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Genetics of Breast and Ovarian Cancer (PDQ®)
Health Professional Version   Last Modified: 09/15/2008



Purpose of This PDQ Summary






Introduction






Major Genes






Low Penetrance Predisposition to Breast and Ovarian Cancer






Interventions






Psychosocial Issues in Inherited Breast Cancer Syndromes






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Low Penetrance Predisposition to Breast and Ovarian Cancer

Background
Confirmed Candidate Breast Cancer Susceptibility Genes
        CHEK2
        ATM
        BRIP1
        PALB2
        CASP8 and TGFB1
Genome-Wide Searches



Background

Mutations in BRCA1, BRCA2, and the genes involved in other rare syndromes discussed above account for less than 25% of the excess familial risk of breast cancer.[1] Despite intensive genetic linkage studies, there do not appear to be other BRCA1/BRCA2-like high-penetrance genes that account for a significant fraction of the remaining multiple-case familial clusters.[2] These observations suggest that the remaining breast cancer susceptibility is polygenic in nature, meaning that a relatively large number of low-penetrance genes are involved.[3] Each locus would be expected to have a relatively small effect on breast cancer risk and would not produce dramatic familial aggregation or influence patient management. However in combination with other genetic loci and/or environmental factors, particularly given how common these can be, variants of this kind might significantly alter breast cancer risk. These types of genetic variations are sometimes referred to as “polymorphisms”, meaning that the gene or locus occurs in several “forms” within the population (and more formally defined as polymorphic when at least 1% of chromosomes at a position vary from each other). Most loci that are polymorphic have no influence on disease risk or human traits (benign polymorphisms), while those that are associated with a difference in risk of disease or a human trait (however subtle) are sometimes termed “disease-associated polymorphisms” or “functionally relevant polymorphisms.” This polygenic model of susceptibility is consistent with the observed patterns of familial aggregation of breast cancer.[4] Although the clinical significance and causality of associations with breast cancer are often difficult to evaluate and establish, genetic polymorphisms may account for why some women are more sensitive than others to environmental carcinogens.

Polymorphisms underlying polygenic susceptibility to breast cancer are considered low penetrance, a term often applied to sequence variants associated with a minimal to moderate risk. This is in contrast to “high-penetrance” variants or alleles that are typically associated with more severe phenotypes, for example those BRCA1/BRCA2 mutations leading to an autosomal dominant inheritance patterns in a family. The definition of a “moderate” risk of cancer is arbitrary, but it is usually considered to be in the range of a relative risk of 1.5–2.0. Because these types of sequence variants (also called low-penetrance genes, alleles, mutations, and polymorphisms) are relatively common in the population, their contribution to total cancer risk is estimated to be much higher than the attributable risk in the population from mutations in BRCA1 and BRCA2. For example, it is estimated by segregation analysis that half of all breast cancer occurs in 12% of the population that is deemed most susceptible.[3] There are no known low-penetrance variants in BRCA1/BRCA2. The N372H variation in BRCA2, initially thought to be a low-penetrance allele, was not verified in a large combined analysis.[5]

Two strategies have been taken to identify low-penetrance polymorphisms leading to breast cancer susceptibility: candidate gene and genome-wide searches. Both involve the epidemiologic case-control study design. The candidate gene approach involves selecting genes based on their known or presumed biological function, relevance to carcinogenesis or organ physiology, and searching for or testing known genetic variants for an association with cancer risk. This strategy relies on imperfect and incomplete biological knowledge, and has been relatively disappointing despite some confirmed associations, as described below. It has largely been replaced by the genome-wide association studies (GWAS) in which a very large number of single nucleotide polymorphisms (SNPs) (potentially 1,000,000 or more) are chosen within the genome and tested largely without regard to their possible biological function, but instead to capture more uniformly all genetic variation throughout the genome.

Confirmed Candidate Breast Cancer Susceptibility Genes

CHEK2

CHEK2 (OMIM), a gene involved in the DNA damage repair response pathway, was initially evaluated as a potential cause of Li-Fraumeni syndrome (LFS).[6] While it does not appear to be a common cause of LFS,[7] based on numerous studies, a single polymorphism, 1100delC, appears to be a rare, low-penetrance susceptibility allele.[8-13] The deletion was present in 1.2% of the European controls, 4.2% of the European BRCA1/2-negative familial breast cancer cases, and 1.4% of unselected female breast cancer cases.[8] In a group of 1,479 Dutch women younger than 50 years with invasive breast cancer, 3.7% were found to have the CHEK2 1100delC mutation.[14] In both Europe and the United States (where the mutation appears to be slightly less common), additional studies, including a large prospective study,[15] have detected the mutation in 4% to 11% of familial cases of breast cancer and overall have found an approximately 1.5-fold to 3-fold increased risk of female breast cancer[16-19]. A multicenter combined analysis and reanalysis of nearly 20,000 subjects from ten case-control studies, however, has verified a significant 2.3-fold excess of breast cancer among mutation carriers.[20] One study suggests the risk associated with a CHEK2 1100delC mutation was stronger in the families of probands ascertained because of bilateral breast cancer.[21] At least one study has also suggested that the mutation may be associated with both breast and colorectal cancer.[17] Although the initial report suggested that male mutation carriers were at a significantly increased risk of breast cancer,[13] several follow-up studies have failed to confirm the association.[22-25] The contribution of CHEK2 mutations to breast cancer may be dependent on the population studied. A study of 3,228 women diagnosed with breast cancer before age 51 years, and 5,496 population controls demonstrated that three founder alleles in CHEK2 contributed to 8% of early onset breast cancer in Poland.[26] Although a meta-analysis of 1100delC mutation carriers estimated the risk of breast cancer to be 42% by age 70 years in women with a family history of breast cancer,[27] the clinical applicability of this finding remains uncertain due to low mutation prevalence and lack of guidelines for clinical management.[28]

ATM

Ataxia telangiectasia (AT) (OMIM) is an autosomal recessive disorder characterized by neurologic deterioration, telangiectasias, immunodeficiency states, and hypersensitivity to ionizing radiation. It is estimated that 1% of the general population may be heterozygote carriers of ATM mutations(OMIM).[29] More than 300 mutations in the gene have been identified to date, most of which are truncating mutations.[30] (Refer to the ATM online database for more information on AT mutations) ATM proteins have been shown to play a role in cell cycle control.[31-33] In vitro, AT cells are sensitive to ionizing radiation and radiomimetic drugs, and lack cell cycle regulatory properties after exposure to radiation.[34]

Initial studies searching for an excess of ATM mutations among breast cancer patients provided conflicting results, perhaps due to study design and mutation testing strategies.[35-45] However, two large epidemiologic studies have demonstrated a statistically increased risk of breast cancer among female heterozygote carriers, with an estimated relative risk of approximately 2.0.[45,46] Despite this convincing epidemiologic association, the clinical application of testing for ATM mutations is unclear due to the wide mutational spectrum and the logistics of testing. Because the presence of a mutation could pose a risk in screening-related radiation exposure, further work is needed.

BRIP1

BRIP1 (also known as BACH1) encodes a helicase that interacts with the BRCT domain of BRCA1. This gene also has a role in BRCA1-dependent DNA repair and cell cycle checkpoint function. Biallellic mutations in BRIP1 are a cause of Fanconi anemia,[47-49] much like such mutations in BRCA2. Inactivating mutations of BRIP1 are associated with an increased risk of breast cancer. Over 3,000 individuals from BRCA1/BRCA2 mutation negative families were examined for BRIP1 mutations. Mutations were identified in 9 of 1,212 individuals with breast cancer but in only 2 of 2,081 controls (P = 0.003). The relative risk of breast cancer was estimated to be 2.0 (95% confidence interval (CI), 1.2-3.2, P = 0.012). Of note, in families with BRIP1 mutations and multiple cases of breast cancer, there was incomplete segregation of the mutation with breast cancer, consistent with a low penetrance allele and similar to that seen with CHEK2.[50]

PALB2

PALB2 (partner and localizer of BRCA2) interacts with the BRCA2 protein and plays a role in homologous recombination and double stranded DNA repair. Similar to BRIP1 and BRCA2, biallelic mutations in PALB2 have also been shown to cause Fanconi anemia.[51] PALB2 mutations were found in 10 of 923 (1.1%) individuals with BRCA1 and BRCA2 mutation negative familial breast cancer, compared to none of 1084 (0%) controls (P = 0.0004). One of the ten families with a PALB2 mutation included a case of male breast cancer, raising the possibility that male breast cancer is included in the spectrum of PALB2. Similar to BRIP1 and CHEK2, there was incomplete segregation of PALB2 mutations in families with hereditary breast cancer.[52]

CASP8 and TGFB1

The Breast Cancer Association Consortium (BCAC) investigated single nucleotide polymorphisms identified in previous studies as possibly associated with excess breast cancer risk in 15,000 to 20,000 cases and 15,000 to 20,000 controls. Two SNPs, CASP80 D302H and TGFB1 L10P, were associated with invasive breast cancer with relative risks of 0.88 (95% CI, 0.84-0.92) and 1.08 (95% CI, 1.04-1.11) respectively.[53]

Genome-Wide Searches

In contrast to assessing candidate genes and/or alleles, genome wide association studies involve comparing a very large set of genetic variants spread throughout the genome. The current paradigm uses sets of 100,000 to 1,000,000 SNPs that are chosen to capture a large portion of common variation within the genome based on the HapMap project.[54,55] By comparing allele frequencies between a large number of cases and controls, typically 1,000 or more of each, and validating promising signals in replication sets of subjects, very robust statistical signals of association have been obtained.[56-58] The strong correlation between many SNPs that are physically close to each other on the chromosome (linkage disequilibrium) allows one to “scan” the genome for susceptibility alleles even if the biologically relevant variant is not within the tested set of SNPs. While this between-SNP correlation allows one to interrogate the majority of the genome without having to assay every SNP, when a validated association is obtained, it is not usually obvious which of the many correlated variants is the causal one.

Genome-wide searches are showing great promise in identifying common, low-penetrance susceptibility alleles for many complex diseases[59] including breast cancer.[60-62] The first and most comprehensive study involved an initial scan in familial breast cancer cases followed by replication in two large sample sets of sporadic breast cancer, the final being a collection of over 20,000 cases and 20,000 controls from the BCAC, an international group of investigators.[60] Five distinct genomic regions were identified that were within or near the FGFR2, TNRC9, MAP3K1, and LSP1 genes or at the chromosome 8q region. Subsequent genome-wide studies from the Nurses Health Study, from an Icelandic study, and from a large cohort of Ashkenazi Jewish individuals, clearly replicated the FGFR2[62,63] and TNRC9[61] loci and pointed to additional susceptibility loci at chromosomes 2q35[61] and 6q22.33.[63]

Although the statistical evidence for an association between genetic variation at these loci and breast cancer risk is overwhelming, the biologically relevant variants and the mechanism by which they lead to increased risk are unknown and will require further genetic and functional characterization. Additionally, these loci are associated with very modest risk, with the largest odds ratio among heterozygous carriers being 1.23 (95% CI, 1.18–1.28). More risk variants are likely to be identified. Until their individual and collective influences on cancer risk are evaluated prospectively, they are not considered clinically relevant.

References

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  51. Reid S, Schindler D, Hanenberg H, et al.: Biallelic mutations in PALB2 cause Fanconi anemia subtype FA-N and predispose to childhood cancer. Nat Genet 39 (2): 162-4, 2007.  [PUBMED Abstract]

  52. Rahman N, Seal S, Thompson D, et al.: PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nat Genet 39 (2): 165-7, 2007.  [PUBMED Abstract]

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