Neoplasia Chromosomal Microarray Analysis

Methodology

Chromosomal microarray analysis is done using the Illumina Infinium CytoSNP-850K BeadChip, which contains 850,000 probes for SNP markers.  Analysis in the CGL 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: Chromosomal 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°C.  Ship on minimum of 10 lb of dry ice in insulated container by overnight courier.
• FFPE Tumor Slides: If tumor content is <70% send 10 unstained 10μm FFPE slides and one image of an H&E stained slide that has the area of tumor marked.  If tumor content is >70% send 10 x 10μm curls in two 1.5 mL tubes (5 per tube). 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: Please send curls or slides if possible.  Contact lab if block is the only option.
• 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 water.  Keep at room temperature.  We can only accept DNA isolated in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the College of American Pathologists and/or the Centers for Medicare and Medicaid Services.

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 CGL Neoplasia Test Request Form, including billing information.
2. Collect sample.
3. Deliver to Clinical Genomics Laboratory as soon as possible.  Specimens are accepted Monday through Friday.

Ship sample overnight to:

Clinical Genomics Laboratory
University of Washington Health Sciences Building
Room H-561
1959 NE Pacific St
Seattle, WA 98195

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.