81162

BRCA1, BRCA2 (BRCA1, BRCA2-associated breast cancer 1 and 2) (eg, hereditary breast and ovarian cancer) gene analysis; full sequence analysis and full duplication/deletion analysis

CPT code 81162 describes a comprehensive molecular genetic pathology procedure designed to evaluate the BRCA1 and BRCA2 genes, which are strongly associated with hereditary breast and ovarian cancer (HBOC) syndrome. This exhaustive genomic analysis includes both full sequence analysis and full duplication/deletion analysis of both genes. The BRCA1 and BRCA2 genes are tumor suppressor genes responsible for repairing DNA double-strand breaks through homologous recombination. Pathogenic variants or mutations in these genes significantly elevate an individual's lifetime risk for developing breast, ovarian, prostate, pancreatic, and other malignancies. The procedure involves extracting high-quality genomic DNA from a patient specimen, typically peripheral blood or a buccal swab/saliva sample. The laboratory then employs advanced methodologies such as Next-Generation Sequencing (NGS) to analyze the entire coding region, as well as critical intronic splice site regions, to identify single nucleotide variants (SNVs) and small insertions or deletions (indels). Concurrently or sequentially, the laboratory utilizes techniques like Multiplex Ligation-dependent Probe Amplification (MLPA) or custom microarray analysis to detect large genomic rearrangements, including exon-level or whole-gene duplications and deletions, which might be missed by sequencing alone. Bioinformatic pipelines process the raw genomic data, comparing the patient's sequences to standard human reference genomes. Identified variants are meticulously classified based on the American College of Medical Genetics and Genomics (ACMG) guidelines into categories such as pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, or benign. The final clinical report provides actionable intelligence that oncologists, geneticists, and genetic counselors use to tailor medical management, which may include enhanced surveillance, prophylactic surgeries (such as bilateral risk-reducing mastectomy or salpingo-oophorectomy), or targeted therapeutics like PARP inhibitors for patients with active malignancies.

Clinical Indications

  • Personal history of early-onset breast cancer (e.g., diagnosed at age 45 or younger).
  • Personal history of triple-negative breast cancer diagnosed at age 60 or younger.
  • Personal history of ovarian, fallopian tube, or primary peritoneal cancer at any age.
  • Personal history of male breast cancer at any age.
  • Personal history of metastatic prostate cancer or pancreatic cancer.
  • Known family history of a BRCA1 or BRCA2 pathogenic variant.
  • Multiple primary breast cancers or bilateral breast cancer.
  • Ashkenazi Jewish ancestry with a personal or family history of BRCA-associated malignancies.

Procedure Steps

  1. Specimen collection (venipuncture for whole blood or collection of saliva/buccal swab) and proper labeling.
  2. Transportation of the specimen to a CLIA-certified molecular genetics laboratory.
  3. Extraction and purification of genomic DNA from the collected specimen.
  4. Quantification and quality assessment of the isolated DNA.
  5. Targeted enrichment of BRCA1 and BRCA2 coding exons and adjacent intronic splice sites.
  6. Full sequence analysis using Next-Generation Sequencing (NGS) or Sanger sequencing.
  7. Full duplication and deletion analysis via Multiplex Ligation-dependent Probe Amplification (MLPA) or array comparative genomic hybridization (aCGH).
  8. Bioinformatics processing to align reads, call variants, and detect large rearrangements against a reference genome.
  9. Variant curation and classification according to ACMG/AMP standards.
  10. Generation and sign-out of a comprehensive clinical laboratory report by a board-certified molecular pathologist or clinical geneticist.

Coding Guidelines

  • Code 81162 represents a combined service encompassing both full sequence and full duplication/deletion analysis of BRCA1 and BRCA2; do not report together with 81163, 81164, 81165, 81166, or 81167.
  • Prior authorization is nearly universally required by commercial and government payers; ensure medical necessity documentation includes detailed family history and prior genetic counseling.
  • Do not use 81162 if testing is limited to known familial variants; use targeted mutation analysis codes (e.g., 81215 or 81217) instead.
  • Do not report 81162 for Ashkenazi Jewish founder mutation screening alone; use CPT code 81212.
  • If only full sequence analysis is performed without duplication/deletion analysis, report 81163.
  • Ensure appropriate ICD-10 diagnostic codes reflecting personal or family history of cancer, or genetic susceptibility, are linked to establish medical necessity.

Associated ICD-10 Codes