BRCAplus-EXPANDED

BRCAplus-Expanded is a next generation sequencing panel that simultaneously analyzes 8 genes associated with increased risk for breast cancer, including BRCA1 and BRCA2.

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BRCAplus-Expanded is a next generation sequencing panel that simultaneously analyzes 8 genes associated with increased risk for breast cancer, including BRCA1 and BRCA2.

BRCAplus-Expanded is a next generation sequencing (NGS) panel of 8 genes associated with breast cancer (ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, PTEN, and TP53). These genes all have associated published clinical management guidelines. Full gene sequencing and gross deletion/duplication analysis is performed for all 8 genes. Specific Site Analysis is available for individual gene mutations identified in a family.

Disease Name 
Breast cancer
Hereditary cancer
Hereditary breast and ovarian cancer (HBOC)
Disease Information 

Breast cancer is the most common cancer in women in developed countries, affecting about 1 in 8 (12.5%) women in their lifetime.1 The National Cancer Institute (NCI) estimates that approximately 231,840 new cases of female breast cancer will be diagnosed in the U.S. in 2015.2 The majority of breast cancers is sporadic, but 5-10% are due to inherited causes. Hereditary breast cancers tend to occur earlier in life than non-inherited sporadic cases, and are more likely to occur in both breasts. The highly penetrant genes, BRCA1 and BRCA2, appear to be responsible for around half of hereditary breast cancer.3-5 However, additional genes have been discovered that are associated with increased breast cancer risk as well.3-7 Mutations in the genes on the BRCAplus-Expanded panel can confer an estimated 20–87% lifetime risk for breast cancer. Some of these genes have also been associated with increased lifetime risks for other cancers, such as pancreatic cancer with PALB2, ovarian cancer with BRCA1 and BRCA2, and sarcoma with TP53.8-11

BRCAplus-Expanded Panel Genes:

ATM is a gene associated with an autosomal recessive condition called ataxia-telangiectasia (AT). AT is characterized by progressive cerebellar ataxia with onset between ages 1 and 4, telangiectases of the conjunctivae, oculomotor apraxia, immune defects, and a predisposition to malignancy, particularly leukemia and lymphoma. Women who carry ATM mutations also have an estimated 2-4 fold increased risk for breast cancer.12 Cancer risk estimates for male ATM mutation carriers are not currently available. Recent studies have also reported ATM germline mutations in individuals with familial pancreatic cancer. In one of these studies, ATM mutations were identified in 4/87 (4.6%) families with more than three affected members.13

BRCA1 and BRCA2 are tumor suppressor genes inherited in an autosomal dominant pattern. Mutations in these two highly penetrant genes increase the chance for cancer of the breast, ovaries (including primary peritoneal and fallopian tube), pancreas and prostate. Studies suggest female BRCA1 mutation carriers have a 57-87% lifetime risk to develop breast cancer and a 39-40% lifetime risk to develop ovarian cancer by age 70.8-10,14-16 Male BRCA1 mutation carriers have a cumulative breast cancer lifetime risk of about 1.2% by age 70.17,18 Similar studies suggest female BRCA2 mutation carriers have a 45-84% lifetime risk to develop breast cancer and an 11-18% risk to develop ovarian cancer by age 70.8-10,19, 20 Male BRCA2 mutation carriers have up a 15% lifetime prostate cancer risk and a cumulative lifetime breast cancer risk of 6.8% by ages 65 and 70 respectively.17,18,20,21 BRCA1/2 mutation carriers may also be at an increased risk for melanoma, pancreatic cancer, and potentially other cancers.22 BRCA2 is also known as FANCD1. Individuals who inherit a BRCA2/FANCD1 mutation from each parent may have a rare autosomal recessive condition called Fanconi-anemia type D1 (FA-D1), which affects multiple body systems.

CHEK2 is a gene that receives signals from damaged DNA, transmitted via ATM. CHEK2 interacts in vivo with BRCA1, BRCA2, and TP53, which have all been implicated in cellular processes responsible for the maintenance of genomic stability. Multiple studies indicate that mutations in CHEK2 confer an increased risk of developing many types of cancer including breast, colon, and other cancers. Mutations are more likely to be found among women with bilateral versus unilateral breast cancers. A female CHEK2 mutation carrier has approximately a two-fold increase in lifetime breast cancer risk, and has a 1% risk per year of developing a second breast primary cancer. Lifetime risks for other associated cancers are unknown. An increased risk for ovarian cancer has also been suggested. 23, 24-36

CDH1 germline mutations are associated with hereditary diffuse gastric cancer (HDGC) and lobular breast cancer in women. In one published study, the estimated cumulative risk of gastric cancer for CDH1 mutation carriers by age 80 years was 67% for men and 83% for women.27 Patients with HDGC typically present with diffuse-type gastric cancer, with signet ring cells diffusely infiltrating the wall of the stomach and, at advanced stages, linitis plastica. An elevated risk of lobular breast cancer in women is also associated with HDGC, with an estimated lifetime breast cancer risk of 39-52%.28

PALB2 germline mutations have been associated with an increased lifetime risk for pancreatic cancer, breast cancer, and Fanconi anemia-type N (FA-N). Familial pancreatic and/or breast cancer due to PALB2 mutations is inherited in an autosomal dominant pattern, while FA-N is a rare autosomal recessive condition affecting multiple body systems. Females with a PALB2 mutation have a 2- to 4-fold increase in risk for breast cancer.30,31 A 2014 article concluded that in the context of a strong family history, mutations in PALB2 may be associated with up to a 58% risk of female breast cancer. Without a family history, the risk for female breast cancer was estimated to be 33% (the difference attributed to genetic and/or environmental modifiers).32 Studies have identified PALB2 mutations in 1-3% of families with pancreatic cancer; however, the exact lifetime pancreatic cancer risk has not yet been established.33,34 Additionally, recent studies have shown an increased risk for ovarian cancer.23,44

PTEN is a gene associated with Cowden syndrome (CS), PTEN hamartoma tumor syndrome (PHTS), Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome and autism spectrum disorder. CS is a multiple hamartoma syndrome with a high risk of developing tumors of the thyroid, breast, and endometrium. Mucocutaneous lesions, thyroid abnormalities, fibrocystic disease, multiple uterine leiomyomata, and macrocephaly can also be seen. Affected individuals have a lifetime risk of up to 50% for breast cancer, 10% for thyroid cancer, and 5-10% for endometrial cancer. Over 90% of individuals with CS will express some clinical manifestations by their twenties.35,36 Recent studies noted increased risks for renal cell cancer, colorectal cancer, and other cancers.37,38 One study quotes up to a 31-fold increase in RCC risk for PTEN mutation carriers as compared to the general population.39

TP53 is a tumor suppressor gene, and germline mutations within it are associated with Li-Fraumeni syndrome (LFS). An individual carrying a TP53 mutation has a 21-49% lifetime risk of developing cancer by age 30 and a lifetime cancer risk of 68-93%.40 The most common tumor types observed in LFS families include soft tissue and osteosarcomas, breast cancer, brain tumors (including astrocytomas, glioblastomas, medulloblastomas and choroid plexus carcinomas), and adrenocortical carcinoma (ACC); other cancers, including colorectal, gastric, ovarian, pancreatic, and renal, have also been reported.11,41 Studies have shown that a small percentage of women with early onset breast cancer who do not carry BRCA1 and BRCA2 mutations are identified to have mutations in TP53.26,42,43

Testing Benefits & Indication 

Indications for Testing:
Families with a combination of the cancers below and some common red flags for hereditary cancer would be appropriate to consider for BRCAplus-Expanded.

  • Early-onset breast cancer (diagnosed ≤45 years of age)
  • Male breast cancer at any age
  • Breast and ovarian cancer in the same woman
  • >3 cases of breast cancer*
  • >3 cases of breast, ovarian, and/or pancreatic cancer*
  • >3 cases of breast, uterine, and/or thyroid cancer*
    *On the same side of the family

Common Red Flags for Hereditary Cancer

  • Cancer diagnosed at a younger age than expected for the general population (≤ 50 years, for most cancers)
  • Cancer diagnosed across generations, and in multiple generations within a family, especially if diagnosed younger than average
  • Individual with multiple primary cancers (either in paired organs or in different organs)
  • A pattern of cancer in the family that is typical of a known cancer predisposition syndrome (for example, breast and diffuse gastric cancer with CDH1 mutations, or breast and thyroid cancer with PTEN mutations)

If increased risk of a hereditary cancer syndrome is suspected, the American Congress (formerly College) of Obstetricians and Gynecologists (ACOG) recommends referral to a specialist in cancer genetics or a healthcare provider with expertise in genetics for complete hereditary cancer risk assessment, which may lead to genetic testing.29 Establishing a molecular diagnosis can help guide preventive measures, direct surgical options and estimate personal and familial cancer risk.

Benefits of Testing:
Identifying patients with an inherited susceptibility for certain cancers can help with medical management. For example, this information can:

  • Modify breast cancer surveillance options and age of initial screening
  • Suggest specific risk-reduction measures (e.g. considering prophylactic oophorectomy, after childbearing is complete, for women with increased risk for breast/ovarian cancer)
  • Offer treatment guidance (e.g. avoidance of radiation-based treatment methods for individuals with a TP53 mutation)
  • Identify other at-risk family members
  • Provide guidance with new gene-specific treatment options and risk reduction measures as they emerge
Test Description 

BRCAplus-Expanded analyzes 8 genes (listed above). All genes are evaluated by next generation sequencing (NGS) or Sanger sequencing of all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions. In addition, sequencing of the promoter region is performed for PTEN (c.-1300 to c.-745). The BRCA2 Portuguese founder mutation, c.156_157insAlu (also known as 384insAlu) is detected by NGS and confirmed by PCR and agarose gel electrophoresis. 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. 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.45 Gross deletion/duplication analysis is performed for the covered exons and untranslated regions of all 8 genes using read-depth from NGS data with confirmatory multiplex ligation-dependent probe amplification (MLPA) and/or targeted chromosomal microarray.

Mutation Detection Rate 

BRCAplus-Expanded can detect >99.9% of described mutations in the included genes listed above, when present (analytic sensitivity).

Specimen Requirements 

Complete specimen requirements are available here or by downloading the PDF found above in the Quick Links section at the top of this page.

Turnaround Time 
TEST CODE TECHNIQUE TURNAROUND TIME (days)
8837 BRCAplus-Expanded 14 - 21

 

Specialty 
Genes 
ATM
BRCA1
BRCA2
CDH1
CHEK2
PALB2
PTEN
TP53
References 
  1. National Cancer Institute. Cancer Stat Fact Sheets. Accessed October 22, 2014. Available from: http://seer.cancer.gov/.
  2. National Cancer Institute. Accessed January 14, 2016. Available from: http://www.cancer.gov/.
  3. Castera L, et al. Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes. Eur J Hum Genet. 2014. 22(11):1305-13.
  4. Walsh T, et al. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci U S A. 2010. 107(28):12629-33.
  5. van der Groep PE, et al. Pathology of hereditary breast cancer. Cell Oncol (Dordr). 2011. 34(2):71-88.
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  8. Antoniou A, et al. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet. 2003. 72(5):1117-30.
  9. Chen S and Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007. 25(11):1329-33.
  10. Ford D, et al. Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet. 1998. 62(3):676-89.
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  13. Roberts NJ, et al. ATM Mutations in patients with hereditary pancreatic cancer. Cancer Discovery. 2011. 2(1):OF1-OF6.
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  15. Ferla R, et al. Founder mutations in BRCA1 and BRCA2 genes. Ann Oncol. 2007. 18 Suppl 6:vi93-8.
  16. Tulinius H, et al. The effect of a single BRCA2 mutation on cancer in Iceland. J Med Genet. 2002. 39(7):457-62.
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  24. Bahassi EM, et al. The checkpoint kinases Chk1 and Chk2 regulate the functional associations between hBRCA2 and Rad51 in response to DNA damage. Oncogene. 2008. 27(28):3977-85.
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  27. Pharoah PD, et al. Incidence of gastric cancer and breast cancer in CDH1 (E-cadherin) mutation carriers from hereditary diffuse gastric cancer families. Gastroenterology. 2001. 121(6):1348-53.
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  39. Mester JL, et al. Papillary renal cell carcinoma is associated with PTEN hamartoma tumor syndrome. Urology. 2012. 79(5):1187 e1-7.
  40. Hwang SJ, et al., Germline p53 mutations in a cohort with childhood sarcoma: sex differences in cancer risk. Am J Hum Genet. 2003. 72(4):975-83.
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  44. Norquist BM, et al. Inherited mutations in women with ovarian carcinoma. JAMA Oncol. 2015 Dec 30:1-9. [Epub ahead of print].
  45. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.