Test Details
Methodology
Next-generation sequencing to identify genetic variants, including single nucleotide variants (SNVs), insertions, deletions and copy number variants (CNVs).
The number of hexanucleotide repeat units in intron 1 of the C9orf72 gene is assessed by repeat-primed PCR (RP-PCR) with fluorescently labeled primers followed by fragment size analysis of the resulting amplicons via capillary electrophoresis (CE). A secondary round of RP-PCR + CE, utilizing a non-overlapping set of primers to amplify the locus from the opposite direction, is used to confirm the initial call for allele sizes of 22 or more repeat units. This test can accurately (+/-1 repeat unit) determine repeat size up to 31 repeat units (Pathogenic full mutation cut-off), but it is not designed to determine the exact number of repeat units above 31.
Confirmation of the presence and location of reportable variants is performed as needed based on stringent criteria using one of several validated orthogonal approaches.1
Result Turnaround Time
10 - 21 days; in some cases, additional time may be required for confirmatory or reflex tests.
Turnaround time is defined as the usual number of days from the date of pickup of a specimen for testing to when the result is released to the ordering provider. In some cases, additional time should be allowed for additional confirmatory or additional reflex tests. Testing schedules may vary.
Test Includes
This test includes the following gene: C9orf72.
Use
This test is used for genetic testing of C9orf72-related Frontotemporal Dementia and Amyotrophic Lateral Sclerosis. This repeat expansion test analyzes hexanucleotide (GGGGCC) repeat expansions within an intronic region of the C9orf72 gene.
Special Instructions
Test orders must include an attestation that the provider has the patient's informed consent for genetic testing.
Limitations
Technologies used do not detect germline mosaicism and do not rule out the presence of large chromosomal aberrations, including rearrangements and gene fusions, or variants in regions or genes not included in this test, or possible inter/intragenic interactions between variants or repeat expansions.
Variant classification and/or interpretation may change with time if more information becomes available. False positive or false negative results may occur for reasons that include: rare genetic variants, sex chromosome abnormalities, pseudogene interference, blood transfusions, bone marrow transplantation, somatic or tissue-specific mosaicism, mislabeled samples or erroneous representation of family relationships.
This test was developed and its performance characteristics determined by Labcorp. It has not been cleared or approved by the Food and Drug Administration.
Specimen Requirements
Specimen
Whole blood or Oragene Dx 500 saliva kit or ORAcollect Dx OCD-100 buccal swabs or genomic DNA (gDNA) extracted from non-fetal, non-tumor sources only
Volume
4 mL whole blood or Oragene Dx 500 saliva kit or 2 ORAcollect Dx OCD-100 buccal swabs or 5 micrograms (μg) of gDNA with a concentration of 50 ng/μL
Minimum Volume
3 mL whole blood or Oragene Dx 500 saliva kit or 2 ORAcollect Dx OCD-100 buccal swabs or 5 μg of extracted DNA at a minimum concentration of 50 ng/μL
Container
Lavender-top (EDTA) tube or Oragene Dx 500 saliva collection kit or ORAcollect Dx OCD-100 buccal swabs or 2 mL microcentrifuge tube with screw cap
Collection Instructions
Standard phlebotomy; follow Oragene Dx 500 saliva kit collection instructions. Follow ORAcollect Dx OCD-100 buccal swab collection instructions. Do not eat, drink, smoke or chew gum 30 minutes prior to saliva or buccal collection. For gDNA, DNA must be extracted in a CLIA-certified laboratory.
Stability Requirements
- Whole blood: 90 days at room temperature or 4°C
- Saliva: 60 days at room temperature
- Buccal: 60 days at room temperature
- gDNA: room temperature (preferred) or refrigerate 3 years at 4°C
Storage Instructions
For blood, saliva and buccal, maintain specimen at room temperature or refrigerate at 4°C. Do not freeze.
For gDNA, room temperature is preferred, or refrigerate at 4°C. Frozen also is accepted if shipped on ice packs.
Causes for Rejection
Hemolyzed; quantity not sufficient for analysis; improper container; improper storage temperature; specimen from an individual who has undergone allogeneic bone marrow transplant
Footnotes
1. Lincoln SE, Truty R, Lin CF, et al. A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing. J Mol Design. 2019 Mar;21(2):318-329. PubMed 30610921