title: Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus.
abstract: Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk.
  
  
  
  We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation.
  
  
  
  Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05.
  
  
  
  This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk.
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authors.forename: Daehee
authors.initials: D
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authors.affiliation: Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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authors.initials: BY
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authors.affiliation: Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland.
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authors.affiliation: Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.
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authors.initials: E
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authors.affiliation: Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos", Athens, Greece.
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authors.affiliation: Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer, Israel.
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authors.initials: Y
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authors.affiliation: Vesalius Research Center, Leuven, Belgium.|Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium.
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authors.forename: Conxi
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authors.affiliation: University of Hawaii Cancer Center, Honolulu, HI, USA.
authors.forename: Loic
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authors.forename: Chuen Neng
authors.initials: CN
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authors.affiliation: Department of Surgery, Soonchunhyang University and Hospital, Seoul, South Korea.
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authors.initials: MH
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authors.affiliation: Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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authors.affiliation: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
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authors.forename: Annelie
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authors.forename: Annika
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authors.affiliation: Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK.
authors.forename: Artitaya
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authors.initials: J
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authors.affiliation: Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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authors.affiliation: Cancer Center, Kuopio University Hospital, Kuopio, Finland.|Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.|Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
authors.forename: Arto
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authors.forename: Siranoush
authors.initials: S
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authors.forename: Sara
authors.initials: S
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authors.forename: Frederik
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authors.affiliation: Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan.
authors.forename: Keitaro
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authors.initials: A
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authors.forename: Florence
authors.initials: F
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authors.initials: M
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authors.forename: Kenneth
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authors.affiliation: Laboratory Medicine Program, University Health Network, Toronto, ON, Canada.|Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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authors.initials: AM
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authors.initials: KL
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authors.affiliation: Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.
authors.forename: Heli
authors.initials: H
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authors.initials: K
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authors.forename: Edith
authors.initials: E
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authors.initials: OI
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authors.initials: C
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authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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authors.initials: Y
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authors.initials: B
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authors.initials: J
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authors.initials: P
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authors.initials: MU
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authors.initials: G
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authors.forename: Anja
authors.initials: A
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authors.initials: R
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authors.initials: EJ
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authors.affiliation: Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
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authors.initials: MK
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authors.affiliation: Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany.|Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany.|Center for Integrated Oncology, University Hospital of Cologne, Cologne, Germany.|Center for Molecular Medicine, University Hospital of Cologne, Cologne, Germany.
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authors.initials: RK
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authors.initials: MJ
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authors.initials: CY
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authors.affiliation: Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA.
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authors.affiliation: Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA.
authors.forename: Xiao-Ou
authors.initials: XO
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authors.initials: A
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authors.initials: CF
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authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
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authors.initials: S
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authors.affiliation: Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, QC, Canada.
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authors.initials: P
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authors.affiliation: Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Australia.
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authors.initials: M
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authors.affiliation: Hannover Medical School, Hannover, Germany.
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authors.initials: D
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authors.affiliation: Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.|Division of Breast Cancer Research, The Institute of Cancer Research, London, UK.
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authors.initials: A
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authors.affiliation: National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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authors.initials: CI
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authors.affiliation: Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
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authors.initials: S
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authors.initials: SH
authors.lastname: Teo
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authors.initials: MB
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authors.affiliation: McGill University and Génome Québec Innovation Centre, Montréal, Canada.
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authors.forename: Alex
authors.initials: A
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authors.affiliation: Department of Clinical Genetics, Odense University Hospital, Odense, C, Denmark.
authors.forename: Mads
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authors.affiliation: Latvian Biomedical Research and Study Centre, Riga, Latvia.
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authors.initials: L
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authors.affiliation: Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, QC, Canada.|Currently at Medical School Cambridge University, Cambridge, UK.
authors.forename: Marc
authors.initials: M
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authors.affiliation: Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
authors.forename: Amanda E
authors.initials: AE
authors.lastname: Toland
authors.affiliation: Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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authors.initials: N
authors.lastname: Tung
authors.affiliation: Section of Cancer Genetics, The Institute of Cancer Research, London, UK.
authors.forename: Clare
authors.initials: C
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authors.affiliation: Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
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authors.initials: AM
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authors.affiliation: Department of Genetics, University of Pretoria, Pretoria, South Africa.
authors.forename: Elizabeth J
authors.initials: EJ
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authors.affiliation: Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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authors.initials: D
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authors.affiliation: Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.|Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Joseph
authors.initials: J
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authors.affiliation: Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany.
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authors.initials: S
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authors.initials: JN
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authors.initials: R
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authors.affiliation: Singapore Eye Research Institute, National University of Singapore, Singapore, Singapore.
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authors.initials: TY
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authors.initials: JC
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authors.affiliation: Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.|Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.
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authors.initials: PD
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authors.affiliation: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
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authors.initials: P
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authors.affiliation: Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia.|Peter MacCallum Cancer Center, The University of Melbourne, Melbourne, Australia.
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authors.affiliation: Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.
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authors.affiliation: Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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authors.initials: FJ
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authors.affiliation: Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
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authors.initials: AC
authors.lastname: Antoniou
authors.affiliation: Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.|Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.
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authors.initials: DF
authors.lastname: Easton
authors.affiliation: Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA. wei.zheng@vanderbilt.edu.
authors.forename: Wei
authors.initials: W
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mesh_terms: D000483:Alleles; D019313:BRCA1 Protein / Q000235:genetics; D001943:Breast Neoplasms / Q000453:epidemiology* / Q000235:genetics*; D016022:Case-Control Studies; D002874:Chromosome Mapping; D002881:Chromosomes, Human, Pair 12; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D004742:Enhancer Elements, Genetic; D044127:Epigenesis, Genetic; D005260:Female; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D009154:Mutation; D016017:Odds Ratio; D020641:Polymorphism, Single Nucleotide; D011159:Population Surveillance; D011401:Promoter Regions, Genetic; D040641:Quantitative Trait Loci; D012306:Risk; D044465:White People / Q000235:genetics
chemical_list: D019313:BRCA1 Protein
keywords: BRAC1 mutation carriers; Breast cancer; CCDC91; Fine-scale mapping; Genetic risk factor; PTHLH