Droplet digital PCR (ddPCR)

Test Guide

Droplet digital PCR (ddPCR) is most often used to test family members for deletions or duplications initially detected by cytogenomic microarray analysis (CMA).  It is a less expensive option than CMA.  ddPCR allows for detection of deletions and duplications that are too small to be seen using FISH or CMA.  ddPCR also targets only the deletion or duplication of interest.  This avoids the possibility of incidentally detecting a different copy number variant.

Methodology

Genomic DNA extracted from the patient sample is amplified by fluorescence based PCR.  Before the amplification, the PCR sample is partitioned into 20,000 droplets using Bio-Rad QX200 droplet generator. After amplification, droplets containing target sequence are detected by fluorescence and scored as positive, and droplets without fluorescence are scored as negative, using Bio-Rad QX200 droplet reader and QuantaSoft Software.  Poisson statistical analysis (built in QuantaSoft™ Software) of the numbers of positive and negative droplets yields absolute quantitation of the target sequence.  CN can be determined by comparing the concentration of the target and reference genes/regions (RPP30). Additional details about this assay can be found at: http://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_6407.pdf

Limitations of the test: Droplet digital PCR (ddPCR) is performed for the sole purpose of identifying targeted genomic copy number gains (duplications or amplifications) and copy number losses (deletions) of the regions being interrogated.  ddPCR will not detect low-level mosaicism (<20%). ddPCR will not detect imbalances in the genome outside of the interrogated regions or other types of genomic alterations (e.g. point mutations).  The failure to detect a CNV at the regions being interrogated does not rule out other types of genomic abnormalities that may be responsible for the clinical phenotype.

Specimen Requirements

Sample Types:

  • Peripheral Blood: 3-4 ml 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: 30-50mg fresh tissue in sterile transport media containing antibiotics (e.g. Alpha-MEM media, RPMI) or two T-25 flasks 80-100% confluent.  If identifiable tissue in products of conception, send chorionic villi.  If material is small and unidentifiable, send entire sample.  For stillbirths, send fascia lata, lung, or kidney if possible.  Keep refrigerated.
  • Amniotic Fluid: 15-20ml of amniotic fluid OR two T-25 flasks that are 80-100% confluent.  Keep at room temperature.
  • Chorionic Villi: Two T-25 flasks that are 80-100% confluent.  Keep at room temperature.
  • DNA: 2 micrograms (minimum 1 microgram) at a concentration of 50 nanograms per microliter (or higher), suspended in water.  Keep at room temperature.
  • Saliva: 0.5mL in Oragene•ONE(ON-500) Collection KitKeep at room temperature.

Special Instructions

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

Turnaround Time: 4 weeks from receipt of adequate sample

  • For prenatal testing, add 7 days 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 CCL Constitutional Test Request Form, including billing information.
2. Collect sample.
3. Deliver to Clinical Cytogenomics Laboratory as soon as possible.  Samples 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.

Prior Insurance Authorization:  When this is required by a patient’s insurance plan, we can do it for you.  Download and complete the CPDx INSURANCE VERIFICATION FORM.

CPT Code & Cost

81479
$595

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