• Test Code:
    6520
  • Department:
  • Test Synonyms:
    Melanoma arrayMelanoma copy number analysisMelanoma targeted region
  • CPT Code(s):
    81406
Background:

The distinction between melanocytic nevi and melanoma can prove diagnostically challenging.  The melanoma targeted region microarray may be a useful molecular methodology for discriminating malignant neoplasms from benign nevi.  For instance, benign nevi are generally normal on chromosomal microarray (see note*) whereas melanomas very often show large (regional) deletion and duplications (Ardakani et al. 2017 Pathology 49; Chandler et al. 2012 Arch Pathol Lab Med 136).  Expectedly, such gains and losses overlap and contain known oncogenes and tumor suppressor genes, respectively.  Additionally, the SNP microarray used here can detect copy number neutral absence of heterozygosity (AOH), which is not detectable by FISH and may impact relevant regions (Chandler et al. 2012). 

Currently, the Melanoma Microarray Targeted Region Panel focuses on regional gains and losses that are typical in melanomas, such as (in order of prevalence):

Losses: 9p, 9q, 10q, 10p, 11q, 6q, 5q, 14q, 3p, 3q, 11q, 16q, 1p and 11p
Gains: 6p, 7q, 7p, 1q, 8q and 20q.

*Note:  Spitz nevi may show isolated gain of 11p, which is not seen in melanomas; Bastian et al. 2003 Am J Pathol 163).

Methodology:

After pathologist review and tumor identification, DNA is macro-dissected from FFPE slides, isolated, fluorescently labeled and hybridized (with labeled reference DNA) to an Oxford Genome Technology-designed CCMC oncology array, printed by Agilent.  The CCMC+SNP array is comprised of a collection of oligonucleotide probes covering 495 oncology-associated genes at gene-level resolution, plus region-specific and backbone probes; additionally, SNP probes are used to determine copy number neutral (LOH); 180,000 elements in total (oligos+SNP) on each array.

Specimen Requirements:

  • Unstained FFPE slides at room temperature.
  • Preferred slice thickness is 5 micrometer on positively charged slides.
  • Please submit 10 unstained slides; 15 sections for small biopsies.
  • Contact Client Services with questions.
  • Tumor samples should be selected from viable areas, with as little normal or necrotic material as possible.
  • After collection, keep at room temperature until shipping.
  • Contact Client Services at (855) 535-1522 for shipping kits and instructions.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information.

Test Performed (Days):

Weekly

Turn Around Time:

7-12 Days - Contact Lab at 855-KDL-1LAb (535-1522)

Shipment Sensitivity Requirements:

  • Keep specimen at room temperature during transit.
  • Do not use the cold pack provided in the KDL shipping kit.
  • Ship the specimen overnight express, using the FedEx priority overnight label provided.

References:

Additional Info:

The Knight Cancer Institute at Oregon Health & Science University is a pioneer in the field of precision cancer medicine. The institute's director, Brian Druker, M.D., helped prove it was possible to shut down just the cells that enable cancer to grow. This breakthrough has made once-fatal forms of the disease manageable and transformed how cancer is treated. The OHSU Knight Cancer Institute is the only National Cancer Institute-designated Cancer Center between Sacramento and Seattle – an honor earned only by the nation's top cancer centers. It is headquarters for one of the National Cancer Institute's largest research collaboratives, SWOG, in addition to offering the latest treatments and technologies as well as hundreds of research studies and clinical trials.

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