Test Overview
This Chromosomal Microarray Analysis is performed using the Thermo Fisher OncoScan platform. 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 numbers, the assay has a resolution of 50-100 kb in selected 900 cancer genes and of 300 kb outside of the cancer genes. Gains and losses that include a known clinically significant cancer gene, or are greater than 3Mb outside clinical oncology significant regions, and loss of heterozygosity greater than 10Mb are reported. Results are analyzed and interpreted using Thermo Fisher Chromosome Analysis Suite software (ChAS).
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% of 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, the 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.
* Reference ranges may change over time. Please refer to the original patient report when evaluating results.
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 resulting 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
Specimen Requirements
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. Most insurance carriers require prior authorization for payment. Testing will not begin until insurance prior authorization is received, it is confirmed that prior authorization is not required, or the patient has agreed to pay out of pocket. A completed Michigan Medicine Request and Consent for Genetic Testing form is required and is available by calling 800-862-7284 or online: https://mlabs.umich.edu/media/188.
Additional Information
Appropriate FISH testing on a separate sample may be performed at an additional charge to confirm, clarify, or further characterize the Chromosomal Microarray Analysis results if necessary. By ordering this test the clinician acknowledges that additional reflex testing will be performed and billed at a separate additional charge if indicated. Also, by ordering this test the clinician acknowledges that informed consent has been obtained from the patient as required by applicable state or federal laws.