BRCA1 and BRCA2 Sequencing and Deletion/Duplication Testing


At this time, this test may only be ordered by healthcare providers within the Mount Sinai Health System. For any questions, please contact customer support.



Related Gene(s): BRCA1, BRCA2

Hereditary breast and ovarian cancer (HBOC) is an autosomal dominant cancer predisposition syndrome caused by germline mutations in the BRCA1 and BRCA2 genes. Mutations in these two highly-penetrant genes increase the chance for cancer of the breast, ovaries and Fallopian tubes, pancreas, and prostate.

BRCA1 coding exons 1-22, BRCA2 coding exons 1-26, and well into the 5’ and 3’ ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis is used to determine gene copy number for BRCA1 coding exons 1-22 and BRCA2 coding exons 1-26. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using a standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next-generation sequencing. Additional Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing. Gross deletion/duplication analysis of BRCA1 and BRCA2 using the multiplex ligation-dependent probe amplification (MLPA) kit is also performed.

Single gene testing and genetic testing for a known familial mutation can also be ordered. If there is a previously-identified mutation in a family member, please include a copy of the test report with the requisition form.


Specimen Requirements

  • Whole blood: Two 4.5 mL EDTA tubes (lavender top)
  • For transfusion patients, please wait at least 2 weeks after a packed cell/platelet transfusion, and at least 4 weeks after a whole blood transfusion prior to blood draw for testing
  • For chemotherapy patients, the DNA quality may be affected if patient has received chemotherapy within the last 120 days. Sema4 may request an additional specimen if DNA quality is insufficient

  • Saliva: 2 mL of freshly-collected saliva in an Oragene container per kit’s specific instructions
  • Fill up to black line with 2 mL of saliva and close the lid. Once the lid is closed, it automatically adds 2 mL of buffer, for a total volume of 4 mL
  • Please note that 2 containers are required for all pediatric saliva testing kits

Saliva and blood are the most common specimen types we receive. For questions regarding other specimen types and requirements for patients with a significant medical history (including allogenic transplant and hematological diseases), please call us at 203-483-3459 to discuss before sample submission.


Ordering Information

Shipping

  • Ship at room temperature

Turnaround Time

  • 6-10 days from receipt of specimen
  • If required by insurance, benefits investigation and pretest genetic counseling may delay test results


Resources

Hereditary Cancer Requisition
Hereditary Cancer Genetic Testing Consent