Hereditary Breast and Ovarian Cancer - Expanded and Lynch Syndrome Panel

Hereditary breast and ovarian cancer (HBOC) cases tend to arise prior to age 50, and tumors often occur bilaterally. Multiple family members are often affected (including males with breast cancer). HBOC occurs with a high predisposition in specific ethnic groups. Individuals with Ashkenazi Jewish ancestry, for example, have an increased risk for HBOC. There are three specific founder genetic variants known to be common in this population: BRCA1 c.68_69delAG, BRCA1 c.5266dupC, and BRCA2 c.5946delT (Petrucelli et al. 2013. PubMed ID: 20301425). Approximately 1 in 40 individuals with Ashkenazi Jewish ancestry has at least one of these variants. One in ten women of Ashkenazi Jewish ancestry who have breast cancer will have one of these variants; for women with Ashkenazi Jewish ancestry and ovarian cancer, 1 in 3 will have one of the three variants (cancer.net).

Lynch syndrome, the most prevalent colorectal cancer syndrome, is caused by pathogenic variants in mismatch repair (MMR) genes, mainly the MSH2 gene. MMR proteins are involved in numerous cellular functions including repairing DNA synthesis errors, repairing double stranded breaks, and apoptosis. Lynch syndrome generally has an early onset and is characterized by predominantly right-sided colon cancer (Jang et al. 2010. PubMed ID: 20559516). Lynch syndrome is estimated to account for approximately 3-5% of colorectal cancer (Jang et al. 2010. PubMed ID: 20559516; Bonadona et al. 2015. PubMed ID: 21642682). Based on the Amsterdam criteria, families with Lynch syndrome have at least three relatives with colorectal cancer, one being a first degree relative, at least two successive generations involved, and at least one relative with onset of cancer before age 50 (Kohlman and Gruber. 2018. PubMed ID: 20301390; cancer.org).

Hereditary breast and ovarian cancer (HBOC) syndrome is a disorder that follows an autosomal dominant pattern of inheritance. It is associated with tumors mainly in the breast and ovaries and is primarily a result of alterations in the high-penetrance genes BRCA1, BRCA2, and TP53 (Seal et al. 2006. PubMed ID: 17033622).

The BRCA1 tumor suppressor gene is associated with hereditary breast and ovarian cancer. Its protein product is essential for processes such as DNA repair, cell cycle checkpoint control, and maintenance of genomic stability (Wang et al. 2009. PubMed ID: 19261749). Women carrying a pathogenic variant in BRCA1 have a 46-65% risk of developing breast cancer, and an approximately 39% risk of developing ovarian cancer by age 70 (Berlinear et al. 2013. PubMed ID: 23188549). Men who have pathogenic variants in the BRCA1 gene have a lifetime risk of 7-8% of developing breast cancer compared to the average man whose risk is approximately 0.1% (Berlinear et al. 2013. PubMed ID: 23188549).

BRCA2 is a tumor suppressor gene, and along with RAD51 has a major role in DNA damage repair and genome stability (Tan et al. 2008. PubMed ID: 18682420). Women with a pathogenic variant in the BRCA2 gene are at a 43-45% risk of developing breast cancer by age 70, and an 11% risk of developing ovarian cancer (Berlinear et al. 2013. PubMed ID: 23188549).

Hereditary breast and/or ovarian cancers can sometimes be associated with other hereditary cancer syndromes including Li-Fraumeni, Cowden, Peutz-Jeghers, hereditary diffuse gastric cancer, and Lynch syndrome (Berlinear et al. 2013. PubMed ID: 23188549). Variants in TP53 have been implicated as the cause of Li-Fraumeni syndrome. Breast cancer appears as a feature of this syndrome, and carriers of TP53 pathogenic variants are at high risk of developing early-onset breast cancer (Antoniou et al. 2006. PubMed ID: 16998504).

Individuals with Cowden syndrome caused by pathogenic variants in PTEN have a lifetime risk of 50% for breast cancer and 5-10% for endometrial cancer (Hearle et al. 2006. PubMed ID: 16707622).

Peutz-Jeghers syndrome, caused by pathogenic variants in STK11, can reach a breast cancer incidence of 32% by 60 years of age (Lim et al. 2004. PubMed ID: 15188174).

Other genes that are thought to confer low to moderate risk of breast and ovarian cancer have been identified:

Pathogenic variants in CDH1 have been shown to be associated with the development of invasive lobular carcinoma. It is also thought to be a gene that causes an intermediate risk of hereditary breast cancer (Masciari et al. 2007. PubMed ID: 17660459).

CHEK2 truncating variants have been shown to confer moderate risk of breast cancer development (Meijers-Heijboer et al. 2002. PubMed ID: 11967536; Tan et al. 2008. PubMed ID: 18682420).

Variants in ATM that cause ataxia telangiectasia in biallelic carriers confer a two-fold increased risk of breast cancer in monoallelic carriers (Tan et al. 2008. PubMed ID: 18682420).

Inactivating, truncating BRIP1 variants cause Fanconi anemia in biallelic carriers and confer susceptibility to breast cancer in monoallelic carriers (Seal et al. 2006. PubMed ID: 17033622). Ovarian tumors from carriers of BRIP1 pathogenic variants show loss of the wild type allele, suggesting its tumor suppressor capabilities. Frameshift variants in BRIP1 also lead to an increased risk of invasive ovarian cancer (Rafnar et al. 2011. PubMed ID: 21964575).

PALB2 is also considered a gene with moderate risk alleles and can cause a 2 to 4 fold increased risk of breast cancer (Caminsky et al. 2016. PubMed ID: 26898890).

RAD51C, essential for homologous recombination repair, has been reported to be a hereditary breast and ovarian cancer susceptibility gene; several pathogenic variants have been identified in BRCA1/2-negative HBOC families (Clague et al. 2011. PubMed ID: 21980511). RAD51C variants are found in 1-5% of individuals with a family history of breast and ovarian cancer (Meindl et al. 2011. PubMed ID: 21637635).

The relative risk of ovarian and breast cancer for RAD51D pathogenic variant carriers was estimated to be 6.3 and 1.3, respectively (Loveday et al. 2011. PubMed ID: 21822267).

Large, multi-exon deletions and insertions in BARD1 may substantially contribute to familial breast and ovarian cancer risk (Klonowska et al. 2015. PubMed ID: 25994375).

NBN pathogenic variants are associated with a 2-fold increased risk of breast cancer (Walsh et al. 2007. PubMed ID: 17292821).

Pathogenic variants in the MUTYH gene have been associated with hereditary breast cancer. In a study of 278 early-onset breast cancer patients, 2.2% of the patients had heterozygous variants in MUTYH, and 1 patient with a personal history of early-onset colon cancer and two primary breast cancers was compound heterozygous for a known pathogenic variant and a likely pathogenic variant in MUTYH (Maxwel et al. 2014. PubMed ID: 25503501).

Other genes thought to confer an increased risk of HBOC and Lynch syndrome include CHEK1 (Dutil et al. 2019. PubMed ID: 31780696), DICER1 (Jalkh et al. 2017. PubMed ID: 28202063), FANCA (Litim et al. 2013. PubMed ID: 23021409; Jalkh et al. 2017. PubMed ID: 28202063), FANCC (Liu et al. 2017. PubMed ID: 28135048; Hirasawa et al. 2017. PubMed ID: 29348823), FANCM (Figlioli et al. 2020. PubMed ID: 31991861), MRE11 (Heikkinen et al. 2003. PubMed ID: 14684699), RAD1(Lopes et al. 2019. PubMed ID: 31078449), RAD50 (van der Merwe et al. 2017. PubMed ID: 28241424; Sung et al. 2017. PubMed ID: 28961279), RECQL5 (Tavera-Tapia et al. 2019. PubMed ID: 30817846), SMARCA4 (Witkowski et al. 2014. PubMed ID: 24658002; Hayano et al. 2016. PubMed ID: 27701467), TP53I3 (Lopes et al. 2019. PubMed ID: 31078449), and XRCC2 (Park et al. 2012. PubMed ID: 22464251).

Lynch syndrome is an autosomal dominant disease mainly caused by variants in MMR genes: MLH1, MSH2, MSH6, and PMS2. Approximately 90% of causative variants are in MLH1, and MLH2, and approximately 10% occur in MSH6 and PMS2. Germline deletions in EPCAM, which is not a mismatch repair gene, inactivates MSH2 in about 1% of individuals with Lynch syndrome (Jang et al. 2010. PubMed ID: 20559516; Bonadona et al. 2015. PubMed ID: 21642682; Kohlman and Gruber. 2018. PubMed ID: 20301390). Germline pathogenic variants in the Lynch syndrome genes have also been shown to be associated with ovarian cancer (Watson et al. 2008. PubMed ID: 18398828).

Less than 1% of the general population has a pathogenic variant in the BRCA1 or BRCA2 genes according to current estimates, and 10-15% of women diagnosed with breast cancer have a pathogenic variant in one of these genes (Tan et al. 2008. PubMed ID: 18682420; Turnbull et al. 2008. PubMed ID: 18544032). In the German population, CHEK2 pathogenic variants are found in around 4% of all cases of hereditary breast cancer. The prevalence of PALB2 pathogenic variants in the populations of both Germany and England is approximately 1% (Meindl et al. 2011. PubMed ID: 21637635). Approximately 6% of patients with hereditary ovarian cancers who do not have pathogenic variants in BRCA1 or BRCA2 have pathogenic variants in genes such BRIP1, CHEK2, NBN, PALB2, RAD51C, RAD51D, and TP53 (Walsh et al. 2007. PubMed ID: 17292821; Loveday et al. 2011. PubMed ID: 21822267). Highly penetrant variants in other genes such as STK11, CDH1, and PTEN account for approximately 1% of all breast cancer cases that aggregate in families. Approximately 1.5% of XRCC2 and ~0.4% MRE11 and FANCC pathogenic variants occur in breast cancer cases (Park et al. 2012. PubMed ID: 22464251; Hirasawa et al. 2017. PubMed ID: 29348823). Another 5% of familial breast cancer cases may be explained by variants in genes such as ATM, CHEK2, NBN, RAD50, RAD51B and RAD51D (Klonowska et al. 2015. PubMed ID: 25994375).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.8% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. 

CNVs detected in STK11, NF1, PMS2 are confirmed via Multiplex Ligation-dependent Probe Amplification (MLPA).

DNA analysis of the PMS2 gene is complicated due to the presence of several pseudogenes. One particular pseudogene, PMS2CL, has high sequence similarity to PMS2 exons 11 to 15 (Blount et al. 2018. PubMed ID: 29286535). Next-generation sequencing (NGS) based copy number variant (CNV) analysis can detect deletions and duplications involving exons 1 to 10 of PMS2 but has less sensitivity for exons 11 through 15. Multiplex ligation-dependent probe amplification (MLPA) can detect deletions and duplications involving PMS2 exons 1 to 15. Of note, PMS2 MLPA is not typically included in this test but can be ordered separately using test code 6062, if desired.