Chromosomal Microarray Analysis for Constitutional Abnormalities [UWMC Clinical Genomics Lab]

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General Information

Lab Name
Lab Code
534
Description

This test detects genomic deletions and duplications much smaller than what can be seen with traditional karyotyping or FISH. It also detects regions of absence of heterozygosity (AOH) caused by uniparental disomy or identity by descent. Ordering providers must choose whether or not variants of uncertain clinical significance are reported. Testing is performed by UWMC - Montlake DLMP Clinical Genomics Laboratory.

Epic Ordering:

  • Test Name: SNP Microarray, Constitutional.
  • Order Code: LAB017.
  • For orders submitted electronically via Epic, a separate requisition form is not required.

SPS Note: If request specifies SNP Microarray to Seattle Children's Hospital, refer to OLTG #459.

Forms & Requisitions

Outside Providers: CGL Constitutional Test Request Form

Synonyms
Absence of Heterozygosity, AOH, CGH, Chromosome Microarray Analysis, CMA, CNV, Comparative Genomic Hybridization, Constitutional, Copy Number Variant, Genomic Microarray, LAB017, Microdeletion, Microduplication, Single Nucleotide Polymorphism Array, SNP Array, SNP Microarray, Uniparental Disomy, UPD

Interpretation

Interferences and Limitations

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

Ordering & Collection

Specimen Type
Amniotic Fluid or Cultured Amniocytes, Chorionic Villi, Extracted DNA, Fetal Tissue, Peripheral Blood, Products of Conception, Saliva, Skin Biopsy, Umbilical Cord Blood
Collection

Peripheral Blood:

  • 3-4 mL for adults or 1-2 mL for infants in EDTA (lavender top vacutainer). Keep at room temperature.

Cord Blood:

  • 1-2 mL in EDTA (lavender top vacutainer). Keep at room temperature.

Skin Biopsies, Products of Conception, Fetal Tissue:

  • For products of conception, send villi when identifiable. If material is small and unidentifiable, send entire sample. For fetal tissue, send fascia lata, lung, or kidney if possible.
  • Fresh tissue: 30-50mg in sterile transport media containing antibiotics (e.g. Alpha-MEM media, RPMI) or two T-25 flasks 80-90% confluent. Keep refrigerated.
  • Frozen tissue (-20 degrees): 30-50 mg. Remove media before freezing. Keep frozen (-20 degrees) during transport.
  • FFPE tissue: Send curls or slides if possible. Contact lab if block is the only option. If sample is mixed maternal and fetal, send 10 unstained 10μm FFPE slides and one image of an H&E stained slide that has the area of villi marked. If sample is entirely fetal, send 10 x 10μm curls in two 1.5 mL tubes (5 per tube). Send at 20-25°C and protect from excessive heat.

Amniotic Fluid:

  • 15-20mL of amniotic fluid obtained under sterile conditions. Discard the first 1mL of fluid to minimize risk of maternal cell contamination.
  • Two T-25 flasks of cultured amniocytes that are 80-90% confluent.
  • Keep at room temperature.

Chorionic Villi:

  • Two T-25 flasks of cultured chorionic villi that are 80-90% confluent. Keep at room temperature.
  • Contact lab to discuss direct testing of cleaned but uncultured villi.

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

Saliva:

Forms & Requisitions

Outside Providers: CGL Constitutional 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

Processing

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.

Performance

LIS Dept Code
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

Frequency
Performed weekly. TATs: amniotic fluid, amniocytes, CVS for ongoing pregnancy: 1-2 weeks. Newborn cord blood: 1-2 weeks. Peripheral blood, Saliva, Extracted DNA: 2-3 weeks. Fetal tissue, products of conception: 3-4 weeks after insurance pre-authorization is approved.
Available STAT?
Yes

Billing & Coding

CPT codes
Billing Comments

CPT code: 81229

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

LOINC