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Familial genetic variant detection (SNV and small indel) by Sanger sequencing – Saskatoon

Discipline

Genetics and Genomics

Overview

Description

Ordering recommendations

  • Sanger sequencing is to specifically detect the familial genetic variant including single nucleotide variants (SNV) and small indel.
  • The Division of Medical Genetics is able to order this test
  • If the requisition is incomplete or the test is ordered by a physician who is not approved, DNA will be extracted and sent to RRPL for banking until testing can proceed
  • DNA may also be extracted at RRPL and sent to RUH Genomics Lab for testing
  • A positive control DNA/specimen should be identified and submitted if possible.

Ordering requirements

Specimen Information

Specimen types accepted

  • Peripheral blood/whole blood
  • Genomic DNA extracted at RUH Genomics Lab or RRPL

Specimen collection container

Collection procedure

  • Invert tube several times to mix
  • Specimen must be accompanied by a completed test requisition, signed by physician
  • Failure to include relevant patient information may result in test results being delayed or discontinued

Required volume

  • Optimal volume: 4 - 7mL
  • Minimum volume for adult: 2 mL blood
  • Minimum volume for pediatric patient: 1 mL of peripheral blood or cord blood

(Submitting the minimum volume makes it impossible to repeat the test or perform confirmatory/reflex testing. In some situations, a minimum volume may require a second collection.)

Transport and stability

  • Ship specimens at ambient temperature
  • Specimens may be stored at 2 - 8°C

Rejection criteria

Performance

Methodology

  • Sanger sequencing, also known as the “chain termination method,” is a method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication.
  • Sanger sequencing is performed to specifically detect the familial variant. Rare variants that prevent amplification of both alleles equally in the PCR process or lie within probe/ligation sites affecting probe binding may lead to false positive or false negative results.
  • Variants are described using HGVS nomenclature (GRCh37).

Days/times performed

Availability

  • Specimens accepted Monday to Friday, 8:00 am to 5:00 pm at the RUH Genomics Laboratory

Maximum laboratory time

For familial variants

  • Turnaround time for routine test is 28 days
  • Turnaround time for STAT is 14 days

Specimen retention time

  • DNA banking specimens are stored and retained at RRPL as their banking policy

Last Updated: April 11, 2024