Array CGH for Melanoma, Tumor
Microarray CGH for Melanoma, Tumor
SNP Microarray for Melanoma, Tumor
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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.
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.
Interpretive report provided.
* Reference ranges may change over time. Please refer to the original patient report when evaluating results.
Submit a formalin-fixed, paraffin-embedded (FFPE) block containing tumor tissue. If a block is not available and examination of a representative H&E tissue section reveals that more than 50% of the cells are tumor cells, submit 10 FFPE tissue rolls cut at 10-micron thickness in a clean 1.5 ul tube. If examination of a representative H&E tissue section reveals that less than 50% of the cells are tumor cells, submit 10 FFPE unstained sections at 10-microns thickness on regular slides, unbaked and one H&E slide obtained as serial sections.
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.