number gains (including amplification) and losses as well as regions of copy neutral loss of heterozygosity by SNP analysis in FFPE tissue samples from neoplastic lesions. This assay is particularly useful for detecting genomic abnormalities in FFPE tissues which usually generate degraded DNA and low DNA yield. At least 25% malignant cells must be present in the sample submitted for this assay. For melanocytic lesions this test is used to aid in the diagnosis of histologically ambiguous melanocytic neoplasms. Most melanomas have an unstable genome with multiple segmental DNA abnormalities, while the majority of benign melanocytic nevi have no chromosomal aberrations or have isolated chromosomal gains and losses that by themselves are not commonly seen in melanomas. In the setting of a histologically ambiguous melanocytic neoplasm, detection of multiple segmental genomic abnormalities favors a diagnosis of melanoma. Published data report a sensitivity of 96% and a specificity of 98% using copy number alterations to diagnose melanoma. Results from this test should not be used alone in diagnosing a melanocytic lesion and correlation with clinical history, histological examination and other standard diagnostic procedures is necessary for diagnosis.

Reference Range *

Interpretive report provided.

Test Limitations

Although SNP Array is a powerful diagnostic tool for the evaluation of chromosomal copy number changes, this assay will not detect balanced chromosomal aberrations, unbalanced genomic aberrations of regions not represented on the microarray, point mutations or a tetraploid genome resulted from duplication of a diploid genome. The test may not detect genomic imbalances in samples with less than 25% tumor burden or mosaicism changes. This test is employed to detect only acquired aberrations.

Test Details
Days Set Up
Monday – Friday , 8:30 am - 5:30 pm
Analytic Time

3 weeks

Soft Order Code
MiChart Code
Chromosomal Microarray Analysis-Melanoma (Dermatopathology Molecular Diagno
  • Microarray CGH for Melanoma, Tumor
  • Array CGH for Melanoma, Tumor
  • SNP Microarray for Melanoma, Tumor
Dermatopathology Molecular Testing Lab
Dermatopathology Molecular Testing Lab
Specimen Requirements
Collection Instructions

Submit a formalin-fixed, paraffin-embedded (FFPE) block containing tumor tissue (preferred specimen). If a block is not available submit 10 FFPE unstained sections at 10-micron thickness on regular slides, unbaked and one regular H&E obtained as serial sections; store at room temperature.

Rejection Criteria
Small samples with insufficient amount of DNA are not acceptable. At least 25% malignant cells must be present in the sample submitted for this test.
Additional Information

By ordering this test the clinician acknowledges that informed consent has been obtained from the patient as required by applicable state or federal laws.

CPT Code
Fee Code
NY State Approved