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Yu C, Dugué PA, Dowty JG, Hammet F, Joo JE, Wong EM, Hosseinpour M, Giles GG, Hopper JL, Nguyen-Dumont T, MacInnis RJ, Southey MC. Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay. BMC Res Notes 2021; 14:394. [PMID: 34689793 PMCID: PMC8543877 DOI: 10.1186/s13104-021-05809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE In previous studies using Illumina Infinium methylation arrays, we have identified DNA methylation marks associated with cancer predisposition and progression. In the present study, we have sought to find appropriate technology to both technically validate our data and expand our understanding of DNA methylation in these genomic regions. Here, we aimed to assess the repeatability of methylation measures made using QIAseq targeted methyl panel and to compare them with those obtained from the Illumina HumanMethylation450 (HM450K) assay. We included in the analysis high molecular weight DNA extracted from whole blood (WB) and DNA extracted from formalin-fixed paraffin-embedded tissues (FFPE). RESULTS The repeatability of QIAseq-methylation measures was assessed at 40 CpGs, using the Intraclass Correlation Coefficient (ICC). The mean ICCs and 95% confidence intervals (CI) were 0.72 (0.62-0.81), 0.59 (0.47-0.71) and 0.80 (0.73-0.88) for WB, FFPE and both sample types combined, respectively. For technical replicates measured using QIAseq and HM450K, the mean ICCs (95% CI) were 0.53 (0.39-0.68), 0.43 (0.31-0.56) and 0.70 (0.59-0.80), respectively. Bland-Altman plots indicated good agreement between QIAseq and HM450K measurements. These results demonstrate that the QIAseq targeted methyl panel produces reliable and reproducible methylation measurements across the 40 CpGs that were examined.
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Affiliation(s)
- Chenglong Yu
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Fleur Hammet
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - JiHoon E Joo
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Mahnaz Hosseinpour
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
| | - Robert J MacInnis
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia.
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia.
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia.
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2
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Nguyen-Dumont T, Steen JA, Winship I, Park DJ, Pope BJ, Hammet F, Mahmoodi M, Tsimiklis H, Theys D, Clendenning M, Giles GG, Hopper JL, Southey MC. Mismatch repair gene pathogenic germline variants in a population-based cohort of breast cancer. Fam Cancer 2021; 19:197-202. [PMID: 32060697 DOI: 10.1007/s10689-020-00164-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The advent of gene panel testing is challenging the previous practice of using clinically defined cancer family syndromes to inform single-gene genetic screening. Individual and family cancer histories that would have previously indicated testing of a single gene or a small number of related genes are now, increasingly, leading to screening across gene panels that contain larger numbers of genes. We have applied a gene panel test that included four DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2) to an Australian population-based case-control-family study of breast cancer. Altogether, eight pathogenic variants in MMR genes were identified: six in 1421 case-families (0.4%, 4 MSH6 and 2 PMS2) and two in 833 control-families (0.2%, one each of MLH1 and MSH2). This testing highlights the current and future challenges for clinical genetics in the context of anticipated gene panel-based population-based screening that includes the MMR genes. This testing is likely to provide additional opportunities for cancer prevention via cascade testing for Lynch syndrome and precision medicine for breast cancer treatment.
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Affiliation(s)
- Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Jason A Steen
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia
| | | | - Daniel J Park
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Bernard J Pope
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Fleur Hammet
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia
| | - Maryam Mahmoodi
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia
| | - Helen Tsimiklis
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia
| | - Derrick Theys
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia
| | - Mark Clendenning
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, VIC, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, VIC, 3010, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Science at Monash Health, Monash University Clayton, Melbourne, VIC, 3168, Australia.
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia.
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3
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Nguyen-Dumont T, Dowty J, Steen JA, Renault AL, Hammet F, Mahmoodi M, Theys D, Rewse A, Tsimiklis H, Winship I, Giles GG, Milne RL, Hopper JL, Southey MC. Population-based estimates of the age-specific cumulative risk of breast cancer for pathogenic variants in CHEK2: Findings from the Australian Breast Cancer Family Registry. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
551 Background: Case-control studies of breast cancer have consistently shown that pathogenic variants in CHEK2 are associated with about a 3-fold increased risk of breast cancer. Information about the recurrent protein truncating variant CHEK2c.1100delC dominates this estimate. There have been no formal estimates of age-specific cumulative risk of breast cancer for all CHEK2 pathogenic (including likely pathogenic) variants combined. Methods: We conducted a genetic screen of CHEK2 in an Australian population-based case-control-family study of breast cancer. This study is focused on disease at an early age and participants were unselected for family history. The age-specific cumulative risk (penetrance) of breast cancer was estimated using segregation analysis. Results: The estimated hazard ratio for carriers of pathogenic CHEK2 variants (combined) was 4.9 (95% CI 2.5-9.5; p < 0.0001) relative to non-carriers. The HR for carriers of the CHEK2 c.1100delC variant was estimated to be 3.5 (95% CI 1.02-11.6) and the HR for carriers of all other CHEK2 variants combined was estimated to be 5.7 (95% CI 2.5-12.9). The age-specific cumulative risk of breast cancer was estimated to be 18% (95% CI 11-30%) and 33% (95% CI 21-48%) to age 60 and 80 years, respectively. Conclusions: These findings provide important information for the clinical management of breast cancer risk for women carrying pathogenic variants in CHEK2.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
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Nguyen-Dumont T, Dowty J, Tucker K, Kirk J, James P, Trainer A, Winship I, Pachter N, Poplawski N, Grist S, Park DJ, Renault AL, Hammet F, Mahmoodi M, Tsimiklis H, Steen JA, Theys D, Rewse A, Willis A, Morrow A, Speechly C, Harris R, Riaz M, Sebra R, Schadt E, Lacaze P, McNeil J, Hopper JL, Southey MC. Abstract PS7-04: Population-based estimates of breast cancer risk for germline pathogenic variants identified by gene-panel testing: An Australian perspective. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-ps7-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BRA-STRAP is an Australia-wide study of breast cancer predisposition that brings together gene-panel data from 30,000 adult Australian women of all ages, across the breast cancer risk spectrum, with and without a diagnosis of breast cancer. The “BRA-STRAP panel” includes 24 genes* that are involved in, or putatively associated with, predisposition to breast and/or ovarian cancer. Despite insufficient evidence for clinical translation for some of these genes, all 24 are commonly included on panel tests for breast cancer predisposition.
We present findings from the population-based case-control sub-study of BRA-STRAP, which involved 1451 women diagnosed with breast cancer and 857 age-matched controls participating in the Australian Breast Cancer Family Registry (ABCFR), and 6101 healthy, elderly Australian women enrolled in the ASPREE study. These analyses focus on rare genetic variants predicted to lead to loss of function and/or classified as pathogenic/likely pathogenic (P/LP) in ClinVar. Odds ratios (ORs) for their associations with breast cancer were estimated by aggregating genetic variants for each gene.
For the women diagnosed with breast cancer, the median age at diagnosis (inter-quartile range, IQR) was 40.0 (14.0) years and the overall frequency of P/LP variant carriers across all genes was 156/1451 (10.8%). The median age (IQR) of the ABCFR and ASPREE controls were 39.4 (14.9) and 73.9 (5.8) years, respectively. The frequencies of P/LP variant carriers were 33/857 (3.9%) and 268/6101 (4.4%) in the ABCFR and ASPREE controls, respectively. We combined both control datasets and, after adjusting for age and other potential confounders, the ORs associated with P/LP variants in BRCA1 and BRCA2 were 4.1 [95% confidence interval (CI): 1.8-10.2] and 2.9 [95% CI: 1.5-6], respectively. We also found that the OR for P/LP variants in ATM was 4.0 [95% CI: 1.5-10.4] and the OR for P/LP variants in PALB2 was 2.2 [95% CI: 0.75-5.7] although this did not reach statistical significance.
These results contribute to international efforts to refine the breast cancer risk estimates for genetic variants identified from population-based screening of unselected women using genes that are included on panel tests and thought to be potentially breast cancer predisposition genes.The case-control-family design of the ABCFR will also allow us to estimate the age specific cumulative risk (penetrance) of these genetic variants, which is important for genetic counselling and the clinical management of carrier families.
*ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, FANCM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, RECQL, STK11 and TP53
Citation Format: Tu Nguyen-Dumont, James Dowty, Katherine Tucker, Judy Kirk, Paul James, Alison Trainer, Ingrid Winship, Nicholas Pachter, Nicola Poplawski, Scott Grist, Daniel J Park, Anne-Laure Renault, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Jason A Steen, Derrick Theys, Amanda Rewse, Amanda Willis, April Morrow, Catherine Speechly, Rebecca Harris, Moeen Riaz, Robert Sebra, Eric Schadt, Paul Lacaze, John McNeil, John L Hopper, Melissa C Southey. Population-based estimates of breast cancer risk for germline pathogenic variants identified by gene-panel testing: An Australian perspective [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS7-04.
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Affiliation(s)
| | - James Dowty
- 2The University of Melbourne, Parkville, Australia
| | | | - Judy Kirk
- 4Westmead Institute for Cancer Research, Sydney, Australia
| | - Paul James
- 5Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | - Nicola Poplawski
- 8South Australian Clinical Genetics Service, Adelaide, Australia
| | - Scott Grist
- 9SA Pathology, Flinders Medical Centre, Adelaide, Australia
| | | | | | | | | | | | | | | | | | | | | | | | - Rebecca Harris
- 4Westmead Institute for Cancer Research, Sydney, Australia
| | | | - Robert Sebra
- 11Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eric Schadt
- 11Icahn School of Medicine at Mount Sinai, New York, NY
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5
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Nguyen-Dumont T, MacInnis RJ, Steen JA, Theys D, Tsimiklis H, Hammet F, Mahmoodi M, Pope BJ, Park DJ, Mahmood K, Severi G, Bolton D, Milne RL, Giles GG, Southey MC. Rare germline genetic variants and risk of aggressive prostate cancer. Int J Cancer 2020; 147:2142-2149. [PMID: 32338768 DOI: 10.1002/ijc.33024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/10/2020] [Accepted: 04/01/2020] [Indexed: 01/02/2023]
Abstract
Few genetic risk factors have been demonstrated to be specifically associated with aggressive prostate cancer (PrCa). Here, we report a case-case study of PrCa comparing the prevalence of germline pathogenic/likely pathogenic (P/LP) genetic variants in 787 men with aggressive disease and 769 with nonaggressive disease. Overall, we observed P/LP variants in 11.4% of men with aggressive PrCa and 9.8% of men with nonaggressive PrCa (two-tailed Fisher's exact tests, P = .28). The proportion of BRCA2 and ATM P/LP variant carriers in men with aggressive PrCa exceeded that observed in men with nonaggressive PrCa; 18/787 carriers (2.3%) and 4/769 carriers (0.5%), P = .004, and 14/787 carriers (0.02%) and 5/769 carriers (0.01%), P = .06, respectively. Our findings contribute to the extensive international effort to interpret the genetic variation identified in genes included on gene-panel tests, for which there is currently an insufficient evidence-base for clinical translation in the context of PrCa risk.
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Affiliation(s)
- Tú Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Robert J MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason A Steen
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Derrick Theys
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Helen Tsimiklis
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Fleur Hammet
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Maryam Mahmoodi
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Bernard J Pope
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,The University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, Victoria, Australia.,Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel J Park
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gianluca Severi
- CESP Inserm U1018, Faculté de Médecine - Université Paris-Sud, Faculté de Médecine - UVSQ, Université Paris-Saclay, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Damien Bolton
- Department of Surgery, The University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,The University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, Victoria, Australia
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6
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Pope BJ, Hammet F, Nguyen-Dumont T, Park DJ. Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing. Methods Mol Biol 2018; 1712:53-70. [PMID: 29224068 DOI: 10.1007/978-1-4939-7514-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.
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Affiliation(s)
- Bernard J Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Fleur Hammet
- Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Tu Nguyen-Dumont
- Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Park
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia.
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7
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Nguyen-Dumont T, Teo ZL, Hammet F, Roberge A, Mahmoodi M, Tsimiklis H, Park DJ, Pope BJ, Lonie A, Kapuscinski MK, Mahmood K, Goldgar DE, Giles GG, Winship I, Hopper JL, Southey MC. Is RNASEL:p.Glu265* a modifier of early-onset breast cancer risk for carriers of high-risk mutations? BMC Cancer 2018; 18:165. [PMID: 29422015 PMCID: PMC5806316 DOI: 10.1186/s12885-018-4028-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 01/23/2018] [Indexed: 11/10/2022] Open
Abstract
Background Breast cancer risk for BRCA1 and BRCA2 pathogenic mutation carriers is modified by risk factors that cluster in families, including genetic modifiers of risk. We considered genetic modifiers of risk for carriers of high-risk mutations in other breast cancer susceptibility genes. Methods In a family known to carry the high-risk mutation PALB2:c.3113G>A (p.Trp1038*), whole-exome sequencing was performed on germline DNA from four affected women, three of whom were mutation carriers. Results RNASEL:p.Glu265* was identified in one of the PALB2 carriers who had two primary invasive breast cancer diagnoses before 50 years. Gene-panel testing of BRCA1, BRCA2, PALB2 and RNASEL in the Australian Breast Cancer Family Registry identified five carriers of RNASEL:p.Glu265* in 591 early onset breast cancer cases. Three of the five women (60%) carrying RNASEL:p.Glu265* also carried a pathogenic mutation in a breast cancer susceptibility gene compared with 30 carriers of pathogenic mutations in the 586 non-carriers of RNASEL:p.Glu265* (5%) (p < 0.002). Taqman genotyping demonstrated that the allele frequency of RNASEL:p.Glu265* was similar in affected and unaffected Australian women, consistent with other populations. Conclusion Our study suggests that RNASEL:p.Glu265* may be a genetic modifier of risk for early-onset breast cancer predisposition in carriers of high-risk mutations. Much larger case-case and case-control studies are warranted to test the association observed in this report.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Zhi L Teo
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Fleur Hammet
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Alexis Roberge
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Maryam Mahmoodi
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Helen Tsimiklis
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Bernard J Pope
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Andrew Lonie
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Miroslav K Kapuscinski
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Khalid Mahmood
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | | | | | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia.,Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Ingrid Winship
- Department of Medicine, The University of Melbourne, Melbourne, VIC, Australia.,The Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia. .,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.
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Nguyen-Dumont T, Myszka A, Karpinski P, Sasiadek MM, Akopyan H, Hammet F, Tsimiklis H, Park DJ, Pope BJ, Slezak R, Kitsera N, Siekierzynska A, Southey MC. FANCM and RECQL genetic variants and breast cancer susceptibility: relevance to South Poland and West Ukraine. BMC Med Genet 2018; 19:12. [PMID: 29351780 PMCID: PMC5775547 DOI: 10.1186/s12881-018-0524-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022]
Abstract
Background FANCM and RECQL have recently been reported as breast cancer susceptibility genes and it has been suggested that they should be included on gene panel tests for breast cancer predisposition. However, the clinical value of testing for mutations in RECQL and FANCM remains to be determined. In this study, we have characterised the spectrum of FANCM and RECQL mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine. Methods We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron-exon junctions of FANCM and RECQL in germline DNA from unrelated women affected with breast cancer (n = 338) and ovarian cancer (n = 89) from Poland (n = 304) and Ukraine (n = 123). These women were at high-risk of carrying a genetic predisposition to breast and/or ovarian cancer due to a family history and/or early-onset disease. Results Among 427 women screened, we identified one carrier of the FANCM:c.1972C > T nonsense mutation (0.23%), and two carriers of the frameshift insertion FANCM:c.1491dup (0.47%). None of the variants we observed in RECQL were predicted to be loss-of-function mutations by standard variant effect prediction tools. Conclusions Our study of the Polish and Ukrainian populations has identified a carrier frequency of truncating mutations in FANCM consistent with previous reports. Although initial reports suggesting that mutations in RECQL could be associated with increased breast cancer risk included women from Poland and identified the RECQL:c.1667_1667 + 3delAGTA mutation in 0.23–0.35% of breast cancer cases, we did not observe any carriers in our study cohort. Continued screening, both in research and diagnostic settings, will enable the accumulation of data that is needed to establish the clinical utility of including RECQL and FANCM on gene panel tests. Electronic supplementary material The online version of this article (10.1186/s12881-018-0524-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Aleksander Myszka
- Institute of Obstetrics and Emergency Medicine, University of Rzeszow, Rzeszow, Poland
| | - Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Hayane Akopyan
- Institute of Obstetrics and Emergency Medicine, University of Rzeszow, Rzeszow, Poland.,Institute of Hereditary Pathology of National Academy of Medical Sciences, Lviv, Ukraine
| | - Fleur Hammet
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Helen Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia.,Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Bernard J Pope
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Victoria, Australia
| | - Ryszard Slezak
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Nataliya Kitsera
- Institute of Hereditary Pathology of National Academy of Medical Sciences, Lviv, Ukraine
| | | | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Australia.
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Nguyen-Dumont T, Pope BJ, Hammet F, Southey MC, Park DJ. A high-plex PCR approach for massively parallel sequencing. Biotechniques 2015; 55:69-74. [PMID: 23931594 DOI: 10.2144/000114052] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/20/2013] [Indexed: 11/23/2022] Open
Abstract
Current methods for targeted massively parallel sequencing (MPS) have several drawbacks, including limited design flexibility, expense, and protocol complexity, which restrict their application to settings involving modest target size and requiring low cost and high throughput. To address this, we have developed Hi-Plex, a PCR-MPS strategy intended for high-throughput screening of multiple genomic target regions that integrates simple, automated primer design software to control product size. Featuring permissive thermocycling conditions and clamp bias reduction, our protocol is simple, cost- and time-effective, uses readily available reagents, does not require expensive instrumentation, and requires minimal optimization. In a 60-plex assay targeting the breast cancer predisposition genes PALB2 and XRCC2, we applied Hi-Plex to 100 ng LCL-derived DNA, and 100 ng and 25 ng FFPE tumor-derived DNA. Altogether, at least 86.94% of the human genome-mapped reads were on target, and 100% of targeted amplicons were represented within 25-fold of the mean. Using 25 ng FFPE-derived DNA, 95.14% of mapped reads were on-target and relative representation ranged from 10.1-fold lower to 5.8-fold higher than the mean. These results were obtained using only the initial automatically-designed primers present in equal concentration. Hi-Plex represents a powerful new approach for screening panels of genomic target regions.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Victoria, Australia
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10
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Nguyen-Dumont T, Hammet F, Mahmoodi M, Tsimiklis H, Teo ZL, Li R, Pope BJ, Terry MB, Buys SS, Daly M, Hopper JL, Winship I, Goldgar DE, Park DJ, Southey MC. Mutation screening of PALB2 in clinically ascertained families from the Breast Cancer Family Registry. Breast Cancer Res Treat 2015; 149:547-54. [PMID: 25575445 DOI: 10.1007/s10549-014-3260-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 12/22/2014] [Indexed: 11/28/2022]
Abstract
Loss-of-function mutations in PALB2 are associated with an increased risk of breast cancer, with recent data showing that female breast cancer risks for PALB2 mutation carriers are comparable in magnitude to those for BRCA2 mutation carriers. This study applied targeted massively parallel sequencing to characterize the mutation spectrum of PALB2 in probands attending breast cancer genetics clinics in the USA. The coding regions and proximal intron-exon junctions of PALB2 were screened in probands not known to carry a mutation in BRCA1 or BCRA2 from 1,250 families enrolled through familial cancer clinics by the Breast Cancer Family Registry. Mutation screening was performed using Hi-Plex, an amplicon-based targeted massively parallel sequencing platform. Screening of PALB2 was successful in 1,240/1,250 probands and identified nine women with protein-truncating mutations (three nonsense mutations and five frameshift mutations). Four of the 33 missense variants were predicted to be deleterious to protein function by in silico analysis using two different programs. Analysis of tumors from carriers of truncating mutations revealed that the majority were high histological grade, invasive ductal carcinomas. Young onset was apparent in most families, with 19 breast cancers under 50 years of age, including eight under the age of 40 years. Our data demonstrate the utility of Hi-Plex in the context of high-throughput testing for rare genetic mutations and provide additional timely information about the nature and prevalence of PALB2 mutations, to enhance risk assessment and risk management of women at high risk of cancer attending clinical genetic services.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia,
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11
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Nguyen-Dumont T, Mahmoodi M, Hammet F, Tran T, Tsimiklis H, Giles GG, Hopper JL, Southey MC, Park DJ. Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots. Anal Biochem 2014; 470:48-51. [PMID: 25447460 DOI: 10.1016/j.ab.2014.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 11/28/2022]
Abstract
Many genetic epidemiology resources have collected dried blood spots (predominantly as Guthrie Cards) as an economical and efficient means of archiving sources of DNA, conferring great value to genetic screening methods that are compatible with this medium. We applied Hi-Plex to screen the breast cancer predisposition gene PALB2 in 93 Guthrie Card-derived DNA specimens previously characterized for PALB2 genetic variants via DNA derived from lymphoblastoid cell lines, whole blood, and buffy coat. Of the 93 archival Guthrie Card-derived DNAs, 92 (99%) were processed successfully and sequenced using approximately half of a MiSeq run. From these 92 DNAs, all 59 known variants were detected and no false-positive variant calls were yielded. Fully 98.13% of amplicons (5417/5520) were represented within 15-fold of the median coverage (2786 reads), and 99.98% of amplicons (5519/5520) were represented at a depth of 10 read-pairs or greater. With Hi-Plex, we show for the first time that a High-Plex amplicon-based massively parallel sequencing (MPS) system can be applied effectively to DNA prepared from dried blood spot archival specimens and, as such, can dramatically increase the scopes of both method and resource.
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Affiliation(s)
- T Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - M Mahmoodi
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - F Hammet
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - T Tran
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - H Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | | | - G G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
| | - J L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Parkville, Victoria 3010, Australia
| | | | - M C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - D J Park
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
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Park DJ, Tao K, Le Calvez-Kelm F, Nguyen-Dumont T, Robinot N, Hammet F, Odefrey F, Tsimiklis H, Teo ZL, Thingholm LB, Young EL, Voegele C, Lonie A, Pope BJ, Roane TC, Bell R, Hu H, Shankaracharya, Huff CD, Ellis J, Li J, Makunin IV, John EM, Andrulis IL, Terry MB, Daly M, Buys SS, Snyder C, Lynch HT, Devilee P, Giles GG, Hopper JL, Feng BJ, Lesueur F, Tavtigian SV, Southey MC, Goldgar DE. Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers. Cancer Discov 2014; 4:804-15. [PMID: 25050558 PMCID: PMC4234633 DOI: 10.1158/2159-8290.cd-14-0212] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
UNLABELLED Approximately half of the familial aggregation of breast cancer remains unexplained. A multiple-case breast cancer family exome-sequencing study identified three likely pathogenic mutations in RINT1 (NM_021930.4) not present in public sequencing databases: RINT1 c.343C>T (p.Q115X), c.1132_1134del (p.M378del), and c.1207G>T (p.D403Y). On the basis of this finding, a population-based case-control mutation-screening study was conducted that identified 29 carriers of rare (minor allele frequency < 0.5%), likely pathogenic variants: 23 in 1,313 early-onset breast cancer cases and six in 1,123 frequency-matched controls [OR, 3.24; 95% confidence interval (CI), 1.29-8.17; P = 0.013]. RINT1 mutation screening of probands from 798 multiple-case breast cancer families identified four additional carriers of rare genetic variants. Analysis of the incidence of first primary cancers in families of women carrying RINT1 mutations estimated that carriers were at increased risk of Lynch syndrome-spectrum cancers [standardized incidence ratio (SIR), 3.35; 95% CI, 1.7-6.0; P = 0.005], particularly for relatives diagnosed with cancer under the age of 60 years (SIR, 10.9; 95% CI, 4.7-21; P = 0.0003). SIGNIFICANCE The work described in this study adds RINT1 to the growing list of genes in which rare sequence variants are associated with intermediate levels of breast cancer risk. Given that RINT1 is also associated with a spectrum of cancers with mismatch repair defects, these findings have clinical applications and raise interesting biological questions.
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Affiliation(s)
- Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | | | - Nivonirina Robinot
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon
| | - Fleur Hammet
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | - Zhi L Teo
- Genetic Epidemiology Laboratory, Department of Pathology
| | | | | | - Catherine Voegele
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon
| | | | - Bernard J Pope
- Department of Computing and Information Systems; Victorian Life Sciences Computation Initiative
| | | | | | - Hao Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shankaracharya
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jonathan Ellis
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Jun Li
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Igor V Makunin
- The QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; Departments of
| | - Esther M John
- Cancer Prevention Institute of California, Fremont; Department of Health Research and Policy, Stanford Cancer Institute, Stanford, California
| | - Irene L Andrulis
- Department of Molecular Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mary B Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Mary Daly
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Saundra S Buys
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Carrie Snyder
- Department of Preventive Medicine, Creighton University, Omaha, Nebraska
| | - Henry T Lynch
- Department of Preventive Medicine, Creighton University, Omaha, Nebraska
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne; Centre for Cancer Epidemiology, The Cancer Council Victoria, Carlton, Victoria
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne; School of Public Health, Seoul National University, Seoul, Korea
| | - Bing-Jian Feng
- Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Fabienne Lesueur
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon; Genetic Epidemiology of Cancer Team, Institut National de la Santé et de la Recherche Medicale (INSERM), U900, Institut Curie, Mines ParisTech, Paris, France
| | | | | | - David E Goldgar
- Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine; Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah;
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Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ. ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets. Source Code Biol Med 2014; 9:3. [PMID: 24461215 PMCID: PMC3904415 DOI: 10.1186/1751-0473-9-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/08/2014] [Indexed: 01/03/2023]
Abstract
Background We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end sequencing can achieve complete overlap of read pairs. Variant calling from Hi-Plex-derived datasets can thus rely on the identification of variants appearing in both reads of read-pairs, permitting stringent filtering of sequencing chemistry-induced errors. These principles underly ROVER software (derived from Read Overlap PCR-MPS variant caller), which we have recently used to report the screening for genetic mutations in the breast cancer predisposition gene PALB2. Here, we describe the algorithms underlying ROVER and its usage. Results ROVER enables users to quickly and accurately identify genetic variants from PCR-targeted, overlapping paired-end MPS datasets. The open-source availability of the software and threshold tailorability enables broad access for a range of PCR-MPS users. Methods ROVER is implemented in Python and runs on all popular POSIX-like operating systems (Linux, OS X). The software accepts a tab-delimited text file listing the coordinates of the target-specific primers used for targeted enrichment based on a specified genome-build. It also accepts aligned sequence files resulting from mapping to the same genome-build. ROVER identifies the amplicon a given read-pair represents and removes the primer sequences by using the mapping co-ordinates and primer co-ordinates. It considers overlapping read-pairs with respect to primer-intervening sequence. Only when a variant is observed in both reads of a read-pair does the signal contribute to a tally of read-pairs containing or not containing the variant. A user-defined threshold informs the minimum number of, and proportion of, read-pairs a variant must be observed in for a ‘call’ to be made. ROVER also reports the depth of coverage across amplicons to facilitate the identification of any regions that may require further screening. Conclusions ROVER can facilitate rapid and accurate genetic variant calling for a broad range of PCR-MPS users.
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Affiliation(s)
| | | | | | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, Medical Building, The University of Melbourne, Melbourne, Victoria 3010, Australia.
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Nguyen-Dumont T, Teo ZL, Pope BJ, Hammet F, Mahmoodi M, Tsimiklis H, Sabbaghian N, Tischkowitz M, Foulkes WD, Giles GG, Hopper JL, Southey MC, Park DJ. Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2. BMC Med Genomics 2013; 6:48. [PMID: 24206657 PMCID: PMC3829211 DOI: 10.1186/1755-8794-6-48] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/05/2013] [Indexed: 11/16/2022] Open
Abstract
Background Massively parallel sequencing (MPS) has revolutionised biomedical research and offers enormous capacity for clinical application. We previously reported Hi-Plex, a streamlined highly-multiplexed PCR-MPS approach, allowing a given library to be sequenced with both the Ion Torrent and TruSeq chemistries. Comparable sequencing efficiency was achieved using material derived from lymphoblastoid cell lines and formalin-fixed paraffin-embedded tumour. Methods Here, we report high-throughput application of Hi-Plex by performing blinded mutation screening of the coding regions of the breast cancer susceptibility gene PALB2 on a set of 95 blood-derived DNA samples that had previously been screened using Sanger sequencing and high-resolution melting curve analysis (n = 90), or genotyped by Taqman probe-based assays (n = 5). Hi-Plex libraries were prepared simultaneously using relatively inexpensive, readily available reagents in a simple half-day protocol followed by MPS on a single MiSeq run. Results We observed that 99.93% of amplicons were represented at ≥10X coverage. All 56 previously identified variant calls were detected and no false positive calls were assigned. Four additional variant calls were made and confirmed upon re-analysis of previous data or subsequent Sanger sequencing. Conclusions These results support Hi-Plex as a powerful approach for rapid, cost-effective and accurate high-throughput mutation screening. They further demonstrate that Hi-Plex methods are suitable for and can meet the demands of high-throughput genetic testing in research and clinical settings.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia.
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Nguyen-Dumont T, Pope BJ, Hammet F, Mahmoodi M, Tsimiklis H, Southey MC, Park DJ. Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing. Anal Biochem 2013; 442:127-9. [PMID: 23933242 DOI: 10.1016/j.ab.2013.07.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 07/31/2013] [Indexed: 12/11/2022]
Abstract
Although per-base sequencing costs have decreased during recent years, library preparation for targeted massively parallel sequencing remains constrained by high reagent cost, limited design flexibility, and protocol complexity. To address these limitations, we previously developed Hi-Plex, a polymerase chain reaction (PCR) massively parallel sequencing strategy for screening panels of genomic target regions. Here, we demonstrate that Hi-Plex applied with hybrid adapters can generate a library suitable for sequencing with both the Ion Torrent and the TruSeq chemistries and that adjusting primer concentrations improves coverage uniformity. These results expand Hi-Plex capabilities as an accurate, affordable, flexible, and rapid approach for various genetic screening applications.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Victoria 3010, Australia
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Dite GS, Mahmoodi M, Bickerstaffe A, Hammet F, Macinnis RJ, Tsimiklis H, Dowty JG, Apicella C, Phillips KA, Giles GG, Southey MC, Hopper JL. Using SNP genotypes to improve the discrimination of a simple breast cancer risk prediction model. Breast Cancer Res Treat 2013; 139:887-96. [PMID: 23774992 DOI: 10.1007/s10549-013-2610-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/09/2013] [Indexed: 10/26/2022]
Abstract
It has been shown that, for women aged 50 years or older, the discriminatory accuracy of the Breast Cancer Risk Prediction Tool (BCRAT) can be modestly improved by the inclusion of information on common single nucleotide polymorphisms (SNPs) that are associated with increased breast cancer risk. We aimed to determine whether a similar improvement is seen for earlier onset disease. We used the Australian Breast Cancer Family Registry to study a population-based sample of 962 cases aged 35-59 years, and 463 controls frequency matched for age and for whom genotyping data was available. Overall, the inclusion of data on seven SNPs improved the area under the receiver operating characteristic curve (AUC) from 0.58 (95 % confidence interval [CI] 0.55-0.61) for BCRAT alone to 0.61 (95 % CI 0.58-0.64) for BCRAT and SNP data combined (p < 0.001). For women aged 35-39 years at interview, the corresponding improvement in AUC was from 0.61 (95 % CI 0.56-0.66) to 0.65 (95 % CI 0.60-0.70; p = 0.03), while for women aged 40-49 years at diagnosis, the AUC improved from 0.61 (95 % CI 0.55-0.66) to 0.63 (95 % CI 0.57-0.69; p = 0.04). Using previously used classifications of low, intermediate and high risk, 2.1 % of cases and none of the controls aged 35-39 years, and 10.9 % of cases and 4.0 % of controls aged 40-49 years were classified into a higher risk group. Including information on seven SNPs associated with breast cancer risk, improves the discriminatory accuracy of BCRAT for women aged 35-39 years and 40-49 years. Given, the low absolute risk for women in these age groups, only a small proportion are reclassified into a higher category for predicted 5-year risk of breast cancer.
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Affiliation(s)
- Gillian S Dite
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Level 3/207 Bouverie Street, Carlton, VIC 3053, Australia
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Garcia-Closas M, Couch FJ, Lindstrom S, Michailidou K, Schmidt MK, Brook MN, orr N, Rhie SK, Riboli E, Feigelson HS, Le Marchand L, Buring JE, Eccles D, Miron P, Fasching PA, Brauch H, Chang-Claude J, Carpenter J, Godwin AK, Nevanlinna H, Giles GG, Cox A, Hopper JL, Bolla MK, Wang Q, Dennis J, Dicks E, Howat WJ, Schoof N, Bojesen SE, Lambrechts D, Broeks A, Andrulis IL, Guénel P, Burwinkel B, Sawyer EJ, Hollestelle A, Fletcher O, Winqvist R, Brenner H, Mannermaa A, Hamann U, Meindl A, Lindblom A, Zheng W, Devillee P, Goldberg MS, Lubinski J, Kristensen V, Swerdlow A, Anton-Culver H, Dörk T, Muir K, Matsuo K, Wu AH, Radice P, Teo SH, Shu XO, Blot W, Kang D, Hartman M, Sangrajrang S, Shen CY, Southey MC, Park DJ, Hammet F, Stone J, Veer LJV, Rutgers EJ, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Peto J, Schrauder MG, Ekici AB, Beckmann MW, Silva IDS, Johnson N, Warren H, Tomlinson I, Kerin MJ, Miller N, Marme F, Schneeweiss A, Sohn C, Truong T, Laurent-Puig P, Kerbrat P, Nordestgaard BG, Nielsen SF, Flyger H, Milne RL, Perez JIA, Menéndez P, Müller H, Arndt V, Stegmaier C, Lichtner P, Lochmann M, Justenhoven C, Ko YD, Muranen TA, Aittomäki K, Blomqvist C, Greco D, Heikkinen T, Ito H, Iwata H, Yatabe Y, Antonenkova NN, Margolin S, Kataja V, Kosma VM, Hartikainen JM, Balleine R, Tseng CC, Van Den Berg D, Stram DO, Neven P, Dieudonné AS, Leunen K, Rudolph A, Nickels S, Flesch-Janys D, Peterlongo P, Peissel B, Bernard L, Olson JE, Wang X, Stevens K, Severi G, Baglietto L, Mclean C, Coetzee GA, Feng Y, Henderson BE, Schumacher F, Bogdanova NV, Labrèche F, Dumont M, Yip CH, Taib NAM, Cheng CY, Shrubsole M, Long J, Pylkäs K, Jukkola-Vuorinen A, Kauppila S, knight JA, Glendon G, Mulligan AM, Tollenaar RAEM, Seynaeve CM, Kriege M, Hooning MJ, Van den Ouweland AMW, Van Deurzen CHM, Lu W, Gao YT, Cai H, Balasubramanian SP, Cross SS, Reed MWR, Signorello L, Cai Q, Shah M, Miao H, Chan CW, Chia KS, Jakubowska A, Jaworska K, Durda K, Hsiung CN, Wu PE, Yu JC, Ashworth A, Jones M, Tessier DC, González-Neira A, Pita G, Alonso MR, Vincent D, Bacot F, Ambrosone CB, Bandera EV, John EM, Chen GK, Hu JJ, Rodriguez-gil JL, Bernstein L, Press MF, Ziegler RG, Millikan RM, Deming-Halverson SL, Nyante S, Ingles SA, Waisfisz Q, Tsimiklis H, Makalic E, Schmidt D, Bui M, Gibson L, Müller-Myhsok B, Schmutzler RK, Hein R, Dahmen N, Beckmann L, Aaltonen K, Czene K, Irwanto A, Liu J, Turnbull C, Rahman N, Meijers-Heijboer H, Uitterlinden AG, Rivadeneira F, Olswold C, Slager S, Pilarski R, Ademuyiwa F, Konstantopoulou I, Martin NG, Montgomery GW, Slamon DJ, Rauh C, Lux MP, Jud SM, Bruning T, Weaver J, Sharma P, Pathak H, Tapper W, Gerty S, Durcan L, Trichopoulos D, Tumino R, Peeters PH, Kaaks R, Campa D, Canzian F, Weiderpass E, Johansson M, Khaw KT, Travis R, Clavel-Chapelon F, Kolonel LN, Chen C, Beck A, Hankinson SE, Berg CD, Hoover RN, Lissowska J, Figueroa JD, Chasman DI, Gaudet MM, Diver WR, Willett WC, Hunter DJ, Simard J, Benitez J, Dunning AM, Sherman ME, Chenevix-Trench G, Chanock SJ, Hall P, Pharoah PDP, Vachon C, Easton DF, Haiman CA, Kraft P. Genome-wide association studies identify four ER negative-specific breast cancer risk loci. Nat Genet 2013; 45:392-8, 398e1-2. [PMID: 23535733 PMCID: PMC3771695 DOI: 10.1038/ng.2561] [Citation(s) in RCA: 323] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 01/29/2013] [Indexed: 12/14/2022]
Abstract
Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers.
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Affiliation(s)
- Montserrat Garcia-Closas
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Fergus J Couch
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sara Lindstrom
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Mark N Brook
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Nick orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Suhn Kyong Rhie
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Elio Riboli
- School of Public Health, Imperial College, London, UK
| | | | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, Hawaii, USA
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Penelope Miron
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jane Carpenter
- Australian Breast Cancer Tissue Bank, University of Sydney at the Westmead Millennium Institute, Westmead, New South Wales, Australia
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
- School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Angela Cox
- Cancer Research UK/Yorkshire Cancer Research Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - John L Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ed Dicks
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Will J Howat
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Nils Schoof
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stig E Bojesen
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
- Department of Oncology, University of Leuven, Leuven, Belgium
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Irene L Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Ontario Cancer Genetics Network, Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Pascal Guénel
- University Paris–Sud, Unité Mixte de Recherche Scientifique (UMRS) 1018, Villejuif, France
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), Environmental Epidemiology of Cancer, Villejuif, France
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, DKFZ, Heidelberg, Germany
| | - Elinor J Sawyer
- Division of Cancer Studies, National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Guy’s & St. Thomas’ National Health Service (NHS) Foundation Trust in partnership with King’s College London, London, UK
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus University Medical Center–Daniel Den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics, Biocenter Oulu, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Arto Mannermaa
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, DKFZ, Heidelberg, Germany
| | - Alfons Meindl
- Division for Gynaecological Tumor Genetics, Clinic of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Wei Zheng
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Peter Devillee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Quebec, Canada
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
- Faculty of Medicine (Faculty Division Ahus), Universitetet i Oslo, Oslo, Norway
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California–Irvine, Irvine, California, USA
| | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Kenneth Muir
- Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Soo Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - William Blot
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- International Epidemiology Institute, Rockville, Maryland, USA
| | - Daehee Kang
- Seoul National University College of Medicine, Seoul, Korea
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | | | - Chen-Yang Shen
- Colleague of Public Health, China Medical University, Taichong, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel J Park
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Fleur Hammet
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer Stone
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Laura J Van’t Veer
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Emiel J Rutgers
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | | | | | | | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Michael G Schrauder
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Isabel dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Helen Warren
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Michael J Kerin
- Department of Surgery, Clinical Science Institute, University Hospital and National University of Ireland, Galway, Ireland
| | - Nicola Miller
- Department of Surgery, Clinical Science Institute, University Hospital and National University of Ireland, Galway, Ireland
| | - Federick Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Andreas Schneeweiss
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Christof Sohn
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Therese Truong
- University Paris–Sud, Unité Mixte de Recherche Scientifique (UMRS) 1018, Villejuif, France
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), Environmental Epidemiology of Cancer, Villejuif, France
| | | | - Pierre Kerbrat
- Centre Eugène Marquis, Department of Medical Oncology, Rennes, France
| | - Børge G Nordestgaard
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sune F Nielsen
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Roger L Milne
- Genetic & Molecular Epidemiology Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | | | - Heiko Müller
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, DKFZ, Heidelberg, Germany
| | | | - Peter Lichtner
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Magdalena Lochmann
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Christina Justenhoven
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn, Johanniter Krankenhaus, Bonn, Germany
| | | | - Taru A Muranen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Dario Greco
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Tuomas Heikkinen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Sara Margolin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Jaana M Hartikainen
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Rosemary Balleine
- Western Sydney Local Health District, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
- Nepean Blue Mountains Local Health District, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | | | - Chiu-Chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Patrick Neven
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Anne-Sophie Dieudonné
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Karin Leunen
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Nickels
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Paolo Peterlongo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS INT, Milan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
- Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Janet E Olson
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Xianshu Wang
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kristen Stevens
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Gianluca Severi
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Catriona Mclean
- Department of Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Gerhard A Coetzee
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Natalia V Bogdanova
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - France Labrèche
- Département de Médecine Sociale et Préventive, Département de Santé Environnementale et Santé au Travail, Université de Montréal, Montreal, Quebec, Canada
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Quebec City, Quebec, Canada
| | - Cheng Har Yip
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya, Kuala Lumpur, Malaysia
| | - Ching-Yu Cheng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Singapore Eye Research Institute, National University of Singapore, Singapore
| | - Martha Shrubsole
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jirong Long
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics, Biocenter Oulu, University of Oulu, Oulu University Hospital, Oulu, Finland
| | | | - Saila Kauppila
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Julia A knight
- Ontario Cancer Genetics Network, Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gord Glendon
- Ontario Cancer Genetics Network, Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine, Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Ontario, Canada
| | | | - Caroline M Seynaeve
- Department of Medical Oncology, Erasmus University Medical Center–Daniel Den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Mieke Kriege
- Department of Medical Oncology, Erasmus University Medical Center–Daniel Den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus University Medical Center–Daniel Den Hoed Cancer Center, Rotterdam, The Netherlands
| | | | | | - Wei Lu
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Hui Cai
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Sabapathy P Balasubramanian
- Cancer Research UK/Yorkshire Cancer Research Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Malcolm W R Reed
- Cancer Research UK/Yorkshire Cancer Research Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Lisa Signorello
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Qiuyin Cai
- Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Quebec, Canada
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hui Miao
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Ching Wan Chan
- Department of Surgery, National University Health System, Singapore
| | - Kee Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Ei Wu
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jyh-Cherng Yu
- Department of Surgery, Tri-Service General Hospital, Taipei, Taiwan
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Michael Jones
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Daniel C Tessier
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Anna González-Neira
- Human Genotyping Unit–CEGEN, Human Cancer Genetics Programme, CNIO, Madrid, Spain
| | - Guillermo Pita
- Human Genotyping Unit–CEGEN, Human Cancer Genetics Programme, CNIO, Madrid, Spain
| | - M Rosario Alonso
- Human Genotyping Unit–CEGEN, Human Cancer Genetics Programme, CNIO, Madrid, Spain
| | - Daniel Vincent
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Francois Bacot
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Elisa V Bandera
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, California, USA
- Department of Health Research and Policy, Division of Epidemiology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Gary K Chen
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
- Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jorge L Rodriguez-gil
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
- Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Robert M Millikan
- Department of Epidemiology, Gillings School of Global Public Health, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sandra L Deming-Halverson
- Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Quinten Waisfisz
- Section of Oncogenetics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Helen Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Enes Makalic
- School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Schmidt
- School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Minh Bui
- School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lorna Gibson
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Bertram Müller-Myhsok
- Statistical Genetics Research Group, Max Planck Institute of Psychiatry, Munich, Germany
| | - Rita K Schmutzler
- Centre of Hereditary Breast and Ovarian Cancer, University Hospital, Cologne, Germany
- Centre of Integrated Oncology, University Hospital, Cologne, Germany
| | - Rebecca Hein
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- PMV (Primärmedizinische Versorgung) Research Group, Department of Child and Adolescent Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Norbert Dahmen
- Department of Psychiatry, University of Mainz, Mainz, Germany
| | - Lars Beckmann
- Institute for Quality and Efficiency in Health Care (IQWiG), Cologne, Germany
| | - Kirsimari Aaltonen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Astrid Irwanto
- Human Genetics Division, Genome Institute of Singapore, Singapore
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Hanne Meijers-Heijboer
- Section of Oncogenetics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Andre G Uitterlinden
- Department of Internal Medicine and Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine and Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Curtis Olswold
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan Slager
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert Pilarski
- Department of Internal Medicine, James Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | | | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, Institute of Radioisotopes and Radiodiagnostic Products (IRRP), National Centre for Scientific Research Demokritos, Aghia Paraskevi Attikis, Athens, Greece
| | - Nicholas G Martin
- QIMR GWAS Collective, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Grant W Montgomery
- QIMR GWAS Collective, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Dennis J Slamon
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Medicine, Division of Hematology and Oncology, University of California, Los Angeles, Los Angeles, California, USA
| | - Claudia Rauh
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Michael P Lux
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Sebastian M Jud
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Erlangen, Germany
| | - Thomas Bruning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, Germany
| | - Joellen Weaver
- Biosample Repository, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Priyanka Sharma
- Division of Hematology and Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Will Tapper
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sue Gerty
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lorraine Durcan
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece
- Hellenic Health Foundation, Athens, Greece
| | - Rosario Tumino
- Cancer Registry, Histopathology Unit Civile MPArezzo Hospital, Ragusa, Italy
| | - Petra H Peeters
- Julius Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniele Campa
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federico Canzian
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisabete Weiderpass
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Community Medicine, University of Tromsø, Tromsø, Norway
- Cancer Registry of Norway, Oslo, Norway
| | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Ruth Travis
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Françoise Clavel-Chapelon
- University Paris–Sud, Unité Mixte de Recherche Scientifique (UMRS) 1018, Villejuif, France
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), Environmental Epidemiology of Cancer, Villejuif, France
| | - Laurence N Kolonel
- Département de Médecine Sociale et Préventive, Département de Santé Environnementale et Santé au Travail, Université de Montréal, Montreal, Quebec, Canada
| | - Constance Chen
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Andy Beck
- Department of Pathology, Beth Israel DeaconessMedical Center, Boston, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Susan E Hankinson
- Division of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Christine D Berg
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, USA
| | - Robert N Hoover
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jonine D Figueroa
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Mia M Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Walter C Willett
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - David J Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Quebec City, Quebec, Canada
| | - Javier Benitez
- Human Genotyping Unit–CEGEN, Human Cancer Genetics Programme, CNIO, Madrid, Spain
- Human Genetics Group, CNIO, Madrid, Spain
- Centro de Investigacion en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mark E Sherman
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Georgia Chenevix-Trench
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Stephen J Chanock
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Celine Vachon
- Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
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18
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Pope BJ, Nguyen-Dumont T, Odefrey F, Hammet F, Bell R, Tao K, Tavtigian SV, Goldgar DE, Lonie A, Southey MC, Park DJ. FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets. BMC Bioinformatics 2013; 14:65. [PMID: 23441864 PMCID: PMC3599469 DOI: 10.1186/1471-2105-14-65] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 12/05/2012] [Indexed: 11/12/2022] Open
Abstract
Background Characterising genetic diversity through the analysis of massively parallel sequencing (MPS) data offers enormous potential to significantly improve our understanding of the genetic basis for observed phenotypes, including predisposition to and progression of complex human disease. Great challenges remain in resolving genetic variants that are genuine from the millions of artefactual signals. Results FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of the issues related to the analysis of the vast amount of resulting data, with a focus on relatively rare genetic variants. To the best of our knowledge, no equivalent method has previously been described. The most important and novel aspect of FAVR is the use of signatures in comparator sequence alignment files during variant filtering, and annotation of variants potentially shared between individuals. The FAVR methods use these signatures to facilitate filtering of (i) platform and/or mapping-specific artefacts, (ii) common genetic variants, and, where relevant, (iii) artefacts derived from imbalanced paired-end sequencing, as well as annotation of genetic variants based on evidence of co-occurrence in individuals. We applied conventional variant calling applied to whole-exome sequencing datasets, produced using both SOLiD and TruSeq chemistries, with or without downstream processing by FAVR methods. We demonstrate a 3-fold smaller rare single nucleotide variant shortlist with no detected reduction in sensitivity. This analysis included Sanger sequencing of rare variant signals not evident in dbSNP131, assessment of known variant signal preservation, and comparison of observed and expected rare variant numbers across a range of first cousin pairs. The principles described herein were applied in our recent publication identifying XRCC2 as a new breast cancer risk gene and have been made publically available as a suite of software tools. Conclusions FAVR is a platform-agnostic suite of methods that significantly enhances the analysis of large volumes of sequencing data for the study of rare genetic variants and their influence on phenotypes.
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Affiliation(s)
- Bernard J Pope
- Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria 3010, Australia
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19
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Kirchhoff T, Gaudet MM, Antoniou AC, McGuffog L, Humphreys MK, Dunning AM, Bojesen SE, Nordestgaard BG, Flyger H, Kang D, Yoo KY, Noh DY, Ahn SH, Dork T, Schürmann P, Karstens JH, Hillemanns P, Couch FJ, Olson J, Vachon C, Wang X, Cox A, Brock I, Elliott G, Reed MW, Burwinkel B, Meindl A, Brauch H, Hamann U, Ko YD, Broeks A, Schmidt MK, Van ‘t Veer LJ, Braaf LM, Johnson N, Fletcher O, Gibson L, Peto J, Turnbull C, Seal S, Renwick A, Rahman N, Wu PE, Yu JC, Hsiung CN, Shen CY, Southey MC, Hopper JL, Hammet F, Van Dorpe T, Dieudonne AS, Hatse S, Lambrechts D, Andrulis IL, Bogdanova N, Antonenkova N, Rogov JI, Prokofieva D, Bermisheva M, Khusnutdinova E, van Asperen CJ, Tollenaar RA, Hooning MJ, Devilee P, Margolin S, Lindblom A, Milne RL, Arias JI, Zamora MP, Benítez J, Severi G, Baglietto L, Giles GG, kConFab, Group AOCSS, Spurdle AB, Beesley J, Chen X, Holland H, Healey S, Wang-Gohrke S, Chang-Claude J, Mannermaa A, Kosma VM, Kauppinen J, Kataja V, Agnarsson BA, Caligo MA, Godwin AK, Nevanlinna H, Heikkinen T, Fredericksen Z, Lindor N, Nathanson KL, Domchek SM, SWE-BRCA, Loman N, Karlsson P, Askmalm MS, Melin B, von Wachenfeldt A, HEBON, Hogervorst FBL, Verheus M, Rookus MA, Seynaeve C, Oldenburg RA, Ligtenberg MJ, Ausems MG, Aalfs CM, Gille HJ, Wijnen JT, Gómez García EB, EMBRACE, Peock S, Cook M, Oliver CT, Frost D, Luccarini C, Pichert G, Davidson R, Chu C, Eccles D, Ong KR, Cook J, Douglas F, Hodgson S, Evans DG, Eeles R, Gold B, Pharoah PD, Offit K, Chenevix-Trench G, Easton DF. Breast cancer risk and 6q22.33: combined results from Breast Cancer Association Consortium and Consortium of Investigators on Modifiers of BRCA1/2. PLoS One 2012; 7:e35706. [PMID: 22768030 PMCID: PMC3387216 DOI: 10.1371/journal.pone.0035706] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 03/20/2012] [Indexed: 11/19/2022] Open
Abstract
Recently, a locus on chromosome 6q22.33 (rs2180341) was reported to be associated with increased breast cancer risk in the Ashkenazi Jewish (AJ) population, and this association was also observed in populations of non-AJ European ancestry. In the present study, we performed a large replication analysis of rs2180341 using data from 31,428 invasive breast cancer cases and 34,700 controls collected from 25 studies in the Breast Cancer Association Consortium (BCAC). In addition, we evaluated whether rs2180341 modifies breast cancer risk in 3,361 BRCA1 and 2,020 BRCA2 carriers from 11 centers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Based on the BCAC data from women of European ancestry, we found evidence for a weak association with breast cancer risk for rs2180341 (per-allele odds ratio (OR) = 1.03, 95% CI 1.00-1.06, p = 0.023). There was evidence for heterogeneity in the ORs among studies (I(2) = 49.3%; p = <0.004). In CIMBA, we observed an inverse association with the minor allele of rs2180341 and breast cancer risk in BRCA1 mutation carriers (per-allele OR = 0.89, 95%CI 0.80-1.00, p = 0.048), indicating a potential protective effect of this allele. These data suggest that that 6q22.33 confers a weak effect on breast cancer risk.
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Affiliation(s)
- Tomas Kirchhoff
- Memorial Sloan-Kettering Cancer Center (MSKCC): Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America (TK, MG, KO); Department of Environmental Medicine, New York University Cancer Institute, New York University, New York, New York, United States of America (TK), American Cancer Society, Atlanta, Georgia, United States of America (MG)
| | - Mia M. Gaudet
- Memorial Sloan-Kettering Cancer Center (MSKCC): Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America (TK, MG, KO); Department of Environmental Medicine, New York University Cancer Institute, New York University, New York, New York, United States of America (TK), American Cancer Society, Atlanta, Georgia, United States of America (MG)
| | - Antonis C. Antoniou
- Studies of Epidemiology and Risk Factors in Cancer Heredity (SEARCH): Department of Oncology and Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (ACA, LM, MKH, AMD, PDPP, DFE)
| | - Lesley McGuffog
- Studies of Epidemiology and Risk Factors in Cancer Heredity (SEARCH): Department of Oncology and Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (ACA, LM, MKH, AMD, PDPP, DFE)
| | - Manjeet K. Humphreys
- Studies of Epidemiology and Risk Factors in Cancer Heredity (SEARCH): Department of Oncology and Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (ACA, LM, MKH, AMD, PDPP, DFE)
| | - Alison M. Dunning
- Studies of Epidemiology and Risk Factors in Cancer Heredity (SEARCH): Department of Oncology and Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (ACA, LM, MKH, AMD, PDPP, DFE)
| | - Stig E. Bojesen
- The Copenhagen Breast Cancer Study and The Copenhagen General Population Study (CGPS): Department of Clinical Biochemistry (SEB, BGN); Department of Breast Surgery, Herlev Hospital (HF), Copenhagen University Hospital, University of Copenhagen, Denmark
| | - Børge G. Nordestgaard
- The Copenhagen Breast Cancer Study and The Copenhagen General Population Study (CGPS): Department of Clinical Biochemistry (SEB, BGN); Department of Breast Surgery, Herlev Hospital (HF), Copenhagen University Hospital, University of Copenhagen, Denmark
| | - Henrik Flyger
- The Copenhagen Breast Cancer Study and The Copenhagen General Population Study (CGPS): Department of Clinical Biochemistry (SEB, BGN); Department of Breast Surgery, Herlev Hospital (HF), Copenhagen University Hospital, University of Copenhagen, Denmark
| | - Daehee Kang
- Seoul Breast Cancer Study (SEBCS): Seoul National University College of Medicine and National Cancer Center, Seoul, Korea; Department of Surgery, Ulsan University College of Medicine, Ulsan, Korea (DK, KYY, DYN, SHA)
| | - Keun-Young Yoo
- Seoul Breast Cancer Study (SEBCS): Seoul National University College of Medicine and National Cancer Center, Seoul, Korea; Department of Surgery, Ulsan University College of Medicine, Ulsan, Korea (DK, KYY, DYN, SHA)
| | - Dong-Young Noh
- Seoul Breast Cancer Study (SEBCS): Seoul National University College of Medicine and National Cancer Center, Seoul, Korea; Department of Surgery, Ulsan University College of Medicine, Ulsan, Korea (DK, KYY, DYN, SHA)
| | - Sei-Hyun Ahn
- Seoul Breast Cancer Study (SEBCS): Seoul National University College of Medicine and National Cancer Center, Seoul, Korea; Department of Surgery, Ulsan University College of Medicine, Ulsan, Korea (DK, KYY, DYN, SHA)
| | - Thilo Dork
- Hannover Breast Cancer Study (HABCS): Clinics of Obstetrics and Gynecology and Clinic of Radiation Oncology, Hannover Medical School, Hannover, Germany (TD, PS, JHK, PH)
| | - Peter Schürmann
- Hannover Breast Cancer Study (HABCS): Clinics of Obstetrics and Gynecology and Clinic of Radiation Oncology, Hannover Medical School, Hannover, Germany (TD, PS, JHK, PH)
| | - Johann H. Karstens
- Hannover Breast Cancer Study (HABCS): Clinics of Obstetrics and Gynecology and Clinic of Radiation Oncology, Hannover Medical School, Hannover, Germany (TD, PS, JHK, PH)
| | - Peter Hillemanns
- Hannover Breast Cancer Study (HABCS): Clinics of Obstetrics and Gynecology and Clinic of Radiation Oncology, Hannover Medical School, Hannover, Germany (TD, PS, JHK, PH)
| | - Fergus J. Couch
- Mayo Clinic Breast Cancer Study (MCBCS): Mayo Clinic, Rochester, Minnesota, United States of America (FJC, JO, CV, XW)
- Mayo Clinic Familial Breast and Ovarian Cancer Study (MAYO), Mayo Clinic, Rochester, Minnesota, United States of America (FJC, ZF, NL)
| | - Janet Olson
- Mayo Clinic Breast Cancer Study (MCBCS): Mayo Clinic, Rochester, Minnesota, United States of America (FJC, JO, CV, XW)
| | - Celine Vachon
- Mayo Clinic Breast Cancer Study (MCBCS): Mayo Clinic, Rochester, Minnesota, United States of America (FJC, JO, CV, XW)
| | - Xianshu Wang
- Mayo Clinic Breast Cancer Study (MCBCS): Mayo Clinic, Rochester, Minnesota, United States of America (FJC, JO, CV, XW)
| | - Angela Cox
- Sheffield Breast Cancer Study (SBCS): Department of Oncology, Sheffield University Medical School, Sheffield, United Kingdom (AC, IB, GE, MWRR)
| | - Ian Brock
- Sheffield Breast Cancer Study (SBCS): Department of Oncology, Sheffield University Medical School, Sheffield, United Kingdom (AC, IB, GE, MWRR)
| | - Graeme Elliott
- Sheffield Breast Cancer Study (SBCS): Department of Oncology, Sheffield University Medical School, Sheffield, United Kingdom (AC, IB, GE, MWRR)
| | - Malcolm W.R. Reed
- Sheffield Breast Cancer Study (SBCS): Department of Oncology, Sheffield University Medical School, Sheffield, United Kingdom (AC, IB, GE, MWRR)
| | - Barbara Burwinkel
- German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC): Institute of Human Genetics, German Cancer Research Center, Heidelberg, Germany (BB); Department of Obstetrics and Gynecology, Division of Tumor Genetics, Technical University of Munich, Munich, Germany (AM)
| | - Alfons Meindl
- German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC): Institute of Human Genetics, German Cancer Research Center, Heidelberg, Germany (BB); Department of Obstetrics and Gynecology, Division of Tumor Genetics, Technical University of Munich, Munich, Germany (AM)
| | - Hiltrud Brauch
- Gene Environment Interaction and Breast Cancer in Germany (GENICA): Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University Tübingen, Stuttgart and Tübingen, Germany (HB, Christina Justenhoven); Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany (UH); Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany (YDK,); Institute of Pathology, Medical Faculty of the University of Bonn, Bonn, Germany (Hans-Peter Fischer); Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Bochum, Germany (Thomas Brüning, Beate Pesch, Volker Harth, Sylvia Rabstein)
| | - Ute Hamann
- Gene Environment Interaction and Breast Cancer in Germany (GENICA): Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University Tübingen, Stuttgart and Tübingen, Germany (HB, Christina Justenhoven); Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany (UH); Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany (YDK,); Institute of Pathology, Medical Faculty of the University of Bonn, Bonn, Germany (Hans-Peter Fischer); Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Bochum, Germany (Thomas Brüning, Beate Pesch, Volker Harth, Sylvia Rabstein)
| | - Yon-Dschun Ko
- Gene Environment Interaction and Breast Cancer in Germany (GENICA): Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University Tübingen, Stuttgart and Tübingen, Germany (HB, Christina Justenhoven); Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany (UH); Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany (YDK,); Institute of Pathology, Medical Faculty of the University of Bonn, Bonn, Germany (Hans-Peter Fischer); Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Bochum, Germany (Thomas Brüning, Beate Pesch, Volker Harth, Sylvia Rabstein)
| | - GENICA Network
- Gene Environment Interaction and Breast Cancer in Germany (GENICA): Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University Tübingen, Stuttgart and Tübingen, Germany (HB, Christina Justenhoven); Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany (UH); Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany (YDK,); Institute of Pathology, Medical Faculty of the University of Bonn, Bonn, Germany (Hans-Peter Fischer); Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Bochum, Germany (Thomas Brüning, Beate Pesch, Volker Harth, Sylvia Rabstein)
| | - Annegien Broeks
- Amsterdam Breast Cancer Study (ABCS): Netherlands Cancer Institute, Departments of Experimental Therapy, Epidemiology and Molecular Pathology, Amsterdam, The Netherlands (AB, MKS, LJVV, LMB)
| | - Marjanka K. Schmidt
- Amsterdam Breast Cancer Study (ABCS): Netherlands Cancer Institute, Departments of Experimental Therapy, Epidemiology and Molecular Pathology, Amsterdam, The Netherlands (AB, MKS, LJVV, LMB)
| | - Laura J. Van ‘t Veer
- Amsterdam Breast Cancer Study (ABCS): Netherlands Cancer Institute, Departments of Experimental Therapy, Epidemiology and Molecular Pathology, Amsterdam, The Netherlands (AB, MKS, LJVV, LMB)
| | - Linde M. Braaf
- Amsterdam Breast Cancer Study (ABCS): Netherlands Cancer Institute, Departments of Experimental Therapy, Epidemiology and Molecular Pathology, Amsterdam, The Netherlands (AB, MKS, LJVV, LMB)
| | - Nichola Johnson
- British Breast Cancer Study (BBCS): Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom (NJ, OF); Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom (LG, JP)
| | - Olivia Fletcher
- British Breast Cancer Study (BBCS): Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom (NJ, OF); Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom (LG, JP)
| | - Lorna Gibson
- British Breast Cancer Study (BBCS): Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom (NJ, OF); Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom (LG, JP)
| | - Julian Peto
- British Breast Cancer Study (BBCS): Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom (NJ, OF); Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom (LG, JP)
| | - Clare Turnbull
- ICR Familial Breast Cancer Study (FBCS): Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, United Kingdom (CT, SS, AR, NR)
| | - Sheila Seal
- ICR Familial Breast Cancer Study (FBCS): Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, United Kingdom (CT, SS, AR, NR)
| | - Anthony Renwick
- ICR Familial Breast Cancer Study (FBCS): Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, United Kingdom (CT, SS, AR, NR)
| | - Nazneen Rahman
- ICR Familial Breast Cancer Study (FBCS): Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, United Kingdom (CT, SS, AR, NR)
| | - Pei-Ei Wu
- Taiwanese Breast Cancer Study (TWBCS): Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (CNH, CYS); Taiwan Biobank, Academia Sinica, Taiwan (PEW); Departments of Surgery, Tri-Service General Hospital, Taipei, Taiwan (JCY)
| | - Jyh-Cherng Yu
- Taiwanese Breast Cancer Study (TWBCS): Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (CNH, CYS); Taiwan Biobank, Academia Sinica, Taiwan (PEW); Departments of Surgery, Tri-Service General Hospital, Taipei, Taiwan (JCY)
| | - Chia-Ni Hsiung
- Taiwanese Breast Cancer Study (TWBCS): Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (CNH, CYS); Taiwan Biobank, Academia Sinica, Taiwan (PEW); Departments of Surgery, Tri-Service General Hospital, Taipei, Taiwan (JCY)
| | - Chen-Yang Shen
- Taiwanese Breast Cancer Study (TWBCS): Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (CNH, CYS); Taiwan Biobank, Academia Sinica, Taiwan (PEW); Departments of Surgery, Tri-Service General Hospital, Taipei, Taiwan (JCY)
| | - Melissa C. Southey
- Australian Breast Cancer Family Study (ABCFS): Genetic Epidemiology Laboratory, Department of Pathology (MCS, FH), Centre for Molecular Environmental Genetic and Analytic Epidemiology (JLH), The University of Melbourne, Victoria, Australia
- Melbourne Collaborative Cohort Study (MCCS): Cancer Epidemiology Centre, The Cancer Council, Victoria, Melbourne, Australia and Centre for Molecular Environmental, Genetic, and Analytic Epidemiology, School of Population Health, The University of Melbourne, Australia (GGG, MCS, GS, LB)
| | - John L. Hopper
- Australian Breast Cancer Family Study (ABCFS): Genetic Epidemiology Laboratory, Department of Pathology (MCS, FH), Centre for Molecular Environmental Genetic and Analytic Epidemiology (JLH), The University of Melbourne, Victoria, Australia
| | - Fleur Hammet
- Australian Breast Cancer Family Study (ABCFS): Genetic Epidemiology Laboratory, Department of Pathology (MCS, FH), Centre for Molecular Environmental Genetic and Analytic Epidemiology (JLH), The University of Melbourne, Victoria, Australia
| | - Thijs Van Dorpe
- Leuven Multidisciplinary Breast Centre (LMBC): Katholieke Universiteit Leuven–Multidisciplinary Breast Clinic (TVD, ASD, SH), Vesalius Research Center (DL), Leuven, Belgium
| | - Anne-Sophie Dieudonne
- Leuven Multidisciplinary Breast Centre (LMBC): Katholieke Universiteit Leuven–Multidisciplinary Breast Clinic (TVD, ASD, SH), Vesalius Research Center (DL), Leuven, Belgium
| | - Sigrid Hatse
- Leuven Multidisciplinary Breast Centre (LMBC): Katholieke Universiteit Leuven–Multidisciplinary Breast Clinic (TVD, ASD, SH), Vesalius Research Center (DL), Leuven, Belgium
| | - Diether Lambrechts
- Leuven Multidisciplinary Breast Centre (LMBC): Katholieke Universiteit Leuven–Multidisciplinary Breast Clinic (TVD, ASD, SH), Vesalius Research Center (DL), Leuven, Belgium
| | - Irene L. Andrulis
- Ontario Familial Breast Cancer Registry (OFBCR): Ontario Cancer Genetics Network, Cancer Care Ontario, Ontario, Canada; Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada (ILA)
| | - Natalia Bogdanova
- Hannover-Minsk Breast Cancer Study (HMBCS): N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus (NB, NA, JIR)
| | - Natalia Antonenkova
- Hannover-Minsk Breast Cancer Study (HMBCS): N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus (NB, NA, JIR)
| | - Juri I. Rogov
- Hannover-Minsk Breast Cancer Study (HMBCS): N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus (NB, NA, JIR)
| | - Daria Prokofieva
- Hannover-Ufa Breast Cancer Study (HUBCS): Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia (DP, MB, EK)
| | - Marina Bermisheva
- Hannover-Ufa Breast Cancer Study (HUBCS): Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia (DP, MB, EK)
| | - Elza Khusnutdinova
- Hannover-Ufa Breast Cancer Study (HUBCS): Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia (DP, MB, EK)
| | - Christi J. van Asperen
- Leiden University Medical Center Breast Cancer Study (ORIGO): Department of Medical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands (MJH); Departments of Surgical Oncology (RAEMT), Clinical Genetics (CJVA), Human Genetics and Pathology (PD), Leiden University Medical Center, Leiden, The Netherlands
| | - Robert A.E.M. Tollenaar
- Leiden University Medical Center Breast Cancer Study (ORIGO): Department of Medical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands (MJH); Departments of Surgical Oncology (RAEMT), Clinical Genetics (CJVA), Human Genetics and Pathology (PD), Leiden University Medical Center, Leiden, The Netherlands
| | - Maartje J. Hooning
- Leiden University Medical Center Breast Cancer Study (ORIGO): Department of Medical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands (MJH); Departments of Surgical Oncology (RAEMT), Clinical Genetics (CJVA), Human Genetics and Pathology (PD), Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Devilee
- Leiden University Medical Center Breast Cancer Study (ORIGO): Department of Medical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands (MJH); Departments of Surgical Oncology (RAEMT), Clinical Genetics (CJVA), Human Genetics and Pathology (PD), Leiden University Medical Center, Leiden, The Netherlands
| | - Sara Margolin
- Karolinska Breast Cancer Study (KARBAC): Department of Molecular Medicine and Surgery (AL) and Department of Oncology-Pathology, Karolinska Institutet and Karolinska University, Stockholm, Sweden (SM)
| | - Annika Lindblom
- Karolinska Breast Cancer Study (KARBAC): Department of Molecular Medicine and Surgery (AL) and Department of Oncology-Pathology, Karolinska Institutet and Karolinska University, Stockholm, Sweden (SM)
| | - Roger L. Milne
- Spanish National Cancer Center Breast Cancer Study (CNIO-BCS): Genetic and Molecular Epidemiology Group (RLM) and Human Genetics Group (JB), Spanish National Cancer Centre, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain (JB); Monte Naranco Hospital, Oviedo, Spain (JIA); La Paz University Hospital, Madrid, Spain (MPZ)
| | - José Ignacio Arias
- Spanish National Cancer Center Breast Cancer Study (CNIO-BCS): Genetic and Molecular Epidemiology Group (RLM) and Human Genetics Group (JB), Spanish National Cancer Centre, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain (JB); Monte Naranco Hospital, Oviedo, Spain (JIA); La Paz University Hospital, Madrid, Spain (MPZ)
| | - M. Pilar Zamora
- Spanish National Cancer Center Breast Cancer Study (CNIO-BCS): Genetic and Molecular Epidemiology Group (RLM) and Human Genetics Group (JB), Spanish National Cancer Centre, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain (JB); Monte Naranco Hospital, Oviedo, Spain (JIA); La Paz University Hospital, Madrid, Spain (MPZ)
| | - Javier Benítez
- Spanish National Cancer Center Breast Cancer Study (CNIO-BCS): Genetic and Molecular Epidemiology Group (RLM) and Human Genetics Group (JB), Spanish National Cancer Centre, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain (JB); Monte Naranco Hospital, Oviedo, Spain (JIA); La Paz University Hospital, Madrid, Spain (MPZ)
| | - Gianluca Severi
- Melbourne Collaborative Cohort Study (MCCS): Cancer Epidemiology Centre, The Cancer Council, Victoria, Melbourne, Australia and Centre for Molecular Environmental, Genetic, and Analytic Epidemiology, School of Population Health, The University of Melbourne, Australia (GGG, MCS, GS, LB)
| | - Laura Baglietto
- Melbourne Collaborative Cohort Study (MCCS): Cancer Epidemiology Centre, The Cancer Council, Victoria, Melbourne, Australia and Centre for Molecular Environmental, Genetic, and Analytic Epidemiology, School of Population Health, The University of Melbourne, Australia (GGG, MCS, GS, LB)
| | - Graham G. Giles
- Melbourne Collaborative Cohort Study (MCCS): Cancer Epidemiology Centre, The Cancer Council, Victoria, Melbourne, Australia and Centre for Molecular Environmental, Genetic, and Analytic Epidemiology, School of Population Health, The University of Melbourne, Australia (GGG, MCS, GS, LB)
| | - kConFab
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFaB): Queensland Institute of Medical Research, Brisbane, and the Australian Ovarian Cancer Study Group, Peter MacCallum Cancer Center, Melbourne, Australia (ABS, JB, XC, HH, SH, GCT)
| | - AOCS Study Group
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFaB): Queensland Institute of Medical Research, Brisbane, and the Australian Ovarian Cancer Study Group, Peter MacCallum Cancer Center, Melbourne, Australia (ABS, JB, XC, HH, SH, GCT)
| | - Amanda B. Spurdle
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFaB): Queensland Institute of Medical Research, Brisbane, and the Australian Ovarian Cancer Study Group, Peter MacCallum Cancer Center, Melbourne, Australia (ABS, JB, XC, HH, SH, GCT)
| | - Jonathan Beesley
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFaB): Queensland Institute of Medical Research, Brisbane, and the Australian Ovarian Cancer Study Group, Peter MacCallum Cancer Center, Melbourne, Australia (ABS, JB, XC, HH, SH, GCT)
| | - Xiaoqing Chen
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFaB): Queensland Institute of Medical Research, Brisbane, and the Australian Ovarian Cancer Study Group, Peter MacCallum Cancer Center, Melbourne, Australia (ABS, JB, XC, HH, SH, GCT)
| | - Helene Holland
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFaB): Queensland Institute of Medical Research, Brisbane, and the Australian Ovarian Cancer Study Group, Peter MacCallum Cancer Center, Melbourne, Australia (ABS, JB, XC, HH, SH, GCT)
| | - Sue Healey
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFaB): Queensland Institute of Medical Research, Brisbane, and the Australian Ovarian Cancer Study Group, Peter MacCallum Cancer Center, Melbourne, Australia (ABS, JB, XC, HH, SH, GCT)
| | - Shan Wang-Gohrke
- Genetic Epidemiology Study of Breast Cancer by Age 50 (GESBC): Division of Cancer Epidemiology, German Cancer Research Center [DFKZ], Heidelberg, Germany (JC-C), and Molecular Biology Laboratory, Department of Gynecology and Obstetrics, University of Ulm, Ulm, Germany (SW-G)
| | - Jenny Chang-Claude
- Genetic Epidemiology Study of Breast Cancer by Age 50 (GESBC): Division of Cancer Epidemiology, German Cancer Research Center [DFKZ], Heidelberg, Germany (JC-C), and Molecular Biology Laboratory, Department of Gynecology and Obstetrics, University of Ulm, Ulm, Germany (SW-G)
| | - Arto Mannermaa
- Kuopio Breast Cancer Project (KBCP): Institute of Clinical Medicine, Department of Pathology, University of Eastern Finland, and Kuopio University Hospital, Biocenter Kuopio, Kuopio Finland (AM, VMK, JK); Department of Oncology, Vaasa Central Hospital, Vaasa, Finland, and Department of Oncology, Kuopio University Hospital, Kuopio, Finland (VK)
| | - Veli-Matti Kosma
- Kuopio Breast Cancer Project (KBCP): Institute of Clinical Medicine, Department of Pathology, University of Eastern Finland, and Kuopio University Hospital, Biocenter Kuopio, Kuopio Finland (AM, VMK, JK); Department of Oncology, Vaasa Central Hospital, Vaasa, Finland, and Department of Oncology, Kuopio University Hospital, Kuopio, Finland (VK)
| | - Jaana Kauppinen
- Kuopio Breast Cancer Project (KBCP): Institute of Clinical Medicine, Department of Pathology, University of Eastern Finland, and Kuopio University Hospital, Biocenter Kuopio, Kuopio Finland (AM, VMK, JK); Department of Oncology, Vaasa Central Hospital, Vaasa, Finland, and Department of Oncology, Kuopio University Hospital, Kuopio, Finland (VK)
| | - Vesa Kataja
- Kuopio Breast Cancer Project (KBCP): Institute of Clinical Medicine, Department of Pathology, University of Eastern Finland, and Kuopio University Hospital, Biocenter Kuopio, Kuopio Finland (AM, VMK, JK); Department of Oncology, Vaasa Central Hospital, Vaasa, Finland, and Department of Oncology, Kuopio University Hospital, Kuopio, Finland (VK)
| | - Bjarni A. Agnarsson
- Iceland Landspitali–University Hospital (ILUH): Department of Pathology, Landspitali-University Hospital and University of Iceland School of Medicine, Reykjavik, Iceland (BAA)
| | - Maria A. Caligo
- Division of Surgical, Molecular and Ultrastructural Pathology, Department of Oncology University of Pisa and Pisa University Hospital, Pisa, Italy (MAC)
| | - Andrew K. Godwin
- Fox Chase Cancer Center (FCCC): Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America (AKG)
| | - Heli Nevanlinna
- Helsinki Breast Cancer Study (HEBCS): Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland (HN, TH)
| | - Tuomas Heikkinen
- Helsinki Breast Cancer Study (HEBCS): Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland (HN, TH)
| | - Zachary Fredericksen
- Mayo Clinic Familial Breast and Ovarian Cancer Study (MAYO), Mayo Clinic, Rochester, Minnesota, United States of America (FJC, ZF, NL)
| | - Noralane Lindor
- Mayo Clinic Familial Breast and Ovarian Cancer Study (MAYO), Mayo Clinic, Rochester, Minnesota, United States of America (FJC, ZF, NL)
| | - Katherine L. Nathanson
- The University of Pennsylvania (UPENN): Department of Medicine and Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America (KLN, SMD)
| | - Susan M. Domchek
- The University of Pennsylvania (UPENN): Department of Medicine and Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America (KLN, SMD)
| | - SWE-BRCA
- The Swedish BRCA1 and BRCA2 study collaborators (SWE-BRCA): Department of Oncology, Lund University Hospital, Lund, Sweden (NL); Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden (PK); Department of Oncology, University Hospital, Linköping, Sweden (MSA); Department of Radiation Sciences, Oncology, Umeå University, Umeå Sweden (BM); Department of Oncology, Karolinska University Hospital, Stockholm, Sweden (AVW)
| | - Niklas Loman
- The Swedish BRCA1 and BRCA2 study collaborators (SWE-BRCA): Department of Oncology, Lund University Hospital, Lund, Sweden (NL); Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden (PK); Department of Oncology, University Hospital, Linköping, Sweden (MSA); Department of Radiation Sciences, Oncology, Umeå University, Umeå Sweden (BM); Department of Oncology, Karolinska University Hospital, Stockholm, Sweden (AVW)
| | - Per Karlsson
- The Swedish BRCA1 and BRCA2 study collaborators (SWE-BRCA): Department of Oncology, Lund University Hospital, Lund, Sweden (NL); Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden (PK); Department of Oncology, University Hospital, Linköping, Sweden (MSA); Department of Radiation Sciences, Oncology, Umeå University, Umeå Sweden (BM); Department of Oncology, Karolinska University Hospital, Stockholm, Sweden (AVW)
| | - Marie Stenmark Askmalm
- The Swedish BRCA1 and BRCA2 study collaborators (SWE-BRCA): Department of Oncology, Lund University Hospital, Lund, Sweden (NL); Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden (PK); Department of Oncology, University Hospital, Linköping, Sweden (MSA); Department of Radiation Sciences, Oncology, Umeå University, Umeå Sweden (BM); Department of Oncology, Karolinska University Hospital, Stockholm, Sweden (AVW)
| | - Beatrice Melin
- The Swedish BRCA1 and BRCA2 study collaborators (SWE-BRCA): Department of Oncology, Lund University Hospital, Lund, Sweden (NL); Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden (PK); Department of Oncology, University Hospital, Linköping, Sweden (MSA); Department of Radiation Sciences, Oncology, Umeå University, Umeå Sweden (BM); Department of Oncology, Karolinska University Hospital, Stockholm, Sweden (AVW)
| | - Anna von Wachenfeldt
- The Swedish BRCA1 and BRCA2 study collaborators (SWE-BRCA): Department of Oncology, Lund University Hospital, Lund, Sweden (NL); Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden (PK); Department of Oncology, University Hospital, Linköping, Sweden (MSA); Department of Radiation Sciences, Oncology, Umeå University, Umeå Sweden (BM); Department of Oncology, Karolinska University Hospital, Stockholm, Sweden (AVW)
| | - HEBON
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Frans B. L. Hogervorst
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Martijn Verheus
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Matti A. Rookus
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Caroline Seynaeve
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Rogier A. Oldenburg
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Marjolijn J. Ligtenberg
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Margreet G.E.M. Ausems
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Cora M. Aalfs
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Hans J.P. Gille
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Juul T. Wijnen
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - Encarna B. Gómez García
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON): Coordinating Center: Netherlands Cancer Institute, Amsterdam, The Netherlands (FBLH, MV, MAR); Erasmus Medical Center, Rotterdam, The Netherlands (CS, RAO); Leiden University Medical Center, Leiden, The Netherlands (JTW); Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands (MJL); University Medical Center Utrecht, Utrecht, The Netherlands (MGA); Amsterdam Medical Center, Amsterdam, The Netherlands (CMA); Vrije Universiteit University Medical Center, Amsterdam, The Netherlands (HJPG); University Hospital Maastricht, Maastricht, The Netherlands (EBG)
| | - EMBRACE
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Susan Peock
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Margaret Cook
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Clare T. Oliver
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Debra Frost
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Craig Luccarini
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Gabriella Pichert
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Rosemarie Davidson
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Carol Chu
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Diana Eccles
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Kai-Ren Ong
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Jackie Cook
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Fiona Douglas
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Shirley Hodgson
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - D. Gareth Evans
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Rosalind Eeles
- Epidemiological study of BRCA1 and BRCA2 mutation carriers (EMBRACE): Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (SP, MC, CTO, DF, CL); Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester, United Kingdom (DGE); Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom (RE); Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom (GP); Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, United Kingdom (RD); Yorkshire Regional Genetics Service, Leeds, United Kingdom (CC); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (DE); West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, United Kingdom (KRO); Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, United Kingdom (JC); Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, United Kingdom (FD); Clinical Genetics Department, St Georges Hospital, University of London, London, United Kingdom (SH)
| | - Bert Gold
- National Cancer Institute (NCI): Clinical Genetics Branch, National Cancer Institute, Rockville, Maryland, United States of America (BG)
| | - Paul D.P. Pharoah
- Studies of Epidemiology and Risk Factors in Cancer Heredity (SEARCH): Department of Oncology and Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (ACA, LM, MKH, AMD, PDPP, DFE)
| | - Kenneth Offit
- Memorial Sloan-Kettering Cancer Center (MSKCC): Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America (TK, MG, KO); Department of Environmental Medicine, New York University Cancer Institute, New York University, New York, New York, United States of America (TK), American Cancer Society, Atlanta, Georgia, United States of America (MG)
| | - Georgia Chenevix-Trench
- Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFaB): Queensland Institute of Medical Research, Brisbane, and the Australian Ovarian Cancer Study Group, Peter MacCallum Cancer Center, Melbourne, Australia (ABS, JB, XC, HH, SH, GCT)
| | - Douglas F. Easton
- Studies of Epidemiology and Risk Factors in Cancer Heredity (SEARCH): Department of Oncology and Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom (ACA, LM, MKH, AMD, PDPP, DFE)
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Teo ZL, Park DJ, Odefrey F, Hammet F, Nguyen-Dumont T, Tsimiklis H, Pope BJ, Lonie A, Winship I, Giles GG, Hopper JL, Southey MC. Expanded genetic analysis of a PALB2 c.3113G>A mutation carrying multiple-case breast cancer family via exome sequencing. Hered Cancer Clin Pract 2012. [PMCID: PMC3327032 DOI: 10.1186/1897-4287-10-s2-a92] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Blanc R, Jammot A, Nguyen-Dumont T, Teo ZL, Odefrey FA, Hammet F, Goldgar DE, Park DJ, Southey MC. Early exploration of two candidate breast cancer susceptibility genes identified by whole-exome sequencing. Hered Cancer Clin Pract 2012. [PMCID: PMC3327170 DOI: 10.1186/1897-4287-10-s2-a91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Southey MC, Park DJ, Lesueur F, Odefrey F, Nguyen-Dumont T, Hammet F, Neuhausen SL, John EM, Andrulis IL, Chenevix-Trench G, Baglietto L, Le Calvez-Kelm F, Pertesi M, Lonie A, Pope B, Sinilnikova O, Tsimiklis H, Giles GG, Hopper JL, Tavtigian SV, Goldgar DE. Identification of new breast cancer predisposition genes via whole exome sequencing. Hered Cancer Clin Pract 2012. [PMCID: PMC3327171 DOI: 10.1186/1897-4287-10-s2-a40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Figueroa JD, Garcia-Closas M, Humphreys M, Platte R, Hopper JL, Southey MC, Apicella C, Hammet F, Schmidt MK, Broeks A, Tollenaar RAEM, Van't Veer LJ, Fasching PA, Beckmann MW, Ekici AB, Strick R, Peto J, dos Santos Silva I, Fletcher O, Johnson N, Sawyer E, Tomlinson I, Kerin M, Burwinkel B, Marme F, Schneeweiss A, Sohn C, Bojesen S, Flyger H, Nordestgaard BG, Benítez J, Milne RL, Ignacio Arias J, Zamora MP, Brenner H, Müller H, Arndt V, Rahman N, Turnbull C, Seal S, Renwick A, Brauch H, Justenhoven C, Brüning T, Chang-Claude J, Hein R, Wang-Gohrke S, Dörk T, Schürmann P, Bremer M, Hillemanns P, Nevanlinna H, Heikkinen T, Aittomäki K, Blomqvist C, Bogdanova N, Antonenkova N, Rogov YI, Karstens JH, Bermisheva M, Prokofieva D, Gantcev SH, Khusnutdinova E, Lindblom A, Margolin S, Chenevix-Trench G, Beesley J, Chen X, Mannermaa A, Kosma VM, Soini Y, Kataja V, Lambrechts D, Yesilyurt BT, Chrisiaens MR, Peeters S, Radice P, Peterlongo P, Manoukian S, Barile M, Couch F, Lee AM, Diasio R, Wang X, Giles GG, Severi G, Baglietto L, Maclean C, Offit K, Robson M, Joseph V, Gaudet M, John EM, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Grip M, Andrulis I, Knight JA, Mulligan AM, O'Malley FP, Brinton LA, Sherman ME, Lissowska J, Chanock SJ, Hooning M, Martens JWM, van den Ouweland AMW, Collée JM, Hall P, Czene K, Cox A, Brock IW, Reed MWR, Cross SS, Pharoah P, Dunning AM, Kang D, Yoo KY, Noh DY, Ahn SH, Jakubowska A, Lubinski J, Jaworska K, Durda K, Sangrajrang S, Gaborieau V, Brennan P, McKay J, Shen CY, Ding SL, Hsu HM, Yu JC, Anton-Culver H, Ziogas A, Ashworth A, Swerdlow A, Jones M, Orr N, Trentham-Dietz A, Egan K, Newcomb P, Titus-Ernstoff L, Easton D, Spurdle AB. Associations of common variants at 1p11.2 and 14q24.1 (RAD51L1) with breast cancer risk and heterogeneity by tumor subtype: findings from the Breast Cancer Association Consortium. Hum Mol Genet 2011; 20:4693-706. [PMID: 21852249 PMCID: PMC3209823 DOI: 10.1093/hmg/ddr368] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 07/06/2011] [Accepted: 08/15/2011] [Indexed: 12/14/2022] Open
Abstract
A genome-wide association study (GWAS) identified single-nucleotide polymorphisms (SNPs) at 1p11.2 and 14q24.1 (RAD51L1) as breast cancer susceptibility loci. The initial GWAS suggested stronger effects for both loci for estrogen receptor (ER)-positive tumors. Using data from the Breast Cancer Association Consortium (BCAC), we sought to determine whether risks differ by ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), grade, node status, tumor size, and ductal or lobular morphology. We genotyped rs11249433 at 1p.11.2, and two highly correlated SNPs rs999737 and rs10483813 (r(2)= 0.98) at 14q24.1 (RAD51L1), for up to 46 036 invasive breast cancer cases and 46 930 controls from 39 studies. Analyses by tumor characteristics focused on subjects reporting to be white women of European ancestry and were based on 25 458 cases, of which 87% had ER data. The SNP at 1p11.2 showed significantly stronger associations with ER-positive tumors [per-allele odds ratio (OR) for ER-positive tumors was 1.13, 95% CI = 1.10-1.16 and, for ER-negative tumors, OR was 1.03, 95% CI = 0.98-1.07, case-only P-heterogeneity = 7.6 × 10(-5)]. The association with ER-positive tumors was stronger for tumors of lower grade (case-only P= 6.7 × 10(-3)) and lobular histology (case-only P= 0.01). SNPs at 14q24.1 were associated with risk for most tumor subtypes evaluated, including triple-negative breast cancers, which has not been described previously. Our results underscore the need for large pooling efforts with tumor pathology data to help refine risk estimates for SNP associations with susceptibility to different subtypes of breast cancer.
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Affiliation(s)
- Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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Broeks A, Schmidt MK, Sherman ME, Couch FJ, Hopper JL, Dite GS, Apicella C, Smith LD, Hammet F, Southey MC, Van 't Veer LJ, de Groot R, Smit VTHBM, Fasching PA, Beckmann MW, Jud S, Ekici AB, Hartmann A, Hein A, Schulz-Wendtland R, Burwinkel B, Marme F, Schneeweiss A, Sinn HP, Sohn C, Tchatchou S, Bojesen SE, Nordestgaard BG, Flyger H, Ørsted DD, Kaur-Knudsen D, Milne RL, Pérez JIA, Zamora P, Rodríguez PM, Benítez J, Brauch H, Justenhoven C, Ko YD, Hamann U, Fischer HP, Brüning T, Pesch B, Chang-Claude J, Wang-Gohrke S, Bremer M, Karstens JH, Hillemanns P, Dörk T, Nevanlinna HA, Heikkinen T, Heikkilä P, Blomqvist C, Aittomäki K, Aaltonen K, Lindblom A, Margolin S, Mannermaa A, Kosma VM, Kauppinen JM, Kataja V, Auvinen P, Eskelinen M, Soini Y, Chenevix-Trench G, Spurdle AB, Beesley J, Chen X, Holland H, Lambrechts D, Claes B, Vandorpe T, Neven P, Wildiers H, Flesch-Janys D, Hein R, Löning T, Kosel M, Fredericksen ZS, Wang X, Giles GG, Baglietto L, Severi G, McLean C, Haiman CA, Henderson BE, Le Marchand L, Kolonel LN, Alnæs GG, Kristensen V, Børresen-Dale AL, Hunter DJ, Hankinson SE, Andrulis IL, Mulligan AM, O'Malley FP, Devilee P, Huijts PEA, Tollenaar RAEM, Van Asperen CJ, Seynaeve CS, Chanock SJ, Lissowska J, Brinton L, Peplonska B, Figueroa J, Yang XR, Hooning MJ, Hollestelle A, Oldenburg RA, Jager A, Kriege M, Ozturk B, van Leenders GJLH, Hall P, Czene K, Humphreys K, Liu J, Cox A, Connley D, Cramp HE, Cross SS, Balasubramanian SP, Reed MWR, Dunning AM, Easton DF, Humphreys MK, Caldas C, Blows F, Driver K, Provenzano E, Lubinski J, Jakubowska A, Huzarski T, Byrski T, Cybulski C, Gorski B, Gronwald J, Brennan P, Sangrajrang S, Gaborieau V, Shen CY, Hsiung CN, Yu JC, Chen ST, Hsu GC, Hou MF, Huang CS, Anton-Culver H, Ziogas A, Pharoah PDP, Garcia-Closas M. Low penetrance breast cancer susceptibility loci are associated with specific breast tumor subtypes: findings from the Breast Cancer Association Consortium. Hum Mol Genet 2011; 20:3289-303. [PMID: 21596841 PMCID: PMC3140824 DOI: 10.1093/hmg/ddr228] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 05/10/2011] [Accepted: 05/16/2011] [Indexed: 01/23/2023] Open
Abstract
Breast cancers demonstrate substantial biological, clinical and etiological heterogeneity. We investigated breast cancer risk associations of eight susceptibility loci identified in GWAS and two putative susceptibility loci in candidate genes in relation to specific breast tumor subtypes. Subtypes were defined by five markers (ER, PR, HER2, CK5/6, EGFR) and other pathological and clinical features. Analyses included up to 30 040 invasive breast cancer cases and 53 692 controls from 31 studies within the Breast Cancer Association Consortium. We confirmed previous reports of stronger associations with ER+ than ER- tumors for six of the eight loci identified in GWAS: rs2981582 (10q26) (P-heterogeneity = 6.1 × 10(-18)), rs3803662 (16q12) (P = 3.7 × 10(-5)), rs13281615 (8q24) (P = 0.002), rs13387042 (2q35) (P = 0.006), rs4973768 (3p24) (P = 0.003) and rs6504950 (17q23) (P = 0.002). The two candidate loci, CASP8 (rs1045485, rs17468277) and TGFB1 (rs1982073), were most strongly related with the risk of PR negative tumors (P = 5.1 × 10(-6) and P = 4.1 × 10(-4), respectively), as previously suggested. Four of the eight loci identified in GWAS were associated with triple negative tumors (P ≤ 0.016): rs3803662 (16q12), rs889312 (5q11), rs3817198 (11p15) and rs13387042 (2q35); however, only two of them (16q12 and 2q35) were associated with tumors with the core basal phenotype (P ≤ 0.002). These analyses are consistent with different biological origins of breast cancers, and indicate that tumor stratification might help in the identification and characterization of novel risk factors for breast cancer subtypes. This may eventually result in further improvements in prevention, early detection and treatment.
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Affiliation(s)
- Annegien Broeks
- Department of Experimental Therapy, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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Yang XR, Chang-Claude J, Goode EL, Couch FJ, Nevanlinna H, Milne RL, Gaudet M, Schmidt MK, Broeks A, Cox A, Fasching PA, Hein R, Spurdle AB, Blows F, Driver K, Flesch-Janys D, Heinz J, Sinn P, Vrieling A, Heikkinen T, Aittomäki K, Heikkilä P, Blomqvist C, Lissowska J, Peplonska B, Chanock S, Figueroa J, Brinton L, Hall P, Czene K, Humphreys K, Darabi H, Liu J, Van 't Veer LJ, van Leeuwen FE, Andrulis IL, Glendon G, Knight JA, Mulligan AM, O'Malley FP, Weerasooriya N, John EM, Beckmann MW, Hartmann A, Weihbrecht SB, Wachter DL, Jud SM, Loehberg CR, Baglietto L, English DR, Giles GG, McLean CA, Severi G, Lambrechts D, Vandorpe T, Weltens C, Paridaens R, Smeets A, Neven P, Wildiers H, Wang X, Olson JE, Cafourek V, Fredericksen Z, Kosel M, Vachon C, Cramp HE, Connley D, Cross SS, Balasubramanian SP, Reed MWR, Dörk T, Bremer M, Meyer A, Karstens JH, Ay A, Park-Simon TW, Hillemanns P, Arias Pérez JI, Menéndez Rodríguez P, Zamora P, Benítez J, Ko YD, Fischer HP, Hamann U, Pesch B, Brüning T, Justenhoven C, Brauch H, Eccles DM, Tapper WJ, Gerty SM, Sawyer EJ, Tomlinson IP, Jones A, Kerin M, Miller N, McInerney N, Anton-Culver H, Ziogas A, Shen CY, Hsiung CN, Wu PE, Yang SL, Yu JC, Chen ST, Hsu GC, Haiman CA, Henderson BE, Le Marchand L, Kolonel LN, Lindblom A, Margolin S, Jakubowska A, Lubiński J, Huzarski T, Byrski T, Górski B, Gronwald J, Hooning MJ, Hollestelle A, van den Ouweland AMW, Jager A, Kriege M, Tilanus-Linthorst MMA, Collée M, Wang-Gohrke S, Pylkäs K, Jukkola-Vuorinen A, Mononen K, Grip M, Hirvikoski P, Winqvist R, Mannermaa A, Kosma VM, Kauppinen J, Kataja V, Auvinen P, Soini Y, Sironen R, Bojesen SE, Ørsted DD, Kaur-Knudsen D, Flyger H, Nordestgaard BG, Holland H, Chenevix-Trench G, Manoukian S, Barile M, Radice P, Hankinson SE, Hunter DJ, Tamimi R, Sangrajrang S, Brennan P, McKay J, Odefrey F, Gaborieau V, Devilee P, Huijts PEA, Tollenaar RAEM, Seynaeve C, Dite GS, Apicella C, Hopper JL, Hammet F, Tsimiklis H, Smith LD, Southey MC, Humphreys MK, Easton D, Pharoah P, Sherman ME, Garcia-Closas M. Associations of breast cancer risk factors with tumor subtypes: a pooled analysis from the Breast Cancer Association Consortium studies. J Natl Cancer Inst 2011; 103:250-63. [PMID: 21191117 PMCID: PMC3107570 DOI: 10.1093/jnci/djq526] [Citation(s) in RCA: 513] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Previous studies have suggested that breast cancer risk factors are associated with estrogen receptor (ER) and progesterone receptor (PR) expression status of the tumors. METHODS We pooled tumor marker and epidemiological risk factor data from 35,568 invasive breast cancer case patients from 34 studies participating in the Breast Cancer Association Consortium. Logistic regression models were used in case-case analyses to estimate associations between epidemiological risk factors and tumor subtypes, and case-control analyses to estimate associations between epidemiological risk factors and the risk of developing specific tumor subtypes in 12 population-based studies. All statistical tests were two-sided. RESULTS In case-case analyses, of the epidemiological risk factors examined, early age at menarche (≤12 years) was less frequent in case patients with PR(-) than PR(+) tumors (P = .001). Nulliparity (P = 3 × 10(-6)) and increasing age at first birth (P = 2 × 10(-9)) were less frequent in ER(-) than in ER(+) tumors. Obesity (body mass index [BMI] ≥ 30 kg/m(2)) in younger women (≤50 years) was more frequent in ER(-)/PR(-) than in ER(+)/PR(+) tumors (P = 1 × 10(-7)), whereas obesity in older women (>50 years) was less frequent in PR(-) than in PR(+) tumors (P = 6 × 10(-4)). The triple-negative (ER(-)/PR(-)/HER2(-)) or core basal phenotype (CBP; triple-negative and cytokeratins [CK]5/6(+) and/or epidermal growth factor receptor [EGFR](+)) accounted for much of the heterogeneity in parity-related variables and BMI in younger women. Case-control analyses showed that nulliparity, increasing age at first birth, and obesity in younger women showed the expected associations with the risk of ER(+) or PR(+) tumors but not triple-negative (nulliparity vs parity, odds ratio [OR] = 0.94, 95% confidence interval [CI] = 0.75 to 1.19, P = .61; 5-year increase in age at first full-term birth, OR = 0.95, 95% CI = 0.86 to 1.05, P = .34; obesity in younger women, OR = 1.36, 95% CI = 0.95 to 1.94, P = .09) or CBP tumors. CONCLUSIONS This study shows that reproductive factors and BMI are most clearly associated with hormone receptor-positive tumors and suggest that triple-negative or CBP tumors may have distinct etiology.
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Affiliation(s)
- Xiaohong R Yang
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Sciences, Rockville, MD 20852, USA.
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Hammet F, George J, Tesoriero AA, Jenkins MA, Schroen C, Smith L, Grabosch-Meehan A, Dite G, McCredie MRE, Giles GG, Tavtigian SV, Hopper JL, Southey MC. Is BRCA2 c.9079 G>A a predisposing variant for early onset breast cancer? Breast Cancer Res Treat 2007; 109:177-9. [PMID: 17549625 DOI: 10.1007/s10549-007-9624-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 05/16/2007] [Indexed: 10/23/2022]
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Armes JE, Hammet F, de Silva M, Ciciulla J, Ramus SJ, Soo WK, Mahoney A, Yarovaya N, Henderson MA, Gish K, Hutchins AM, Price GR, Venter DJ. Candidate tumor-suppressor genes on chromosome arm 8p in early-onset and high-grade breast cancers. Oncogene 2004; 23:5697-702. [PMID: 15184884 DOI: 10.1038/sj.onc.1207740] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Loss of genetic material from chromosome arm 8p occurs commonly in breast carcinomas, suggesting that this region is the site of one or more tumor-suppressor genes (TSGs). Comparative genomic hybridization analysis showed that 8p loss is more common in breast cancers from pre-menopausal compared with post-menopausal patients, as well as in high-grade breast cancers, regardless of the menopausal status. Subsequent high-resolution gene expression profiling of genes mapped to chromosome arm 8p, on an extended cohort of clinical tumor samples, indicated a similar dichotomy of breast cancer clinicopathologic types. Some of these genes showed differential downregulation in early-onset and later-onset, high-grade cancers compared with lower-grade, later-onset cancers. Three such genes were analysed further by in situ technologies, performed on tissue microarrays representing breast tumor and normal tissue samples. PCM1, which encodes a centrosomal protein, and DUSP4/MKP-2, which encodes a MAP kinase phosphatase, both showed frequent gene and protein loss in carcinomas. In contrast, there was an excess of cases showing loss of expression in the absence of reduced gene copy number of SFRP1, which encodes a dominant-negative receptor for Wnt-family ligands. These candidate TSGs may constitute some of the molecular drivers of chromosome arm 8p loss in breast carcinogenesis.
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Affiliation(s)
- Jane E Armes
- Molecular Pathology Laboratory, Victorian Breast Cancer Research Consortium, Australia.
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28
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Willis S, Hutchins AM, Hammet F, Ciciulla J, Soo WK, White D, van der Spek P, Henderson MA, Gish K, Venter DJ, Armes JE. Detailed gene copy number and RNA expression analysis of the 17q12-23 region in primary breast cancers. Genes Chromosomes Cancer 2003; 36:382-92. [PMID: 12619162 DOI: 10.1002/gcc.10138] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Chromosome region 17q12-23 commonly shows an increase in DNA copy number in breast cancers, suggesting that several oncogenes are located at this site. We performed a high-resolution expression array and comparative genomic hybridization analysis of genes mapped to the entire 17q12-23 region, to identify novel candidate oncogenes. We identified 24 genes that showed significant overexpression in breast cancers with gain of 17q12-23, compared to cancers without gain. These genes included previously identified oncogenes, together with several novel candidate oncogenes. FISH analysis using specific gene probes hybridized to tissue arrays confirmed the underlying amplification of overexpressed genes. This high-resolution analysis of the 17q12-23 region indicates that several established and novel candidate oncogenes, including a Wnt-signaling pathway member, are amplified and overexpressed within individual primary breast cancer samples. We were also able to confirm the presence of two apparently separate and reciprocally amplified groups of genes within this region. Investigation of these genes and their functional interactions will facilitate our understanding of breast oncogenesis and optimal management of this disease.
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Affiliation(s)
- Simon Willis
- Molecular Pathology Laboratory, Victorian Breast Cancer Research Consortium, University of Melbourne and Peter MacCallum Cancer Institute, Melbourne, Australia
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Allen DG, Hutchins AM, Hammet F, White DJ, Scurry JP, Tabrizi SN, Garland SM, Armes JE. Genetic aberrations detected by comparative genomic hybridisation in vulvar cancers. Br J Cancer 2002; 86:924-8. [PMID: 11953825 PMCID: PMC2364141 DOI: 10.1038/sj.bjc.6600112] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2001] [Revised: 11/21/2001] [Accepted: 11/30/2001] [Indexed: 11/09/2022] Open
Abstract
Squamous cell carcinoma of the vulva is a disease of significant clinical importance, which arises in the presence or absence of human papillomavirus. We used comparative genomic hybridisation to document non-random chromosomal gains and losses within human papillomavirus positive and negative vulvar cancers. Gain of 3q was significantly more common in human papillomavirus-positive cancers compared to human papillomavirus-negative cancers. The smallest area of gain was 3q22-25, a chromosome region which is frequently gained in other human papillomavirus-related cancers. Chromosome 8q was more commonly gained in human papillomavirus-negative compared to human papillomavirus-positive cancers. 8q21 was the smallest region of gain, which has been identified in other, non-human papillomavirus-related cancers. Chromosome arms 3p and 11q were lost in both categories of vulvar cancer. This study has demonstrated chromosome locations important in the development of vulvar squamous cell carcinoma. Additionally, taken together with previous studies of human papillomavirus-positive cancers of other anogenital sites, the data indicate that one or more oncogenes important in the development and progression of human papillomavirus-induced carcinomas are located on 3q. The different genetic changes seen in human papillomavirus-positive and negative vulvar squamous cell carcinomas support the clinicopathological data indicating that these are different cancer types.
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Affiliation(s)
- D G Allen
- Department of Gynecologic Oncology, Mercy Hospital for Women, Melbourne, Australia
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Armes JE, Trute L, White D, Southey MC, Hammet F, Tesoriero A, Hutchins AM, Dite GS, McCredie MR, Giles GG, Hopper JL, Venter DJ. Distinct molecular pathogeneses of early-onset breast cancers in BRCA1 and BRCA2 mutation carriers: a population-based study. Cancer Res 1999; 59:2011-7. [PMID: 10213514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Breast cancers arising in women with and without a germline mutation in the BRCA1 or BRCA2 gene display different histological features, which suggests unique mechanisms of molecular pathogenesis: We used a molecular pathological analysis to define the genetic abnormalities relevant to these specific pathogeneses. Tumor material was studied from 40 women with breast cancer diagnosed before 40 years of age, sampled from a population-based study and stratified by BRCA1 and BRCA2 germline mutation status. Cases were not selected for family history or ethnic origin, and none were known to be genetically related. Thus, germline mutation itself is likely to impact on the molecular pathogenesis of these tumors, with no substantial influence due to modifying genetic or environmental factors. Breast cancers occurring in BRCA1 mutation carriers had significantly higher levels of p53 expression, including the preinvasive (carcinoma in situ) stage of disease, compared with cancers occurring in BRCA2 mutation carriers or women with no detectable germline mutation. These cancers also had a higher proliferation rate as measured by Ki-67 antibody. Expression of the prognostic factors c-erbB-2, cyclin D1, and estrogen receptor was significantly less common in BRCA1 mutation carriers. Lower levels of cyclin D1 were also found in cancers from BRCA2 mutation carriers compared with non-mutation carriers. Direct p53 mutation analysis revealed mutations in 18% of all of the early-onset breast cancers within the study and included rare insertion and deletional mutations in cancers from BRCA1 mutation carriers. Our data indicate that a BRCA1 breast cancer phenotype may be recognized by an exceptionally high proliferation rate and early and frequent p53 overexpression but infrequent selection for overexpression of several other prognostic factor proteins known to be involved in breast oncogenesis. In contrast, breast cancers arising in BRCA2 mutation carriers have a more heterogeneous phenotypic profile.
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Affiliation(s)
- J E Armes
- Molecular Pathology Laboratory, Victorian Breast Cancer Research Consortium, Peter MacCallum Cancer Institute, East Melbourne, Victoria, Australia
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Somers GR, Hammet F, Woollatt E, Richards RI, Southey MC, Venter DJ. Chromosomal localization of the human P2y6 purinoceptor gene and phylogenetic analysis of the P2y purinoceptor family. Genomics 1997; 44:127-30. [PMID: 9286708 DOI: 10.1006/geno.1997.4841] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The G-protein-coupled P2Y purinoceptors mediate a variety of physiological effects in response to extracellular nucleotides. With the recent discovery of several new members from a variety of species, the P2Y purinoceptor family now encompasses types P2Y1 to P2Y6. By fluorescence in situ hybridization and utilization of the National Center for Biotechnology Information (NCBI) database, the human P2Y6 gene was localized to chromosome 11q13.5, between polymorphic markers D11S1314 and D11S916. NCBI database analysis of the remaining human P2Y purinoceptor genes revealed that P2Y2 and P2Y6 mapped to within less than 4 cM, and thus constitute the first described chromosomal clustering of this gene family. Phylogenetic analysis of the P2Y purinoceptor family demonstrated the presence of five evolutionary branches and suggests the occurrence of an ancient gene duplication event.
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Affiliation(s)
- G R Somers
- Department of Pathology, Peter MacCallum Cancer Institute, East Melbourne, Victoria, Australia.
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Southey MC, Hammet F, Hutchins AM, Paidhungat M, Somers GR, Venter DJ. Molecular cloning and sequencing of a novel human P2 nucleotide receptor. Biochim Biophys Acta 1996; 1309:77-80. [PMID: 8950181 DOI: 10.1016/s0167-4781(96)00148-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A novel human P2 nucleotide receptor has been cloned from a T-cell cDNA library. The predicted amino acid sequence shows characteristics of a G-protein-coupled receptor, and shares 88% homology with a recently characterised rat P2 nucleotide receptor sequence. Distinctive features include an extremely short cytoplasmic tail with only one putative protein kinase C phosphorylation site. Northern blot analysis revealed a 1.9 kb transcript expressed in the placenta.
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Affiliation(s)
- M C Southey
- Department of Pathology, Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia
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