Neoplasia Cytogenomic Microarray Analysis

Genes

Whole Genome

Test Guide

Neoplasia cytogenomic microarray analysis, also known as neoplasia chromosomal microarray analysis (CMA), is increasingly relevant in establishing a diagnosis and prognosis for people with cancer (e.g. Gunnarsson, et al. 2008).  With a single test, CMA detects chromosome deletions, chromosome duplications and amplifications, and copy neutral loss of heterozygosity (LOH) across the entire genome.

Cytogenomic microarray analysis is not recommended as a test method for post therapy follow-up or for minimal residual disease detection.

Methodology

Cytogenomic microarray analysis is done using the Illumina Infinium CytoSNP-850K BeadChip, which contains 850,000 probes for SNP markers.  Analysis in the CCL is limited to detecting copy number changes (deletions and duplications) that include at least 10 probes and regions of copy number neutral absence of heterozygosity (AOH) that include at least 500 probes.  We cannot exclude abnormalities below these levels of resolution.  Copy number variations found to have clear or suspected clinical relevance are reported.  Copy number changes containing no genes, found commonly in the general population, or of uncertain clinical significance are not reported.  Telomeric regions of AOH >5Mb in length or interstitial regions of AOH >15 Mb in length are reported.

Limitations of the test: Cytogenomic microarray analysis will not detect imbalances in the regions of the genome not represented on the microarray, low level mosaicism (<20%), balanced alterations (e. g. reciprocal translocation), methylation anomalies and other epigenetic events, or point mutations that may be responsible for a clinical phenotype.

Specimen Requirements

Specimen Types:

  • Leukemic Blood: 1-3 ml in EDTA (lavender top vacutainer).  Keep at room temperature.
  • Bone Marrow: 1-3 ml in EDTA (lavender top vacutainer).  Keep at room temperature.
  • Fresh Frozen Tumor Tissue: 50-150mg (0.15-2.0 cm3) fresh tissue snap-frozen.  Store at -20°CShip on minimum of 10 lb of dry ice in insulated container by overnight courier.
  • FFPE Tumor Slides: 10 unstained 5μm FFPE slides containing adequate amounts of tumor with areas of tumor marked.  Include a copy of corresponding surgical pathology report.  Mail slides in a protected mailing container at room temperature and protect from excessive heat.
  • FFPE Tumor Block: Tissue block containing adequate amounts of tumor with areas of tumor marked.  Include a copy of corresponding surgical pathology report.  Mail at room temperature and protect from excessive heat.
  • Solid Tumor Cultures: Two T-25 flasks that are 80-100% confluent.  Keep at room temperature.
  • Bone Core: Contact the lab (206-598-4488).
  • Lymph Node: Contact the lab (206-598-4488).
  • DNA: 3-10 micrograms (minimum 1 microgram) at a concentration of 100 nanograms per microliter (or higher), suspended in TE-buffer.  Keep at room temperature.

Special Instructions

Return of Results: Results will be faxed to the numbers(s) provided on the requisition form.

Turnaround Time: 7 to 14 days from receipt of adequate sample

  • Cell culturing, culture expansion, karyotyping, or FISH confirmation may increase TAT.

How to Order

Please follow these steps:

Test kits and return shipping are available, as needed.  Please call 206-598-8684 to request kits.

1. Complete CCL Neoplasia Test Request Form, including billing information.
2. Collect sample.
3. Deliver to Clinical Cytogenomics Laboratory as soon as possible.  Specimens are accepted 7 days a week.

Ship sample overnight to:

c/o Cytogenetics and Genomics Laboratory
University of Washington Medical Center
Room NW-125, Box 356100
1959 NE Pacific St
Seattle, WA 98195-6100

Note: Orders cancelled after they have been submitted will incur a prorated charge based on the work that has been completed as of the time of cancellation.

CPT Code & Cost

81406
$ 2,480

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