BRCAssure: BRCA1/2 Ashkenazi Jewish Profile

CPT 81212

Test Details

Cancer Type

Breast, Hereditary breast and ovarian, Hereditary cancer, Ovarian

Technology Used

Molecular, NGS

Use

To screen for three founder mutations in BRCA1 (c.68_69delAG and c.5266dupC) and BRCA2 (c.5946delT) genes in Ashkenazi Jewish population. These mutations are also known by their previous nomenlcature, namely 187delAG and 5382insC for BRCA1 and 6174delT for BRCA2 gene.

Special Instructions

BRCAssure® questionnaire should be submitted with sample submission. Please contact CMBP genetics services at 800-345-4363 to coordinate testing.

Limitations

Technologies used do not detect germline mosaicism and do not rule out the presence of large chromosomal aberrations, including rearrangements, gene fusions, or variants in regions or genes not included in this test, or possible inter/intragenic interactions between variants. 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: genetic variants, pseudogene interference, technical handling, blood transfusions, bone marrow transplantation, mislabeling of samples, or erroneous representation of family relationships. For heterozygous variants in the same gene, the assay cannot determine whether they are on the same or a different chromosome; to determine phase and clinical significance, rarely, parental testing may be required. Exact breakpoints of exon-level deletions/duplications are not determined. The presence of an inherited cancer syndrome due to a different genetic cause cannot be ruled out. Any interpretation should be clinically correlated with information about the patient's presentation and relevant family history.

This test was developed and its performance characteristics determined by LabCorp. It has not been cleared or approved by the Food and Drug Administration.

Methodology

Next-generation sequencing: Genomic regions of interest are selected using a custom capture reagent for target enrichment and sequenced via the Illumina® next generation sequencing platform. Regions of interest include all exons and intron/exon junctions (+/-20 nucleotides) of the BRCA1 (NM_007294.3) and BRCA2 (NM_000059.3) genes. Sequencing reads are aligned with the human genome reference GRCh37/hg19 build. Minimum mean coverage is 40X. Any segment failing minimum read depth coverage is rescued by bi-directional Sanger sequencing to complete sequence analysis. Variants, including SNVs and CNVs, are identified using a custom bioinformatics pipeline.

Reported variants: Pathogenic and likely pathogenic variants and variants of uncertain significance (VUS) are reported. Non-deletion variants are specified using the numbering and nomenclature recommended by the Human Genome Variation Society (HGVS). Benign variants are not reported. Variant classification and confirmation are consistent with ACMG standards and guidelines.1,2 Detailed variant classification information is available upon request. A variant of uncertain significance (VUS) should not be used in clinical decision making; a VUS is classified based on inadequate or conflicting evidence regarding its pathogenicity or clinical relevance.

Specimen Requirements

Information on collection, storage, and volume

Specimen

Whole blood or saliva collected in an Oragene Dx collection kit

Volume

7 mL whole blood, 2.0 mL saliva

Minimum Volume

3 mL whole blood, 0.5 mL saliva

Container

Lavender-top (EDTA) tube or yellow-top (ACD) tube or Oragene Dx 500 saliva collection kit

Storage Instructions

Maintain specimen at room temperature.

Causes for Rejection

Frozen whole blood; serum; leaking tube; clotted blood; grossly hemolyzed specimen; incorrect anticoagulant; saliva collection in incorrect container.

Do not eat, drink, smoke, or chew gum 30 minutes prior to saliva sample collection. See Oragene Dx 500 saliva kit for detailed instructions.