An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Additional file 1: List of ethical committees that approved the access to the data analyzed in this study.

Additional file 2: SNPs selected for downstream analyses.

Additional file 3: Description and results of the procedure used to estimate the accuracy of our haplogroup inference methodology.

Additional file 4: Absolute and relative frequencies of imputed haplogroups by population. Table containing absolute and relative frequencies of imputed haplogroups for BRCA1 and BRCA2 mutation carriers.

Additional file 6: Details of haplogroups inference results for subclade T.

Additional file 7: Methods used to compute coevolution index.

Additional file 5: Correlated evolution index for all non-monomorphic sites observed in short haplotype sequences of subclade T. Table containing correlated evolution index for all non-monomorphic sites observed in short haplotypes sequences of subclade T.

INTRODUCTION : Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. METHODS : We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. RESULTS : We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. CONCLUSIONS : This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.

Higher-level funding: The COGS project is funded through a European Commission Seventh Framework Program grant (agreement number 223175: HEALTH-F2-2009-223175). The CIMBA data management and data analysis were supported by Cancer Research UK grants C12292/A11174 and C1287/A10118. SH is supported by a National Health and Medical Research Council (NHMRC) program grant (to GCT). Individual researcher support: ACA is a Cancer Research UK Senior Cancer Research Fellow (C12292/A11174). DFE is a Principal Research Fellow of Cancer Research UK. GC, MCS and IC are supported by the National Health and Medical Research Council (NHMRC). BK holds an American Cancer Society Early Detection Professorship (SIOP-06-258-01-COUN). MHG and PLM were supported by funding from the Intramural Research Program of the National Cancer Institute, National Institutes of Health. OIO is an American Cancer Society Clinical Research Professor. JS is Chairholder of the Canada Research Chair in Oncogenetics. Funding of constituent studies: The Breast Cancer Family Registry (BCFR) was supported by grant UM1 CA164920 from the National Cancer Institute, National Institutes of Health. The content of this article does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the BCFR, nor does mention of trade names, commercial products or organizations imply endorsement by the US Government or the BCFR. The Baltic Familial Breast Ovarian Cancer Consortium (BFBOCC) is partly supported by Lithuania (BFBOCC-LT): Research Council of Lithuania grant LIG-07/2012; BFBOCC-LV (Latvia) is partly supported by LSC grant 10.0010.08 and in part by a grant from the European Social Fund number 2009/0220/1DP/1.1.1.2.0/09/APIA/VIAA/016 and the Liepāja City Council, Liepāja, Latvia; Beth Israel Deaconess Medical Center Cancer Center is supported by the Breast Cancer Research Foundation; BRCA-gene mutations and breast cancer in South African women (BMBSA) was supported by grants from the Cancer Association of South Africa (CANSA) to Elizabeth J van Rensburg; SLN (Beckman Research Institute, City of Hope, Duarte, CA, USA) was partially supported by the Morris and Horowitz Families Professorship in Cancer Etiology and Outcomes Research; the Copenhagen Breast Cancer Study (CBCS) was supported by the NEYE Foundation; the Spanish National Cancer Research Center (Centro Nacional de Investigaciones Oncológicas (CNIO)) was partially supported by the Spanish Association against Cancer (Asociación Española Contra el Cáncer AECC08), Thematic Network Cooperative Research in Cancer (Red Temática Investigación Cooperativa en Cáncer (RTICC), Centro de Investigación Cáncer, Salamanca, Spain) RTICC 06/0020/1060, Spanish Ministry of Science and Innovation grants FIS PI08 1120 (Fondo de Investigación Sanitaria (FIS)) and SAF2010-20493, and the Fundación Mutua Madrileña (FMMA); the City of Hope Clinical Cancer Genetics Community Network and the Hereditary Cancer Research Registry (COH-CCGCRN), supported in part by award number RC4CA153828 (Principal Investigator: JNW) from the National Cancer Institute and the Office of the Director, National Institutes of Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. CONsorzio Studi ITaliani sui Tumori Ereditari Alla Mammella, Italy (CONSIT Team): Funds from Italian citizens who allocated the “5 × 1,000” share of their tax payment in support of the Fondazione IRCCS Istituto Nazionale Tumori, according to Italian laws (Istituto Nazionale dei Tumori (INT) institutional strategic project “5 × 1,000”) (to SM); the Italian Association for Cancer Research (AIRC) (to LO); National Centre for Scientific Research “Demokritos” has been cofinanced by the European Union (European Social Fund (ESF)) and Greek national funds through the “Education and Lifelong Learning” operational program of the National Strategic Reference Framework (NSRF) – Research Funding Program of the General Secretariat for Research and Technology: ARISTEIA; “Heracleitus II: Investing in knowledge society through the European Social Fund”; the DKFZ study was supported by the Deutsches Krebsforschungszentrum (DKFZ); Epidemiological Study of BRCA1 and BRCA2 Mutation Carriers (EMBRACE) is supported by Cancer Research UK grants C1287/A10118 and C1287/A11990; DGE and FL are supported by a National Institute for Health Research (NIHR) grant to the Biomedical Research Centre, Manchester, UK; the investigators at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust are supported by an NIHR grant to the Biomedical Research Centre at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, London; RE and EB are supported by Cancer Research UK grant C5047/A8385; Kansas University Medical Center: The authors acknowledge support from The University of Kansas Cancer Center (P30 CA168524) and the Kansas Bioscience Authority Eminent Scholar Program; AKG was funded by grants 5U01 CA113916 and R01 CA140323 and by the Chancellors Distinguished Chair in Biomedical Sciences Professorship; The German Consortium of Hereditary Breast and Ovarian Cancer (GC-HBOC) is supported by German Cancer Aid (grant 109076 (to RKS) and by the Center for Molecular Medicine Cologne (CMMC); GC-HBOC is deeply grateful to Dr Sabine Preisler-Adam for providing information and samples; the GEMO Study was supported by the Ligue National Contre le Cancer; the Association “Le cancer du sein, parlons-en!” Award; and the Canadian Institutes of Health Research for the CIHR Team in Familial Risks of Breast Cancer program; G-FAST: KDL is supported by GOA grant BOF10/GOA/019 (Ghent University) and spearhead financing of Ghent University Hospital; the Gynecologic Oncology Group (GOG) was supported by National Cancer Institute grants to the GOG Administrative Office and Tissue Bank (grant CA 27469), the GOG Statistical and Data Center (grant CA 37517) and GOG’s Cancer Prevention and Control Committee (grant CA 101165); HCSC was supported by grants RD12/00369/0006 and 12/00539 from Instituto de Salud Carlos III (ISCIII), Madrid, Spain, partially supported by European Regional Development Fund (Fonds européen de développement régional (FEDER)) funds; the Helsinki Breast Cancer Study (HEBCS) was financially supported by the Helsinki University Central Hospital Research Fund, Academy of Finland (266528), the Finnish Cancer Society and the Sigrid Juselius Foundation; HEBON is supported by the Dutch Cancer Society grants NKI1998-1854, NKI2004-3088 and NKI2007-3756, the Netherlands Organization of Scientific Research grant NWO 91109024, the Pink Ribbon grant 110005 and Biobanking and Molecular Resource Infrastructure (BBMRI) grant NWO 184.021.007/CP46; HEBON thanks the registration teams of the Comprehensive Cancer Centre Netherlands and Comprehensive Centre South (together the Netherlands Cancer Registry) and PALGA (Dutch Pathology Registry) for part of the data collection; the High Risk Breast Cancer Program (HRBCP) is supported by the Hong Kong Hereditary Breast Cancer Family Registry and the Dr Ellen Li Charitable Foundation, Hong Kong; the Hungarian Breast and Ovarian Cancer Study (HUNBOCS) was supported by Hungarian Research and Technological Innovation Fund (KTIA)/Hungarian Scientific Research Fund (Országos Tudományos Kutatási Alapprogramok (OTKA)) research grants KTIA-OTKA CK-80745 and KTIA-OTKA K-112228; Institut Català d’Oncologia (ICO): contract grant sponsor: Asociación Española Contra el Cáncer; Spanish Health Research Foundation; Ramón Areces Foundation; Instituto de Salud Carlos III (ISCIII); Catalan Health Institute; and Autonomous Government of Catalonia; contract grant numbers ISCIIIRETIC RD06/0020/1051, PI09/02483, PI10/01422, PI10/00748, PI13/00285, PI13/00189 2009SGR290 and PI13/00189 2009SGR283; the International Hereditary Cancer Center (Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland) was supported by grant PBZ_KBN_122/P05/2004; Landspitali – The National University Hospital of Iceland was supported by the Icelandic Association “Walking for Breast Cancer Research” and by the Landspitali University Hospital Research Fund; the Interdisciplinary Health Research Internal Team Breast Cancer Susceptibility Study (INHERIT) was supported by the Canadian Institutes of Health Research (CIHR) for the “CIHR Team in Familial Risks of Breast Cancer” program, Canadian Breast Cancer Research Alliance grant 019511 and Ministry of Economic Development, Innovation and Export Trade grant PSR-SIIRI-701; the Istituto Oncologico Veneto Hereditary Breast and Ovarian Cancer Study (IOVHBOCS) is supported by the Ministero della Salute and a “5 × 1,000” Istituto Oncologico Veneto grant; the Portuguese Oncology Institute–Porto Breast Cancer Study (IPOBCS) was supported in part by Liga Portuguesa Contra o Cancro; kConFab is supported by a grant from the National Breast Cancer Foundation and previously by the National Health and Medical Research Council (NHMRC), the Queensland Cancer Fund, the Cancer Councils of New South Wales, Victoria, Tasmania and South Australia, and the Cancer Foundation of Western Australia; the Mayo Clinic is supported by National Institutes of Health (NIH) grants CA 116167, CA 128978 and CA 176785 through the National Cancer Institute (NCI), an NCI Specialized Program of Research Excellence (SPORE) in Breast Cancer (CA116201), a US Department of Defense Ovarian Cancer Idea award (W81XWH-10-1-0341), a grant from the Breast Cancer Research Foundation, a generous gift from the David F and Margaret T Grohne Family Foundation and the Ting Tsung and Wei Fong Chao Foundation; McGill University Jewish General Hospital Weekend to End Breast Cancer, Quebec Ministry of Economic Development, Innovation and Export Trade; Modifier Study of Quantitative Effects on Disease (ModSQuaD) was supported by the Ministry of Health of the Czech Republic to Masaryk Memorial Cancer Institute (MH CZ – DRO) (MMCI 00209805) and by the European Regional Development Fund and the State Budget of the Czech Republic (RECAMO, CZ.1.05/ 2.1.00/03.0101) (to LF), and by Charles University in Prague project UNCE204024 (MZ); Memorial Sloan Kettering Cancer Center (MSKCC) is supported by grants from the Breast Cancer Research Foundation and Robert and Kate Niehaus Clinical Cancer Genetics Initiative; National Cancer Institute, National Institutes of Health: The research of MHG and PLM was supported by the Intramural Research Program of the National Cancer Institute and by support services contracts N02-CP-11019-50 and N02-CP-65504 with Westat, Inc, Rockville, MD, USA; the National Israeli Cancer Control Center (NICCC) is supported by Clalit Health Services in Israel; some of its activities are supported by the Israel Cancer Association and the Breast Cancer Research Foundation (BCRF), New York, NY, USA; NN Petrov Institute of Oncology has been supported by the Russian Federation for Basic Research (grants 11-04-00227, 12-04-00928 and 12-04-01490) and the Federal Agency for Science and Innovations, Russia (contract 02.740.11.0780); The Ohio State University Clinical Cancer Genetics (OSUCCG) is supported by The Ohio State University Comprehensive Cancer Center; the Pisa Breast Cancer Study (PBCS) was supported by Istituto Toscano Tumori (ITT) grants 2011–2013; Sheba Medical Center was partially funded through a grant from the Israel Cancer Association and funding for the Israeli Inherited Breast Cancer Consortium; the Swedish Breast Cancer Study collaborators are supported by the Swedish Cancer Society; The University of Chicago is supported by NCI Specialized Program of Research Excellence (SPORE) in Breast Cancer (CA125183), R01 CA142996 and 1U01CA161032 and by the Ralph and Marion Falk Medical Research Trust, the Entertainment Industry Fund National Women’s Cancer Research Alliance and the Breast Cancer Research Foundation; University of California, Los Angeles Jonsson Comprehensive Cancer Center Foundation: Breast Cancer Research Foundation; University of California, San Francisco Cancer Risk Program and Helen Diller Family Comprehensive Cancer Center; UK Familial Ovarian Cancer Registry (UKFOCR) was supported by a project grant from Cancer Research UK (to Paul DP Pharoah); the University of Pennsylvania: National Institutes of Health (NIH) grants R01 CA102776 and R01 CA083855; the Breast Cancer Research Foundation; the Susan G Komen for the Cure, Basser Center for BRCA; Victorian Familial Cancer Trials Group (VFCTG): Victorian Cancer Agency, Cancer Australia, National Breast Cancer Foundation; The Women’s Cancer Program (WCP) at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, is funded by the American Cancer Society Early Detection Professorship (SIOP-06-258-01-COUN). GEMO Study: National Cancer Genetics Network UNICANCER Genetic Group, France. The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON) coordinating center: Netherlands Cancer Institute, Amsterdam.

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