Familial Breast Cancer Susceptibility Research Articles

Germline pathogenic variants associated with triple-negative breast cancer in US Hispanic and Guatemalan women using hospital and community-based recruitment strategies

PurposeRecruit and sequence breast cancer subjects in Guatemalan and US Hispanic populations. Identify optimum strategies to recruit Latin American and Hispanic women into genetic studies of breast cancer.MethodsWe used targeted gene sequencing to identify pathogenic variants in 19 familial breast cancer susceptibility genes in DNA from unselected Hispanic breast cancer cases in the US and Guatemala.Recruitment across the US was achieved through community-based strategies. In addition, we obtained patients receiving cancer treatment at major hospitals in Texas and Guatemala.ResultsWe recruited 287 Hispanic US women, 38 (13%) from community-based and 249 (87%) from hospital-based strategies. In addition, we ascertained 801 Guatemalan women using hospital-based recruitment. In our experience, a hospital-based approach was more efficient than community-based recruitment. In this study, we sequenced 103 US and 137 Guatemalan women and found 11 and 10 pathogenic variants, respectively. The most frequently mutated genes were BRCA1, BRCA2, CHEK2, and ATM. In addition, an analysis of 287 US Hispanic patients with pathology reports showed a significantly higher percentage of triple-negative disease in patients with pathogenic variants (41% vs. 15%). Finally, an analysis of mammography usage in 801 Guatemalan patients found reduced screening in women with a lower socioeconomic status (p < 0.001).ConclusionGuatemalan and US Hispanic women have rates of hereditary breast cancer pathogenic variants similar to other populations and are more likely to have early age at diagnosis, a family history, and a more aggressive disease. Patient recruitment was higher using hospital-based versus community enrollment. This data supports genetic testing in breast cancer patients to reduce breast cancer mortality in Hispanic women.

Gene- and pathway-level analyses of iCOGS variants highlight novel signaling pathways underlying familial breast cancer susceptibility.

Single‐nucleotide polymorphisms (SNPs) in over 180 loci have been associated with breast cancer (BC) through genome‐wide association studies involving mostly unselected population‐based case‐control series. Some of them modify BC risk of women carrying a BRCA1 or BRCA2 (BRCA1/2) mutation and may also explain BC risk variability in BC‐prone families with no BRCA1/2 mutation. Here, we assessed the contribution of SNPs of the iCOGS array in GENESIS consisting of BC cases with no BRCA1/2 mutation and a sister with BC, and population controls. Genotyping data were available for 1281 index cases, 731 sisters with BC, 457 unaffected sisters and 1272 controls. In addition to the standard SNP‐level analysis using index cases and controls, we performed pedigree‐based association tests to capture transmission information in the sibships. We also performed gene‐ and pathway‐level analyses to maximize the power to detect associations with lower‐frequency SNPs or those with modest effect sizes. While SNP‐level analyses identified 18 loci, gene‐level analyses identified 112 genes. Furthermore, 31 Kyoto Encyclopedia of Genes and Genomes and 7 Atlas of Cancer Signaling Network pathways were highlighted (false discovery rate of 5%). Using results from the “index case‐control” analysis, we built pathway‐derived polygenic risk scores (PRS) and assessed their performance in the population‐based CECILE study and in a data set composed of GENESIS‐affected sisters and CECILE controls. Although these PRS had poor predictive value in the general population, they performed better than a PRS built using our SNP‐level findings, and we found that the joint effect of family history and PRS needs to be considered in risk prediction models.

Absence of the CHEK2 c.1100delC mutation in familial breast and ovarian cancer in Colombia: a case-control study

Background: BRCA1 and BRCA2 have been identified as high-penetrance breast cancer predisposition genes, but they only account for a small fraction of the inherited component of breast cancer. To explain the remaining cases, a polygenic model with a large number of low- to moderate-penetrance genes have been proposed; one of these, is the CHEK2 gene (Checkpoint Kinase 2). The objective of this study was to determine the role of the CHEK2 gene, specifically the c.1100delC mutation in familial breast cancer susceptibility in Colombian patients. Methods: We screened 131 high-risk breast and/or ovarian cancer patients (negative for mutations in BRCA1 and BRCA2) and 131 controls for the germline mutation CHEK2 c.1100delC by allele-specific PCR. Results: None of the cases or controls showed the CHEK2 c.1100delC mutation, neither as a homozygote nor as a heterozygote. Conclusions: Our results suggest that the CHEK2 c.1100delC mutation is not a risk factor for genetic susceptibility to familial breast or ovarian cancer in the Colombian population. The absence of the CHEK2 c.1100delC mutation in our population show the importance of considering ethnic background before offering a genetic test.

Alterations of BRCA1 and PALB2 Define a Novel Class of Complex-Karyotype AML with a Very Bad Prognosis

BRCA1 is one of the most important gene associated with familial breast and ovarian cancer susceptibility and is involved in the DNA damage repair and cell cycle arrest. Alterations in BRCA1 and their consequences are well characterized in breast and ovarian tumors, while little is known about its role in Acute Myeloid Leukemia (AML).We aimed to investigate the frequency and the interplay of BRCA1 alterations and patterns of somatic mutations (SNVs) and copy number variations (CNVs) of in AML patients.We genotyped 118 AML samples at either diagnosis or relapse by Single Nucleotide Polymorphism (SNP) array (SNP6.0 and Cytoscan HD, Affymetrix) to detect CNVs. In addition, we performed Whole-Exome Sequencing (WES, 100 bp paired-end, Illumina) of 56 genotyped AML patients to detect SNVs and small indels (MuTect and Varscan 2.0). Differences in survival were assessed using Kaplan-Meier survival analysis and Long-Rank test, or Breslow when indicated.We detected BRCA1 loss in 14 out of 118 patients (12%), ranging from 1,6 Kb to the loss of the entire chromosome 17, with none of the BRCA1 loss patients having a normal karyotype. Moreover, BRCA1 losses significantly co-occurred with PALB2 and RAD50 losses. Notably, the PALB2 loss (chromosome 16) mostly involved exon 12 and was detected also in patients without the BRCA1 loss, with a frequency of 11 out of 118 cases (9%), suggesting a pivotal and previously undescribed role in AML pathogenesis. BRCA1 loss patients were enriched for copy number alterations in genes involved in the regulation of mitotic recombination, DNA repair and positive regulation of kinase activity compared with BRCA1 wild-type cases (p <0.01). To investigate which genes and biological functions cooperates with the pathways affected by structural alterations, we integrated the analysis with WES data on 56 out of 118 AML patients. We focused on the genes involved in the DNA damage repair (DDR) and we identified somatic SNVs in BRCA1, TP53 and in the Fanconi Anemia genes BRCA2 and FANCE. Analysis of co-occurrence and mutual exclusivity revealed that BRCA1 loss and DDR-related alterations (BRCA1, PALB2, BRCA2, and FANCE) were significantly associated with TP53 alterations (p=0.0001 and p=0.0003, respectively). In addition, alterations in the DDR genes were mutually exclusive with mutations in KRAS, IDH1/2, BCOR, BCORL1, NPM1 and myeloid transcription factors as RUNX1 and CEBPA. Notably, patients without alteration in the DDR genes were enriched for mutations in DNMT3A and FLT3.Finally, BRCA1 and PALB2 alterations defined group of patients with poor overall survival (OS). In particular, patients with alterations of either BRCA1 or PALB2 had a worst prognosis compared to patients without alterations in the two genes (p=0.009 and p=0.001, respectively). Patients harboring PALB2 loss had a poorer prognosis compared with patients with complex karyotype (p=0.021, Breslow test). In addition, double BRCA1 and PALB2 loss, single BRAC1 or PALB2 hits and lack of alterations in BRCA1 and PALB2 defined three different classes of risks in our AML cohort (p<0.001).In summary, we define for the first time a novel subgroup of AML patients characterized by alterations targeting the DDR pathway, and in particular the BRCA1 and PALB2 genes. Our data suggest that a signature of genes involved in the DDR and cell cycle regulation synergize and led to the uncontrolled proliferation, independently of DNA damage accumulation. Our results may help improve patient stratification and define ad hoc therapeutic strategies for this aggressive leukemia type.Acknowledgments: ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), Fondazione del Monte di Bologna e Ravenna, FP7 NGS-PTL project. [Display omitted] DisclosuresGuadagnuolo:CellPly S.r.l.: Employment. Martinelli:Novartis: Speakers Bureau; Genentech: Consultancy; Roche: Consultancy, Speakers Bureau; BMS: Speakers Bureau; Celgene: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau; MSD: Consultancy; Pfizer: Consultancy, Speakers Bureau; Ariad: Consultancy, Speakers Bureau.

Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility.

The signaling events that drive familial breast cancer (FBC) risk remain poorly understood. While the majority of genomic studies have focused on genetic risk variants, known risk variants account for at most 30% of FBC cases. Considering that multiple genes may influence FBC risk, we hypothesized that a pathway‐based strategy examining different data types from multiple tissues could elucidate the biological basis for FBC. In this study, we performed integrated analyses of gene expression and exome‐sequencing data from peripheral blood mononuclear cells and showed that cell adhesion pathways are significantly and consistently dysregulated in women who develop FBC. The dysregulation of cell adhesion pathways in high‐risk women was also identified by pathway‐based profiling applied to normal breast tissue data from two independent cohorts. The results of our genomic analyses were validated in normal primary mammary epithelial cells from high‐risk and control women, using cell‐based functional assays, drug‐response assays, fluorescence microscopy, and Western blotting assays. Both genomic and cell‐based experiments indicate that cell–cell and cell–extracellular matrix adhesion processes seem to be disrupted in non‐malignant cells of women at high risk for FBC and suggest a potential role for these processes in FBC development.

The Dawn of Genomic Medicine: The Role of the 100,000 Genomes Project in Breast Care Management

Department of Clinical Genetics, Leicester Royal Infirmary, Leicester, LE1 5WW, UK *Author for correspondence: Tel.: +44 0 116 258 7597; julian.barwell@uhl-tr.nhs.uk On 25 September 2015, University Hospitals of Leicester National Health Service (NHS) Trust recruited its first family to the 100,000 Genomes Project. This project focuses on patients living in England with rare diseases and their families, and patients with cancer. Sequencing 100,000 genomes will enable scientists and doctors to understand more about specific conditions and how we treat them and will greatly enhance the genomic diagnostic capability in the NHS. Genomics England, a company owned by the Department of Health, is coordinating this work, while 11 NHS Genomic Medicine Centers (GMCs) have been established so far across England. The role of the NHS GMCs is to identify, recruit and consent patients, collect and process samples and capture and submit data through to the validation of the results, to enable clinicians to feed back information to patients and manage the treatment of individuals. University Hospitals of Leicester NHS Trust itself is part of the east of England NHS GMC. The primary aims of the project are: to bring benefit to NHS patients; to create an ethical and transparent program based on consent; to enable new scientific discovery and medical insights and to aid development of a UK genomics industry. This project has the potential to transform the future of healthcare, find conclusive diagnoses for rare diseases and revolutionize treatments. This review discusses familial breast cancer susceptibility, the aims, logistics and vision of the 100,000 Genomes Project and how the patients were recruited to the project [1].

Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

BackgroundWomen with a family history of breast cancer face considerable uncertainty about whether to pursue standard screening, intensive screening, or prophylactic surgery. Accurate and individualized risk-estimation approaches may help these women make more informed decisions. Although highly penetrant genetic variants have been associated with familial breast cancer (FBC) risk, many individuals do not carry these variants, and many carriers never develop breast cancer. Common risk variants have a relatively modest effect on risk and show limited potential for predicting FBC development. As an alternative, we hypothesized that additional genomic data types, such as gene-expression levels, which can reflect genetic and epigenetic variation, could contribute to classifying a person’s risk status. Specifically, we aimed to identify common patterns in gene-expression levels across individuals who develop FBC.MethodsWe profiled peripheral blood mononuclear cells from women with a family history of breast cancer (with or without a germline BRCA1/2 variant) and from controls. We used the support vector machines algorithm to differentiate between patients who developed FBC and those who did not. Our study used two independent datasets, a training set of 124 women from Utah (USA) and an external validation (test) set from Ontario (Canada) of 73 women (197 total). We controlled for expression variation associated with clinical, demographic, and treatment variables as well as lymphocyte markers.ResultsOur multigene biomarker provided accurate, individual-level estimates of FBC occurrence for the Utah cohort (AUC = 0.76 [0.67-84]) . Even at their lower confidence bounds, these accuracy estimates meet or exceed estimates from alternative approaches. Our Ontario cohort resulted in similarly high levels of accuracy (AUC = 0.73 [0.59-0.86]), thus providing external validation of our findings. Individuals deemed to have “high” risk by our model would have an estimated 2.4 times greater odds of developing familial breast cancer than individuals deemed to have “low” risk.ConclusionsTogether, these findings suggest that gene-expression levels in peripheral blood cells reflect genomic variation associated with breast cancer risk and that such data have potential to be used as a non-invasive biomarker for familial breast cancer risk.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0145-6) contains supplementary material, which is available to authorized users.

Genomic Testing and Genomic Care: Are They Talking to Each Other?

The principle of basing medical decisions on the concept of risk is not new. Table 1 shows comparative information on medical management guidance in a number of relatively common scenarios such as the use of statins in hypercholesterolaemia, treatment of hypertension, prevention of sudden death in hypertrophic cardiomyopathy, prevention of berry aneurysm rupture in autosomal dominant polycystic kidney disease, screening for Down Syndrome in pregnancy and the management of familial breast cancer susceptibility (Table 1).

Large BRCA1 and BRCA2 genomic rearrangements in Polish high-risk breast and ovarian cancer families

BRCA1 and BRCA2 are two major genes associated with familial breast and ovarian cancer susceptibility. In Poland standard BRCA gene test is usually limited to Polish founder BRCA1 mutations: 5382insC, C61G and 4153delA. To date, just a few single large genomic rearrangements (LGRs) of BRCA1 gene have been reported in Poland. Here we report the first comprehensive analysis of large mutations in BRCA1 and BRCA2 genes in this country. We screened LGRs in BRCA1 and BRCA2 genes by multiplex ligation-dependent probe amplification in 200 unrelated patients with strong family history of breast/ovarian cancers and negative for BRCA1 Polish founder mutations. We identified three different LGRs in BRCA1 gene: exons 13-19 deletion, exon 17 deletion and exon 22 deletion. No LGR was detected in BRCA2 genes. Overall, large rearrangements accounted for 3.7% of all BRCA1 mutation positive families in our population and 1.5% in high-risk families negative for Polish founder mutation.

Analysis of centrosome localization of BRCA1 and its activity in suppressing centrosomal aster formation

BRCA1, a product of a familial breast and ovarian cancer susceptibility gene, localizes to centrosomes and physically interacts with γ-tubulin, a key centrosomal protein for microtubule nucleation and anchoring at centrosomes. Here, we performed a rigorous analysis of centrosome localization of BRCA1, and found that BRCA1 is specifically associated with mother centrioles in unduplicated centrosomes, and daughter centrioles acquire BRCA1 prior to initiation of duplication, and thus duplicated centrosomes are both bound by BRCA1. We further found that BRCA1 suppresses centrosomal aster formation. In addition, we identified a new domain of BRCA1 critical for γ-tubulin binding, which confers not only its localization to centrosomes, but also its activity to suppress centrosomal aster formation.

BRCA1 and BRCA2 Molecular Testing in Women with Different Risk of Hereditary Breast Cancer: ost/Effectiveness and Psychological Implications

Since the discovery of the familial breast cancer susceptibility genes BRCA1 and BRCA2, genetic counseling and molecular analysis in the identification of mutations responsible for the increased risk of breast and ovarian cancer have become crucial steps in the clinical practice. In fact, the identification of pathogenic BRCA1/2 mutations provides useful information about the risk of a second cancer in the proband, the possible presence of the same mutation in healthy relatives of the patient and the different preventative and therapeutic approaches. However, due to the high costs and some technical limitations, the cost effectiveness ratio of BRCA1/2 gene testing should be carefully evaluated in the different cases, considering the psychological implications related to this kind of analysis. In this review, the different criteria for the selection of patients, the role of genetic counseling and the different approaches for the molecular analysis will be discussed, in order to provide a picture of the different strategies aimed to increase the sensitivity and specificity of BRCA1/2 genetic testing.

Epigenetic control of an oncogenic microRNA, miR-155, by BRCA1

Since its identification in 1994, BRCA1 (Breast Cancer 1) has been established as a familial early onset breast and ovarian cancer susceptibility gene [1]. The protein encoded by this gene is involved in diverse cellular processes such as DNA damage repair, cell cycle control, ubiquitination and transcriptional regulation of target genes [2]. Recently, we uncovered a new function of BRCA1, adding another mechanism of tumor suppression by this multifunctional protein [3]. Using a mouse embryonic stem (mES) cell based assay [4], we examined the functional consequences of a BRCA1 variant, R1699Q, found in some cancer patients. One of the functional readouts of this assay is the ability of BRCA1 variants to rescue the lethality of Brca1 null mES cells. We found R1699Q to result in a 10-fold reduction in survival these ES cells compared to WT human BRCA1. Interestingly, we found R1699Q to have no effect on DNA damage repair or cell cycle regulation, which are regarded as major functions of BRCA1. Instead, microRNA expression analysis in embryoid bodies generated from WT and R1699Q expressing ES cells, showed that some microRNAs were differentially regulated in R1699Q mutant cells. Discovered in 1993, microRNAs are short cellular RNAs (22nt in average) present in eukaryotic cells and are regarded as important regulators of diverse cellular functions [5]. Generally, microRNAs interact with 3'UTR of target mRNAs by complementary sequence matching and consequently, repress the translation or induce the degradation of target mRNA. Among the candidate microRNAs identified, we focused on miR-155 because it showed the highest and most consistent increase in the R1699Q mutant cells. miR-155 is a well-known oncogenic microRNA that is encoded by a non-coding RNA BIC (B-cell Insertion Cluster). A viral insertion on this gene was shown to induce lymphoma. In addition, B-cell specific expression of miR-155 in mouse caused B-cell lymphoma [6]. Based on these findings, we hypothesized that the possible repression of an oncogenic microRNA by BRCA1 may be a novel mode of tumor suppression. Indeed, a series of experiments supported this idea and we found that BRCA1 recruits HDAC2 complex to the miR-155 promoter. Consequently, the promoter is epigenetically silenced through the deacetylation of H2A and H3 histones. More importantly, our study also showed the up-regulation of miR-155 in BRCA1 deficient or BRCA1 mutant human tumors. Finally, based on our observation that the knockdown of miR-155 in a Brca1 mutant tumor cell line attenuates in vivo tumor growth, we proposed a therapeutic potential of anti-miR-155 agent for BRCA1-associated breast cancer. Even though we have described the mechanism of BRCA1-mediated silencing of miR-155 promoter in detail, there are several issues that need to be resolved to fully understand the complex mechanism of the BRCA1 mediated microRNA regulation and its effect on the breast cancer. First, what is the role of miR-155 in BRCA1-meidated tumorigenesis? Because a single microRNA is predicted to regulate up to 200 mRNAs [7], it is important to identify the targets of miR-155 in breast epithelial cells that contribute to tumorigenesis. Second, what other microRNAs are epigenetically regulated by BRCA1? Identification of these other microRNAs and their targets will be a key step towards understanding the BRCA1 regulated microRNA network and its role in tumorigenesis. Interestingly, we found that the knockdown of BRCA1 results in a 2 to 3-fold increase in miR-155 levels. In contrast, we observed 50 to 150-fold increase in miR-155 in human breast cancer cell lines or tumor samples suggesting that this increase may not be caused only by BRCA1 loss. We hypothesize that other transcription factors may activate the miR-155 promoter after it is epigenetically activated due to the loss of BRCA1. Identification of such regulatory factors will help us to fully understand the regulations of this oncogenic microRNA during the tumorigenesis. One of the possible regulatory factors is TGFβ, which has been shown to induce miR-155 expression via SMAD4 [8]. Finally, as a cautionary note, it is worth mentioning that anti-miR-155 agents need to be carefully tested in vivo for their therapeutic effects. Functional studies using miR-155 knockout mice have shown that miR-155 is essential for normal immune function [9]. Considering the systemic inhibition of miR-155 will abrogate the immune function that can be advantageous for the tumor growth, anti-miR-155 agents may have to be delivered directly to the tumor cells. In summary, while our finding that BRCA1 epigenetically silences an oncogenic microRNA is quite significant, many questions remain to be answered. We hope that our efforts to answer these questions will lead to a better understanding of the tumor suppressor function of BRCA1 and allow us to develop novel therapeutic strategies for the breast cancer.

RASSF1A polymorphism in familial breast cancer

Inactivation or loss of the tumour suppressor Ras associated domain family 1 isoform A (RASSF1A) allele has been described in breast cancer. Recently, a missense polymorphism predicting p.A331S in RASSF1A was associated with an increased risk of breast cancer and early-onset breast cancer in BRCA1 and BRCA2 mutation carriers. We genotyped p.A331S RASSF1A in 854 independent, familial, white breast cancer patients (645 BRCA mutation negative, 119 BRCA1 and 90 BRCA2 positive) and compared the genotype in 331 healthy women. The RASSF1A p.A331S variant was not more common in the familial breast cancer cases than in the controls (P = 0.27). Subset analysis demonstrated no association in the BRCA1 (P = 0.26), BRCA2 (P = 0.16) or BRCA negative (P = 0.30) samples. Hence, the RASSF1A p.A331S polymorphism is not confirmed as a significant germline contributor to familial breast cancer susceptibility.

Possible Risk Modification by Polymorphisms of Estrogen Metabolizing Genes in Familial Breast Cancer Susceptibility in an Indian Population

ABSTRACTThis case control study investigated whether polymorphisms of estrogen metabolizing genes CYP1A1 MspI, CYP17 MspAI, COMT Val158 Met, and SULT1A1 Arg213 His have any role in familial breast cancer susceptibility risk. Logistic regression analysis adjusted to age was used to calculate odds ratios (ORs) and 95% confidence intervals (95%CIs). Familial breast cancer risk due to CYP1A1 wt/m1 and m1/m1 genotypes was 2.3 (1.51–3.61)-fold and 7.1 (3.69–13.7)-fold, respectively. In addition to the main effects, certain first-order interactions were also significantly associated with familial breast cancer. Our results favor a possible risk modification by estrogen metabolizing gene polymorphisms in familial breast cancer susceptibility.

Functional Interaction between the Fanconi Anemia D2 Protein and Proliferating Cell Nuclear Antigen (PCNA) via a Conserved Putative PCNA Interaction Motif

Fanconi Anemia (FA) is a rare recessive disease characterized by congenital abnormalities, bone marrow failure, and cancer susceptibility. The FA proteins and the familial breast cancer susceptibility gene products, BRCA1 and FANCD1/BRCA2, function cooperatively in the FA-BRCA pathway to repair damaged DNA and to prevent cellular transformation. Activation of this pathway occurs via the mono-ubiquitination of the FANCD2 protein, targeting it to nuclear foci where it co-localizes with FANCD1/BRCA2, RAD51, and PCNA. The regulation of the mono-ubiquitination of FANCD2, as well as its function in DNA repair remain poorly understood. In this study, we have further characterized the interaction between the FANCD2 and PCNA proteins. We have identified a highly conserved, putative FANCD2 PCNA interaction motif (PIP-box), and demonstrate that mutation of this motif disrupts FANCD2-PCNA binding and precludes the mono-ubiquitination of FANCD2. Consequently, the FANCD2 PIP-box mutant protein fails to correct the mitomycin C hypersensitivity of FA-D2 patient cells. Our results suggest that PCNA may function as a molecular platform to facilitate the mono-ubiquitination of FANCD2 and activation of the FA-BRCA pathway.

Mutational analysis of FANCL , FANCM and the recently identified FANCI suggests that among the 13 known Fanconi Anemia genes, only FANCD1/BRCA2 plays a major role in high-risk breast cancer predisposition

Fanconi Anemia (FA) is a rare recessive syndrome characterized by cellular hypersensitivity to DNA-cross-linking agents. To date, 13 FA complementation groups have been described and all 13 genes associated to each of these groups have been currently identified. Three of the known FA genes are also high-risk (FANCD1/BRCA2) or moderate-risk (FANCN/PALB2 and FANCJ/BRIP1) breast cancer susceptibility genes, which makes all members of the FA pathway particularly attractive breast cancer candidate genes. Most FA genes have been screened for mutations in breast cancer families negative for BRCA1/2 mutations but the role of FANCL, FANCM and the recently identified FANCI has not been evaluated to date. This fact and novel data sustaining greater functional relevance of the three genes within the FA pathway prompted us to scrutinize all coding sequences and splicing sites of FANCI, FANCL and FANCM in 95 BRCA1/2-negative index cases from Spanish high-risk breast cancer families. We identified 68 sequence variants of which 24 were coding and 44 non-coding. Six exonic and 26 non-coding variants had not been described previously. None of the coding changes caused clearly pathogenic changes and computational analysis of all non-described intronic variants did not revealed major impact in splicing. With the present study, all known FA genes have been evaluated within the context of breast cancer high-risk predisposition. Our results rule out a major role of FANCI, FANCL and FANCM in familial breast cancer susceptibility, suggesting that among the 13 known FA genes, only FANCD1/BRCA2 plays a major role in high-risk breast cancer predisposition.

Contribution of XPD (Lys751Gln) and XRCC1 (Arg399Gln) Polymorphisms in Familial and Sporadic Breast Cancer Predisposition and Survival: An Indian Report

The etiology of a significant proportion of familial breast cancers is still poorly understood, with known high penetrance gene mutations accounting for only a small proportion of the cases. The increased risk of breast cancer for the majority of women with a family history likely reflects shared minor low penetrant genetic factors. In the present case-control study undertaken to examine the influence of DNA damage repair gene polymorphisms in familial and sporadic breast cancer susceptibility, 219 Sporadic and 140 familial breast cancer patients and 367 controls were genotyped using PCRRFLP. Odds Ratios (ORs) and 95% Confidence Intervals (95%CIs) were calculated by unconditional logistic regression adjusted to age. Variant genotypes XRCC1 Arg/Gln or Gln/Gln and XPD Lys/Gln or Gln/Gln increased both familial and sporadic breast cancer susceptibility. However, when the intra group risk was compared, the risk due to the XPD polymorphic genotypes Lys/Gln or Gln/Gln was significantly lower among familial breast cancer patients compared to sporadic breast cancer patients [OR = 0.61; 95%CI = 0.39-0.94; p value = 0.024) whereas the risk implied by XRCC1 variant genotype was not significantly different between the familial and nonfamilial groups of breast cancer patients [OR = 0.97; 95%CI = 0.63-1.49; p value = 0.882]. Both these variant genotypes were not associated with the disease characteristics or survival of either familial or sporadic breast cancer patients. This study represents an addition to previous published work on GSTs from the same study population and substantiates the hypothesis that the impact of the low penetrance gene polymorphisms differ by family history of the disease.

Genetic variants of BLM interact with RAD51 to increase breast cancer susceptibility

The role of the familial breast cancer susceptibility genes, BRCA1 and BRCA2, in the homologous recombination (HR) pathway for DNA double-strand break (DSB) repair suggests that the mechanisms involved in HR and DNA DSB repair are of etiological importance during breast tumorigenesis. Bloom (BLM) helicase directly interacts with RAD51 recombinase, which is involved in regulating HR, and it is thus of particular interest to examine whether this interaction is associated with breast cancer susceptibility. This single-nucleotide polymorphism (SNP)-based case-control study was performed to examine this hypothesis using specimens from 933 patients with breast cancer and 1539 healthy controls. The results showed that one SNP (rs2380165) in BLM and two (rs2412546 and rs4417527) in RAD51 were associated with breast cancer risk. Furthermore, haplotype and diplotype analyses based on combinations of five SNPs in RAD51 revealed a strong association between RAD51 polymorphisms and breast cancer risk (P < 0.05). Support for the interaction between BLM and RAD51 in determining breast cancer risk came from the finding that the association between cancer risk and at-risk genotypes/haplotype pairs of RAD51 was stronger and more significant in women harboring homozygous variant alleles of BLM (P for interaction < 0.05). Interestingly, not only the intronic SNP located within the region encoding the helicase domain of BLM but also those within the RAD51-interaction domain-encoding region showed an interaction with RAD51 polymorphisms in determining breast cancer susceptibility. Our results suggest a contribution of BLM and RAD51 to breast cancer development and provide support for the tumorigenic significance of the functional interaction between these two HR proteins.

Analysis of large deletions in BRCA1, BRCA2 and PALB2 genes in Finnish breast and ovarian cancer families

BackgroundBRCA1 and BRCA2 are the two most important genes associated with familial breast and ovarian cancer susceptibility. In addition, PALB2 has recently been identified as a breast cancer susceptibility gene in several populations. Here we have evaluated whether large genomic rearrangement in these genes could explain some of Finnish breast and/or ovarian cancer families.MethodsAltogether 61 index patients of Northern Finnish breast and/or ovarian cancer families were analyzed by Multiplex ligation-dependent probe amplification (MLPA) method in order to identify exon deletions and duplications in BRCA1, BRCA2 and PALB2. The families have been comprehensively screened for germline mutation in these genes by conventional methods of mutation analysis and were found negative.ResultsWe identified one large deletion in BRCA1, deleting the most part of the gene (exon 1A-13) in one family with family history of ovarian cancer. No large genomic rearrangements were identified in either BRCA2 or PALB2.ConclusionIn Finland, women eligible for BRCA1 or BRCA2 mutation screening, when found negative, could benefit from screening for large genomic rearrangements at least in BRCA1. On the contrary, the genomic rearrangements in PALB2 seem not to contribute to the hereditary breast cancer susceptibility.

Evaluation of the BRCA1 interacting genes RAP80 and CCDC98 in familial breast cancer susceptibility

RAP80 and CCDC98 have arisen as new candidate breast cancer susceptibility genes, since they encode for two very recently identified BRCA1 interacting proteins. In this study we have performed the first mutational analysis of both genes in 168 multiple-case breast/ovarian cancer families, negative for mutations in BRCA1 or BRCA2. We have not found truncating mutations in any of the genes and only two missense variants, p.Tyr564His in RAP80, and p.Met299Ile in CCDC98 were found that could be suspected to have a pathogenic effect, although further analyses suggested that they were probably non deleterious. Our analysis suggests that RAP80 and CCDC98 do not play an important role as high penetrance breast cancer susceptibility genes.