Constitutional Chromosomal Microarray Analysis, Familial Variant

Methodology

Chromosomal microarray analysis, Familial Variant is done using the Illumina Infinium CytoSNP-850K BeadChip, which contains 850,000 probes for SNP markers.  This assay only analyzes the region of the specified familial CNV(s) and does not rule out alterations outside of the targeted region.  Analysis in our laboratory is limited to detecting CNVs that include at least 10 SNPs.  Abnormalities below these levels of resolution may not be detected.

Limitations of the test:  Chromosomal microarray analysis, Familial Variant will not detect imbalances in the regions not represented on the microarray, low-level mosaicism (<20%), balanced alterations involving the specified familial region, methylation anomalies and other epigenetic events, single nucleotide variations, or small insertions or deletions.

Specimen Requirements

Sample Types:

• 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.
• Products of Conception and 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: Please 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 (Discard the first 1mL of fluid to minimize risk of maternal cell contamination) OR two T-25 flasks that are 80-90% confluent.  Keep at room temperature.
• Chorionic Villi: Two T-25 flasks that are 80-90% confluent.  Contact lab to discuss direct testing of cleaned but uncultured villi.  Keep at room temperature.
• 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: 0.5mL in Oragene•ONE(ON-500) Collection Kit.  Keep at room temperature.

Special Instructions

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

Turnaround Time: 7 to 14 days for prenatal or newborn samples; 14 to 21 days for pediatric or adult samples; 28 days for products of conception samples.

• For prenatal testing, add 2-3 weeks if sample needs to be cultured (more likely if gestational age <18 weeks).
• Bloody or discolored amniotic fluid samples or amniocyte cell pellets with blood cells present will be cultured to reduce the risk of maternal cell contamination.

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 Constitutional Test Request Form, including billing information.
2. Collect sample.
3. Deliver to Clinical Genomics Laboratory as soon as possible.  Samples 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.

Prior Insurance Authorization:  When this is required by a patient’s insurance plan, our pre-authorization specialists can do it for you.  Contact gpab@uw.edu for details.