Breast Cancer Focus Panel

  • Panel Description
  • Test Description
  • CPT Codes
  • Resources
  • Gene Descriptions

Panel Description

Hereditary Breast Cancer
The Focus Breast Cancer Panel examines 14 genes associated with an increased risk for hereditary breast cancer.

Patients with a personal or family history suggestive of a hereditary breast cancer syndrome. Red flags for hereditary breast cancer could include onset of cancer prior to the age of 50 years, more than one primary cancer in a single person, and multiple affected people within a family. This test is designed to detect individuals with a germline pathogenic variant, and is not validated to detect mosaicism below the level of 20%. It should not be ordered on tumor tissue.

Patients identified with hereditary breast cancer can benefit from increased surveillance and preventative steps to better manage their risk for cancer. Also, your patient’s family members can be tested to help define their risk. If a pathogenic variant is identified in your patient, close relatives (children, siblings, parents) could have as high as a 50% risk to also be at increased risk.

Test Description

  • Sequencing
  • Del/Dup
  • Rush / STAT
  • Exclude VUS
2 - 3 weeks
Call for details
ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MRE11, NBN, PALB2, PTEN, RAD50, STK11, TP53 ( 14 genes )
99% at 50x
Blood (two 4ml EDTA tubes, lavender top) or Extracted DNA (3ug in EB buffer) or Buccal Swab or Saliva (kits available upon request)
Test results and variant interpretation are based on the proper identification of the submitted specimen and use of correct human reference sequences at the queried loci. In very rare instances, errors may result due to mix-up or co-mingling of specimens. Positive results do not imply that there are no other contributions, genetic or otherwise, to the patient's phenotype, and negative results do not rule out a genetic cause for the indication for testing. Result interpretation is based on the collected information and Alamut annotation available at the time of reporting. This assay is not designed or validated for the detection of mosaicism. DNA alterations in regulatory regions or deep intronic regions (greater than 20bp from an exon) will not be detected by this test. There are technical limitations on the ability of DNA sequencing to detect small insertions and deletions. Our laboratory uses a sensitive detection algorithm, however these types of alterations are not detected as reliably as single nucleotide variants. Rarely, due to systematic chemical, computational, or human error, DNA variants may be missed. Although next generation sequencing technologies and our bioinformatics analysis significantly reduce the confounding contribution of pseudogene sequences or other highly-homologous sequences, sometimes these may still interfere with the technical ability of the assay to identify pathogenic variant alleles in both sequencing and deletion/duplication analyses. Deletion/duplication analysis can identify alterations of genomic regions which are a single exon in size. When novel DNA duplications are identified, it is not possible to discern the genomic location or orientation of the duplicated segment, hence the effect of the duplication cannot be predicted. Where deletions are detected, it is not always possible to determine whether the predicted product will remain in-frame or not. Unless otherwise indicated, in regions that have been sequenced by Sanger, deletion/duplication analysis has not been performed.

Patients with Bone Marrow Transplants:
DNA extracted from cultured fibroblasts should be submitted instead of blood/saliva/buccal samples from individuals who have undergone allogeneic bone marrow transplant and from patients with hematologic malignancy.

CPT Code 81162, 81319, 81321

NOTE:  The CPT codes listed on the website are in accordance with Current Procedural Terminology, a publication of the American Medical Association. CPT codes are provided here for the convenience of our clients. Clients who bill for services should make the final decision on which codes to use.
WHY ORDER THIS TEST?

Resources

DescriptionDownload
Hereditary Breast Cancer Information for Patients
Genetic Testing for Hereditary Breast and Ovarian Cancer Webinar

Genetic Testing for Hereditary Cancers Webinar

Gene Descriptions

Gene Reason Reference
ATM Heterozygous pathogenic variants in ATM are associated with an increased risk for breast and pancreatic cancer. Additionally, biallelic pathogenic variants in ATM have been associated with ataxia-telangiectasia. PubMed: 15928302, 22585167, 20301790, 28418444; OMIM: 607585
BARD1 Heterozygous pathogenic variants in the BARD1 gene raise an individual’s risk of developing breast cancer in their lifetime. PubMed:23586058, 28418444; OMIM: 114480
BRCA1 Heterozygous pathogenic variants in the BRCA1 gene are the most common cause of hereditary breast and ovarian cancer syndrome (HBOC). PubMed: 9497246, 12677558, 17416853, 20301425, 22846731
BRCA2 Autosomal dominant mutations in the BRCA2 gene are implicated in the hereditary breast and ovarian cancer syndrome (HBOC). Additionally, biallelic mutations in BRCA2 gene are associated with autosomal recessive Fanconi anemia Types B and D1 . PubMed: 12065746, 12677558, 9497246, 17416853, 18042939, 20301425, 22846731
CDH1 Pathogenic heterozygous variants in the CDH1 gene are associated with an increased risk for gastric and lobular breast cancer. PubMed: 11729114, 20301318; OMIM: 192090
MRE11 Autosomal dominant pathogenic variants in the MRE11 gene, also known as MRE11A, have been associated with a predisposition to breast cancer . Biallelic mutations in the MRE11A gene are associated with MRE11 deficiency, an ataxia telangiectasia-like disorder. PubMed: 26436112, 26328243, 15574463; OMIM: 600814
NBN Heterozygous pathogenic variants in NBN (also known as NBS1) have been associated with a number of malignancies including melanoma, non-Hodkins lymphoma, medulloblastoma, and colorectal, prostate, and breast cancers . Other studies have shown possible associations with aplastic anemia and acute lymphoblastic leukemia. Biallelic pathogenic variants in NBN have been associated with Nijmegen Breakage syndrome (NBS). Individuals with NBS generally have progressive intellectual disability, growth retardation and immunodeficiency, and are at an increased risk for a variety of cancers, including lymphoma, glioma, and medulloblastoma. PubMed: 14973119, 15185344, 16474176, 16770759, 18079974, 19908051, 21514219,15338273,11325820, 20301355; OMIM: 609135, 251260
PTEN Individuals with heterozygous pathogenic PTEN variants are at a significantly increased risk for multiple types of cancers, including breast, thyroid, colorectal, endometrial, renal, and others. Autosomal dominant mutations in PTEN have been associated with a spectrum of disorders sometimes referred to as PTEN hamartoma tumor syndrome. PHTS includes several conditions with overlapping clinical features, including Bannayan-Riley-Ruvalcaba syndrome (BRRS), Cowden syndrome (CWS1), macrocephaly/autism syndrome, and PTEN-related Proteus syndrome (PS). PubMed: 20301661; OMIM: 601728
STK11 Autosomal dominant pathogenic variants in STK11 have been associated with Peutz-Jeghers syndrome (PJS) which is associated with an increased risk for multiple types of cancer, including breast, ovarian, gastric, colorectal, and pancreatic. PubMed: 15121768, 20301443; OMIM: 175200, 260350
TP53 Heterozygous pathogenic variants in the TP53 gene are associated with Li-Fraumeni syndrome, a condition that increases risk for many types of cancer. PubMed: 20301488, 26014290, 2614290; OMIM: 151623, 191170
RAD50 Autosomal dominant pathogenic variants in RAD50 may be associated with a small increased risk for breast cancer, although studies are contradictory. Biallelic pathogenic variants in RAD50 were reported to be associated with Nijmegen breakage syndrome-like disorder (NBSLD) in one individual. PubMed: 19409520, 20301355, 23586058, 26250988, 28418444; OMIM: 613078
CHEK2 Heterozygous pathogenic variants in CHEK2 are associated with approximately a two-fold increased risk for breast cancer, as well as other CHEK2-associated cancers. PubMed: 16998506, 18172190, 21876083, 27595995, 15492928, 11719428, 20597917, 21807500, 21876083, 21956126, 23713947, 23296741, 24240112, 24599715, 24879340, 25431674, 11370630, 15951970, 17164383
PALB2 Autosomal dominant pathogenic variants in PALB2 have been associated with an increased risk of some types of cancer, including breast and pancreatic cancer. Biallelic pathogenic variants in PALB2 have been associated with Fanconi anemia of complementation group N (FANCN) . For women, the risk for breast cancer has been estimated to be two to three times greater than the population risk. PubMed: 17200672, 24870022, 17200668, 21285249, 24141787, 25099575; OMIM: 610355
BRIP1 Heterozygous pathogenic germline variants in the BRIP1 gene are associated with an increased risk for ovarian cancer. A possible association with increased risk for breast cancer has also been suggested, although this has not been proven to date. Biallelic mutations in BRIP1 have been associated with Fanconi anemia of complementation group J (FANCJ). PubMed: 24301948, 28085182, 20301575, 26315354, 28418444 ; OMIM: 609054, 605882