Neoplasia Chromosomal Microarray Analysis [UWMC Clinical Genomics Laboratory]

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General Information

Lab Name
Lab Code
561
Description

This test detects chromosome deletions and duplications much smaller than what can be seen with traditional karyotyping or FISH. It also detects regions of loss of heterozygosity (LOH), which occur frequently in the neoplastic process. Testing is performed by UWMC - Montlake DLMP Clinical Genomics Laboratory.

EPIC Ordering:

  • Test Name: SNP Microarray, Neoplasia
  • Order Code: ARRAYNEOP
  • For orders submitted electronically via Epic, a separate requisition form is not required.
Synonyms
ARRAYNEOP, Cancer Array, Cancer CMA, CGAT, CGH Array, Chromosome Genomic Array Testing, Chromosome Microarray Analysis, CNA, CNV, Comparative Genomic Hybridization, Copy number alteration, Copy Number Variant, Cytogenomic Microarray Analysis, Genomic Microarray, LOH, Loss of Heterozygosity, Neoplasia, Single Nucleotide Polymorphism Microarray, SNP Array, SNP Microarray
Components

Interpretation

Reference Range
Interferences and Limitations

Chromosomal microarray analysis will not detect imbalances smaller than 10 kb on average, imbalances in the regions of the genome not represented on the microarray, low level mosaicism (<20%), tetraploidy, balanced alterations (e. g. reciprocal translocation), methylation anomalies and other epigenetic events, or single nucleotide variants.

Ordering & Collection

Specimen Type
Bone Core, Bone Marrow, Extracted DNA, Fresh or Frozen Tumor, FFPE Slides or Block, Leukemic Blood, Lymph Node, Tumor Culture
Collection

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:

  • 50-150 mg (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.
    • Send 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).
    • Send one H&E stained slide for QC.
  • 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 of cultured tumor cells that are 80-100% confluent. Keep at room temperature.

Bone Core:

  • Contact the lab (206-616-4062).

Lymph Node:

  • Contact the lab (206-616-4062).

Extracted 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.
Forms & Requisitions

Outside Providers: CGL Neoplasia Test Request Form

Handling Instructions

Outside Laboratories:

  • Sample collection kits are available upon request. Kits include sample collection tubes, a biohazard bag with absorbent material, a test requisition, and FedEx shipping materials. Contact the lab at 206.616.4062 to request a kit.
  • A completed request form must accompany all orders.
  • Samples are accepted Monday-Friday.
  • Ship sample to:
    • Clinical Genomics Laboratory
    • University of Washington Health Sciences Building
    • Room H-561
    • 1959 NE Pacific St
    • Seattle, WA 98195
Quantity
Requested: Varies; refer to Collection information.
Minimum: Varies; refer to Collection information.

Processing

Receiving Instructions

Hold samples at room temperature. If sample was frozen when received, keep frozen until pick up.

  • Call UWMC - Montlake DLMP Cytogenetics and Genomics Laboratory at 206.598.4489 for pick up. Cytogenetics is staffed on weekends to accept samples.
  • If no answer or after hours, call 206.598.4488 to leave message.
Misc Sendout

Performance

Lab Department
Frequency
Performed weekly. TAT: 1-2 weeks. Cell culturing, culture expansion, karyotyping, or FISH confirmation may increase TAT
Available STAT?
Yes
Performing Location(s)
Pathology Clinical Genomics Laboratory
206-598-8684
Other Locations/Notes

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

Ph: (206) 616-4062

Billing & Coding

Billing Comments

CPT code: 81277

Prior Insurance Authorization: Contact gpab@uw.edu for details