title: Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2.
abstract: We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88-0.92]; P-value = 1.58 × 10(-25)). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08-1.17]; P-value = 7.89 × 10(-09)) and rs13294895 (OR = 1.09 [1.06-1.12]; P-value = 2.97 × 10(-11)). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06-1.18]; P-value = 2.77 × 10(-05)). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis.
authors: The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and nicholas.orr@icr.ac.uk.
authors: Nick
authors: N
authors: Orr
authors: Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
authors: Frank
authors: F
authors: Dudbridge
authors: The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and.
authors: Nicola
authors: N
authors: Dryden
authors: The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and.
authors: Sarah
authors: S
authors: Maguire
authors: The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and.
authors: Daniela
authors: D
authors: Novo
authors: The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and.
authors: Eleni
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authors: Perrakis
authors: The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and.
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authors: Broeks
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authors: LJ
authors: Van't Veer
authors: Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, The Netherlands.
authors: Frans B
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authors: University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen and David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
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authors: Fasching
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authors: Lothar
authors: L
authors: Haeberle
authors: Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany.
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authors: Ekici
authors: University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen and.
authors: Matthias W
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authors: Lorna
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authors: Gibson
authors: Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
authors: Zoe
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authors: Aitken
authors: Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, UK.
authors: Helen
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authors: Warren
authors: Division of Cancer Studies, Kings College London, Guy's Hospital, London, UK.
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authors: Ian
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authors: Emilie
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authors: Cordina-Duverger
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authors: Anja
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authors: Petra
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authors: IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.
authors: Paolo
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authors: Peterlongo
authors: Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy.
authors: Bernard
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authors: Peissel
authors: IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy, Cogentech Cancer Genetic Test Laboratory, Milan, Italy.
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authors: Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
authors: Seth
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authors: Slettedahl
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authors: Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health and Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.
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authors: Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health and Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia.
authors: Roger L
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authors: Milne
authors: Anatomical Pathology, The Alfred Hospital, Melbourne, VIC, Australia.
authors: Catriona
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authors: McLean
authors: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
authors: Christopher A
authors: CA
authors: Haiman
authors: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
authors: Brian E
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authors: Henderson
authors: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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authors: Jacques
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authors: Simard
authors: Department of Medicine, McGill University, Montreal, QC, Canada, Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, QC, Canada.
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authors: Goldberg
authors: Département de Médecine Sociale et Préventive, Département de Santé Environnementale et Santé au travail, Université de Montréal, Montreal, QC, Canada.
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authors: Labrèche
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authors: Kristensen
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authors: Anne-Lise
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authors: Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
authors: Sandra
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authors: Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics and Biocenter Oulu.
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authors: Irene L
authors: IL
authors: Andrulis
authors: Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada, Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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authors: Devilee
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authors: Tollenaar
authors: Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
authors: Caroline M
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authors: Seynaeve
authors: Department of Clinical Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
authors: Christi J
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authors: Van Asperen
authors: The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
authors: Montserrat
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authors: Garcia-Closas
authors: Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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authors: Jolanta
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authors: Lissowska
authors: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.
authors: Kamila
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authors: Czene
authors: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.
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authors: Darabi
authors: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.
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authors: Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland.
authors: Daniel
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authors: Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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authors: Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
authors: Antoinette
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authors: Hollestelle
authors: Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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authors: van Deurzen
authors: Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
authors: Mieke
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authors: Kriege
authors: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.
authors: Per
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authors: Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore.
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authors: Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore.
authors: Jianjun
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authors: Liu
authors: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.
authors: Keith
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authors: Humphreys
authors: Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield, UK.
authors: Angela
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authors: Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK.
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authors: Centre for Cancer Genetic Epidemiology, Department of Oncology and.
authors: Barbara J
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authors: Perkins
authors: Department of Genetics and Pathology, Pomeranian Medical University, 70-115 Szczecin, Poland.
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authors: Jakubowska
authors: Department of Genetics and Pathology, Pomeranian Medical University, 70-115 Szczecin, Poland.
authors: Jan
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authors: Lubinski
authors: Department of Genetics and Pathology, Pomeranian Medical University, 70-115 Szczecin, Poland.
authors: Katarzyna
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authors: Jaworska-Bieniek
authors: Department of Genetics and Pathology, Pomeranian Medical University, 70-115 Szczecin, Poland.
authors: Katarzyna
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authors: Durda
authors: The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and.
authors: Alan
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authors: Ashworth
authors: Division of Breast Cancer Research and Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
authors: Anthony
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authors: Swerdlow
authors: Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
authors: Michael
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authors: Jones
authors: Division of Breast Cancer Research and Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
authors: Minouk J
authors: MJ
authors: Schoemaker
authors: Division of Gynaecology and Obstetrics, Technische Universität München, 81675 Munich, Germany.
authors: Alfons
authors: A
authors: Meindl
authors: Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne and University Hospital Cologne, Cologne, Germany.
authors: Rita K
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authors: Department of Laboratory Medicine and Pathology and.
authors: Curtis
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authors: Olswold
authors: Department of Laboratory Medicine and Pathology and.
authors: Susan
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authors: Slager
authors: Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
authors: Amanda E
authors: AE
authors: Toland
authors: Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research 'Demokritos', Aghia Paraskevi Attikis, Athens, Greece.
authors: Drakoulis
authors: D
authors: Yannoukakos
authors: Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK, Institute of Population Health, University of Manchester, Manchester, UK.
authors: Kenneth
authors: K
authors: Muir
authors: Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK.
authors: Artitaya
authors: A
authors: Lophatananon
authors: Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK.
authors: Sarah
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authors: Stewart-Brown
authors: Ministry of Public Health, Nonthaburi, Thailand.
authors: Pornthep
authors: P
authors: Siriwanarangsan
authors: Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan.
authors: Keitaro
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authors: Matsuo
authors: Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.
authors: Hidema
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authors: Ito
authors: Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan.
authors: Hiroji
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authors: Iwata
authors: Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan.
authors: Junko
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authors: Ishiguro
authors: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
authors: Anna H
authors: AH
authors: Wu
authors: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
authors: Chiu-Chen
authors: CC
authors: Tseng
authors: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
authors: David
authors: D
authors: Van Den Berg
authors: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
authors: Daniel O
authors: DO
authors: Stram
authors: Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Selangor, Malaysia, Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia.
authors: Soo Hwang
authors: SH
authors: Teo
authors: Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia.
authors: Cheng Har
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authors: Yip
authors: Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Selangor, Malaysia.
authors: Peter
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mesh_terms: D000328:Adult; D000368:Aged; D044466:Asian People / Q000235:genetics; D001943:Breast Neoplasms / Q000235:genetics*; D002874:Chromosome Mapping; D002899:Chromosomes, Human, Pair 9; D004742:Enhancer Elements, Genetic; D047628:Estrogen Receptor alpha / Q000235:genetics; D005260:Female; D050990:GATA3 Transcription Factor / Q000235:genetics; D056726:Genetic Association Studies; D056426:Genetic Loci; D020022:Genetic Predisposition to Disease; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000235:genetics; D006801:Humans; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors / Q000235:genetics; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D012306:Risk; D044465:White People / Q000235:genetics
chemical_list: C506487:ESR1 protein, human; D047628:Estrogen Receptor alpha; C496499:FOXA1 protein, human; D050990:GATA3 Transcription Factor; C494749:GATA3 protein, human; D051541:Hepatocyte Nuclear Factor 3-alpha; C000715467:KLF4 protein, human; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors
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