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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
Cancer Res. Author manuscript; available in PMC Oct 1, 2012.
Published in final edited form as:
PMCID: PMC3319792
NIHMSID: NIHMS357447
19p13.1 is a triple negative-specific breast cancer susceptibility locus
Kristen N. Stevens,1 Zachary Fredericksen,1 Celine M. Vachon,1 Xianshu Wang,2 Sara Margolin,3 Annika Lindblom,3 Heli Nevanlinna,4 Dario Greco,4 Kristiina Aittomäki,5 Carl Blomqvist,6 Jenny Chang-Claude,7 Alina Vrieling,7 Dieter Flesch-Janys,8 Hans-Peter Sinn,9 Shan Wang-Gohrke,10 Stefan Nickels,7 Hiltrud Brauch,11,12 on behalf of the GENICA Network,11,12,13,14,15,16 Yon-Dschun Ko,13 Hans-Peter Fischer,14 Rita K. Schmutzler,17 Alfons Meindl,18 Claus R. Bartram,19 Sarah Schott,20 Christof Engel,21 Andrew K. Godwin,22 JoEllen Weaver,23 Harsh B. Pathak,22 Priyanka Sharma,24 Hermann Brenner,25 Heiko Müller,25 Volker Arndt,25 Christa Stegmaier,26 Penelope Miron,27 Drakoulis Yannoukakos,28 Alexandra Stavropoulou,28 George Fountzilas,29 Helen J. Gogas,30 Ruth Swann,31 Miriam Dwek,31 Annie Perkins,31 Roger L. Milne,32 Javier Benítez,33 M Pilar Zamora,34 José Ignacio Arias Pérez,35 Stig E. Bojesen,36,37 Sune F. Nielsen,36,37 Børge G Nordestgaard,36,37 Henrik Flyger,38 Pascal Guénel,39,40 Thérèse Truong,39,40 Florence Menegaux,39,40 Emilie Cordina-Duverger,39,40 Barbara Burwinkel,20,41 Frederick Marmé,20,42 Andreas Schneeweiss,20,42 Christof Sohn,20 Elinor Sawyer,43 Ian Tomlinson,44 Michael J. Kerin,45 Julian Peto,46 Nichola Johnson,47 Olivia Fletcher,47 Isabel dos Santos Silva,48 Peter A. Fasching,49,50 Matthias W. Beckmann,50 Arndt Hartmann,51 Arif B. Ekici,52 Artitaya Lophatananon,53 Kenneth Muir,53 Puttisak Puttawibul,54 Surapon Wiangnon,55 Marjanka K Schmidt,56 Annegien Broeks,56 Linde M Braaf,56 Efraim H Rosenberg,56 John L. Hopper,57 Carmel Apicella,57 Daniel J. Park,58 Melissa C. Southey,58 Anthony J. Swerdlow,59 Alan Ashworth,60 Nicholas Orr,60 Minouk J. Schoemaker,59 Hoda Anton-Culver,61 Argyrios Ziogas,61 Leslie Bernstein,62 Christina Clarke Dur,63 Chen-Yang Shen,64 Jyh-Cherng Yu,65 Huan-Ming Hsu,65 Chia-Ni Hsiung,64 Ute Hamann,66 Thomas Dünnebier,66 Thomas Rüdiger,67 Hans Ulrich Ulmer,68 Paul P. Pharoah,69,70 Alison M Dunning,69 Manjeet K. Humphreys,70 Qin Wang,70 Angela Cox,71 Simon S. Cross,72 Malcom W. Reed,71 Per Hall,73 Kamila Czene,73 Christine B. Ambrosone,74 Foluso Ademuyiwa,75 Helena Hwang,76 Diana M. Eccles,77 Montserrat Garcia-Closas,78 Jonine D. Figueroa,79 Mark E. Sherman,79 Jolanta Lissowska,80 Peter Devilee,81 Caroline Seynaeve,82 R.A.E.M. Tollenaar,83 Maartje J. Hooning,82 Irene L. Andrulis,84 Julia A. Knight,85 Gord Glendon,86 Anna Marie Mulligan,87 Robert Winqvist,88 Katri Pylkäs,88 Arja Jukkola-Vuorinen,89 Mervi Grip,90 Esther M. John,63 Alexander Miron,27 Grethe Grenaker Alnæs,91,92 Vessela Kristensen,91,92 Anne-Lise Børresen-Dale,93 Graham G. Giles,94,95 Laura Baglietto,94,95 Catriona A McLean,96 Gianluca Severi,94,95 Matthew L. Kosel,1 V.S. Pankratz,1 Susan Slager,1 Janet E. Olson,1 Paolo Radice,97,98 Paolo Peterlongo,97,98 Siranoush Manoukian,99 Monica Barile,100 Diether Lambrechts,101,102 Sigrid Hatse,103 Anne-Sophie Dieudonne,103 Marie-Rose Christiaens,103 Georgia Chenevix-Trench,104 on behalf of kConFab Investigators,105 and the AOCS Group,104,105 Jonathan Beesley,104 Xiaoqing Chen,104 Arto Mannermaa,106 Veli-Matti Kosma,106 Jaana M. Hartikainen,106 Ylermi Soini,106 Douglas F. Easton,68,69 and Fergus J. Couch2*
1Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
2Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
3Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
4Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Biomedicum Helsinki, Helsinki, Finland
5Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
6Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
7Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
8Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
9Department of Pathology, University Hospital Heidelberg, Heidelberg, Germany
10Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
11Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
12University of Tubingen, Tubingen, Germany
13Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
14Institute of Pathology, Medical Faculty of the University of Bonn, Bonn, Germany
15Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
16Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, Germany
17Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, Center of Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany
18Department for Obstetrica and Gynaecology, Dvision for Tumor Genetics, Klinikum rechts der Isar, Technische Universität, Munich, Germany
19Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
20Department of Obstetrics and Gynecology, University Hospital Heidelberg, Heidelberg, Germany
21Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
22Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, USA
23Biosample Repository, Fox Chase Cancer Center, Philadelphia, USA
24Division of Hematology and Oncology, University of Kansas Medical Center, Kansas City, USA
25Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
26Saarland Cancer Registry, Saarbrücken, Germany
27Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
28Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
29Department of Medical Oncology, “Papageorgiou” Hospital, Ring Road, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
30First Department of Medicine, University of Athens, Medical School, Athens, Greece
31Against Breast Cancer Research Unit, School of Life Sciences, University of Westminster, London, UK
32Genetic & Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
33Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
34Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
35Servicio de Cirugía General y Especialidades, Hospital Monte Naranco, Oviedo, Spain
36Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
37The Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
38Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
39Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
40University Paris-Sud, UMRS1018 Villejuif, France
41Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
42National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
43National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Guy’s & St. Thomas’ NHS Foundation Trust in partnership with King’s College London and King’s College Hospital NHS Foundation Trus, London, UK
44Welcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
45NUIG Department of Surgery, Clinical Science Institute, University Hospital Galway, Galway, Ireland
46Department of Nion-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
47Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
48Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
49University of California at Los Angeles, David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, Los Angeles, USA
50University Breast Center Franconia, Department of Gynecology and Obstetrics, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center, Erlangen-Nuremberg, Germany
51Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen-Nuremberg, Germany
52Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen-Nuremberg, Germany
53Health Sciences Research Institute, Warwick Medical School, Warwick University, Coventry, UK
54Department of Surgery, Medical school, Prince Songkla University, Songkla, Thailand
55Department of Pediatrics, Medical school, Khon Kaen University, Khon Kaen, Thailand
56Netherlands Cancer Institute, Amsterdam, Netherlands
57Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia
58Department of Pathology, The University of Melbourne, Melbourne, Australia
59Section of Epidemiology, Institute of Cancer Research., Sutton,, UK
60The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research., London, UK
61Department of Epidemiology, School of Medicine, University of California Irvine, Irvine, CA
62Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute, City of Hope
63Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA
64Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
65Department of Surgery, Tri-Service General Hospital, Taipei, Taiwan
66Molecular Genetics of Breast Cancer, Deutsches Krebsforschungsfzentrum (DKFZ), Heidelberg, Germany
67Institute of Pathology, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
68Women’s Clinic, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
69Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
70Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
71Dept of Oncology, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
72Department of Neuroscience, Faculty of Medicine, Dentistry & Health, University of Sheffield, Sheffield, UK
73Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
74Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, USA
75Department of Medicine, Roswell Park Cancer Institute, Buffalo, USA
76Department of Pathology, Roswell Park Cancer Institute, Buffalo, USA
77Faculty of Medicine, University of Southampton, Southampton, UK
78Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
79Division of Cancer Epidemiology and Genetics, Hormonal and Reproductive Epidemiology Branch, NIH/NCI, Bethesda, USA
80Department of Cancer Epidemiology and Prevention, The M. Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
81Department of Human Genetics & Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
82Department of Medical Oncology, Erasmus Medical Center, Daniel den Hoed Cancer Center, Rotterdam, Netherlands
83Department of Surgical Oncology, Leiden University Medical Center, Leiden, Netherlands
84Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
85Dalla Lana School of Public Health, University of Toronto, Prosserman Centre for Health Research, Toronto, Canada
86Cancer Care Ontario, Princess Margaret Hospital, Toronto, Canada
87Department of Laboratory Medicine, Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
88Department of Clinical Genetics, Institute of Clinical Medicine, Biocenter Oulu, University of Oulu, Oulu University Hospital, Oulu, Finland
89Department of Oncology, University of Oulu, Oulu University Hospital, Oulu, Finland
90Department of Surgery, University of Oulu, Oulu University Hospital, Oulu, Finland
91Institute for Clinical Epidemiology and Molecular Biology (EpiGen), Faculty of Medicine, University of Oslo, Oslo, Norway
92Group of Cancer Genome Variation Department of Genetics, Institute for Cancer Research, Oslo, Norway
93Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
94Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
95Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia
96The Alfred Hospital, Melbourne, Australia
97Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale, Tumori (INT), Milan, Italy
98IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
99Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
100Division of Cancer Prevention and Genetics, Chemoprevention, European Institute of Oncology, Milan, Italy
101Vesalius Research Center, VIB, Leuven, Belgium
102Vesalius Research Center, University of Leuven, Leuven, Belgium
103Multidisciplinary Breast Center, University Hospital Gasthuisberg, Leuven, Belgium
104Queensland Institute of Medical Research, Herston, Australia
105Peter MacCallum Cancer Centre, East Melbourne, Australia
106Institute of Clinical Medicine, Department of Pathology, University of Eastern Finland and Kuopio University Hospital, Biocenter Kuopio, Kuopio, Finland
* Correspondence: Fergus J. Couch, Stabile 2-42, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA. Tel: (507) 284-3623; Fax: (507) 538-1937; couch.fergus/at/mayo.edu
The 19p13.1 breast cancer susceptibility locus is a modifier of breast cancer risk in BRCA1 mutation carriers and is also associated with risk of ovarian cancer. Here we investigated 19p13.1 variation and risk of breast cancer subtypes, defined by estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2) status, using 48,869 breast cancer cases and 49,787 controls from the Breast Cancer Association Consortium (BCAC). Variants from 19p13.1 were not associated with breast cancer overall or with ER-positive breast cancer but were significantly associated with ER-negative breast cancer risk [rs8170 Odds Ratio (OR)=1.10, 95% Confidence Interval (CI) 1.05 – 1.15, p=3.49 × 10-5] and triple negative (TN) (ER, PR and HER2 negative) breast cancer [rs8170 OR=1.22, 95% CI 1.13 – 1.31, p=2.22 × 10-7]. However, rs8170 was no longer associated with ER-negative breast cancer risk when TN cases were excluded [OR=0.98, 95% CI 0.89 – 1.07, p=0.62]. In addition, a combined analysis of TN cases from BCAC and the Triple Negative Breast Cancer Consortium (TNBCC) (n=3,566) identified a genome-wide significant association between rs8170 and TN breast cancer risk [OR=1.25, 95% CI 1.18 – 1.33, p=3.31 × 10-13]. Thus, 19p13.1 is the first triple negative-specific breast cancer risk locus and the first locus specific to a histological subtype defined by ER, PR, and HER2 to be identified. These findings provide convincing evidence that genetic susceptibility to breast cancer varies by tumor subtype and that triple negative tumors and other subtypes likely arise through distinct etiologic pathways.
Keywords: genetic susceptibility, association study, subtype, neoplasms, common variant
It is becoming increasingly apparent that genetic susceptibility to breast cancer varies by expression levels of estrogen receptor (ER) in breast tumors. Studies of genetic loci identified in genome-wide association studies (GWAS) have shown that variants in 5p12, 8q24, 1p11.2, 9p21.3, 10q21.2, and 11q13 are associated with ER-positive breast cancer (18) but not ER-negative breast cancer, whereas variants in FGFR2, 2q35, TOX3, LSP1, MAP3K1, TGFB1, RAD51L1 and ESR1 are associated with both ER-positive and ER-negative disease (810). In addition, only a subset of these genetic risk factors for overall breast cancer (TOX3, 2q35, 5q11, LSP1, RAD51L1 and ESR1) have been associated with triple negative (TN) breast cancer, defined by ER, progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2) expression levels (1012). To date no variants have been specifically associated with ER-negative or TN disease.
The 19p13.1 breast cancer susceptibility locus was first identified in a GWAS of BRCA1 carriers as a modifier of breast cancer risk (9). Single nucleotide polymorphisms (SNPs), rs8170 and either rs8100241 or rs2363956 (r2=1), from 19p13.1 were associated with risk of breast cancer (rs8170 Hazard Ratio (HR)=1.27, p=1.5 × 10−10; rs8100241 HR=0.84, p=1.6 × 10−10; rs2363956 HR=0.84, p=2.4 × 10−10). The same variants have also been associated with risk of ovarian cancer in the general population (13). In addition, replication studies have suggested associations between these SNPs and ER-negative and ER-positive breast cancer (9, 12), and also with triple negative disease (9, 12). The 19p13.1 locus contains the genes c19orf62 (MERIT40), ANKLE1, and ABHD8, but the causal variants underlying these associations with breast and ovarian cancer risk have yet to be identified.
Here we present a study of the 19p13.1 locus and breast cancer risk in the Breast Cancer Association Consortium (BCAC), an international consortium that has identified or confirmed genome-wide significant associations between commonly inherited variants in several loci and breast cancer risk. We investigated associations between rs8170 from the 19p13.1 locus and breast cancer risk using 48,869 breast cancer cases and 49,787 controls, and associations between rs8100241 and rs2363956 from 19p13.1 and breast cancer in a subset of the BCAC cohort. We also directly assessed differences in breast cancer risk by tumor subtype, defined by ER, PR, and HER2 status, and show that 19p13.1 variants are associated specifically with risk of TN breast cancer.
Ethics Statement
Study subjects were recruited on protocols approved by the Institutional Review Boards at each participating institution, and all subjects provided written informed consent.
BCAC studies
Thirty-nine studies from the Breast Cancer Association Consortium (BCAC) contributed genotype data (rs8170, rs8100241 and/or rs2363956) to this study (Supplementary Tables 1, 2). Women of white European ancestry were included from 37 BCAC studies based in Europe, North America, and Australia (49,897 cases, 48,306 controls). Asian women were included from two BCAC studies based in Thailand and Taiwan (1,198 cases, 1,481 controls). BCAC studies are described in detail in Supplementary Table 2. Study participants were recruited under protocols approved by the Institutional Review Board at each institution and all subjects provided written informed consent.
TNBCC studies
Thirteen studies from the Triple Negative Breast Cancer Consortium (TNBCC) were included in the triple negative-specific analysis of rs8170 (Supplementary Tables 1, 2). These studies included 1,350 TN breast cancer cases and 3,852 controls of women of white European ancestry. Samples included from the five TNBCC studies that are also involved in BCAC (BBCC, KARBAC, MCCS, SBCS, POSH) are unique to the TNBCC analysis and were not included in the BCAC analyses presented in this paper. TNBCC studies are described in detail in Supplementary Table 2. Study participants were recruited under protocols approved by the Institutional Review Board at each institution and all subjects provided written informed consent.
Genotyping
Genotyping of rs8170, rs8100241, and rs2363956 in BCAC was performed using a TaqMan allelic discrimination assay or the Sequenom iPLEX platform (Sequenom, San Diego, CA, USA) via standard protocols. Robust quality control criteria, established by BCAC, were applied as detailed in previous consortium studies (4). Briefly, the genotyping concordance was verified with internal duplicates and overall data quality was ensured using independent genotyping of 96 CEU samples by each genotyping center. We excluded all samples from any study with more than two discordant genotypes on the CEU plate. All studies met the specified criteria for call rate (>95%).
Rs8170 and rs8100241 genotyping in TNBCC samples was performed using a single multiplex on the iPLEX Mass Array platform (Sequenom) as part of a larger 22-SNP genotyping project. Samples were plated by study as random mixtures of cases and controls with no-template and CEPH controls in every plate. Genotyping quality for SNPs and samples was evaluated using an iterative quality control process. SNPs and samples were excluded based on the following criteria: SNP call rate <95%, Hardy-Weinberg equilibrium (HWE) p-value <0.01 among controls, and sample call rate <95%.
Pathology and tumor markers
Pathology analyses of BCAC data were conducted using studies of white European women only. All studies except CTS, GC-HBOC, and UKBGS provided data on ER and PR status of tumors, and 25 studies provided data on HER2 (Supplementary Table 3). The collection of pathology and tumor marker information for BCAC has been described previously (14). Briefly, studies provided information on histopathologic subtype, grade of differentiation, tumor size, nodal involvement, and stage at diagnosis of breast tumors. ER/PR status was most commonly defined using data from medical records. ER and PR negative status was defined as <10% of the tumor cells stained. HER2 negative status was typically defined as a score of 0 or 1+ on a HER2 immunohistochemistry (IHC) scale of 0–3+.
TNBCC cases were defined as individuals with an ER–negative, PR–negative and HER2–negative breast cancer. Definition of ER and PR negative status were <1% cells stained positive for DEMOKRITOS, DFCI, FCCC, and MCCS; <10% cells stained positive for BBCC, KARBAC; intensity score (0,1,2,3) percentage of cells stained (0–100%) <50 for SBCS; or an Allred score <3 for RPCI and POSH. Definition of HER2 negative status was score 0 or 1+ by IHC for BBCC, DEMOKRITOS, FCCC, MCCS, POSH, RCPI, SBCS; or IHC score 0, 1+ or 2+ and FISH negative for DFCI, KARBAC. CK5/6 and EGFR IHC data for identification of basal tumors were not available.
Statistical methods
Departure from Hardy-Weinberg equilibrium (HWE) was assessed in controls using a goodness of fit test. Evidence of departure was not observed in any of the participating studies (HWE p≥0.001). Single SNP analyses were conducted using unconditional logistic regression separately for white Europeans and Asians. Analyses utilizing only BCAC case-control studies were adjusted for study, and analyses utilizing all BCAC studies (case-control and case-only studies) were adjusted for country. SNP associations were tested in a log-additive model. To obtain additional information, we also used a 2 degree of freedom test, calculating odds ratios and 95% confidence intervals separately for heterozygotes and rare homozygotes. Consideration of age made no substantial difference to the results, assessed by both the exclusion of studies for which the age of controls was not known and the adjustment for age in 5-year categories and as a continuous covariate. Subtype-specific associations defined by ER, PR and HER2 status were estimated for white Europeans with invasive breast cancer using polytomous logistic regression with control status as the reference outcome, adjusting for country or study where appropriate. SNP associations were tested in a log-additive model. Heterogeneity in the OR by subtypes was tested by applying polytomous logistic regression to cases-only, treating the number of minor alleles as the outcome. Triple-negative specific analyses were conducted among cases with known ER, PR, and HER2 status using polytomous logistic regression with ER-negative (excluding triple negative) and triple negative cases compared to controls as the reference outcome, adjusting for country. BCAC and TNBCC analyses were performed in a combined data set using raw genotype data for rs8170 and rs8100241 from each consortium, and analyses were adjusted for country and consortium. Interaction and haplotype analyses were conducted using the combined BCAC and TNBCC data set adjusting for country. Haplotype analyses were conducted using the haplo.glm function from the haplo.stats package in R with default parameters.
We first evaluated three SNPs in the 19p13.1 locus- rs8170, rs8100241, and rs2363956-for associations with overall risk of invasive breast cancer in BCAC studies of white European women. Rs8170 was genotyped in all 37 studies (47,671 cases and 48,306 controls), while only a subset of studies genotyped rs8100241 (21,645 cases and 21,521 controls) or rs2363956 (17,857 cases and 20,648 controls) (Supplementary Table 1). Neither rs8170 nor rs2363965 was associated with risk of overall invasive breast cancer. However, the A allele of rs8100241 was associated with a small increased risk of breast cancer [Odds Ratio (OR)=1.04, 95% Confidence Interval (CI) 1.01 – 1.08, p=2.88 × 10−3] (Table 1). Results were very similar when excluding four case-only studies (Supplementary Table 4). No associations were observed between rs8170, rs8100241, or rs2363956 and risk of ductal carcinoma in situ (DCIS). Similarly, no association was observed between rs8170 or rs8100241 and risk of invasive breast cancer in two BCAC studies of Asian women including 1,198 breast cancer cases and 1,481 controls, although power to detect an association with rs8170 was limited due to a very low minor allele frequency of 0.20% in this population (Supplementary Table 5). Adjustment for age did not change the magnitude or significance of our results.
Table 1
Table 1
19p13.1 single SNP associations with breast cancer among white European women
Given that the 19p13.1 susceptibility locus was first identified as a modifier of breast cancer risk in BRCA1 mutation carriers (9), who predominantly develop tumors with an ER-negative or TN phenotype, we next evaluated associations between these three SNPs and risk of invasive breast cancer subtypes as defined by ER, PR, and HER2 status (Table 2). Since genotype data were available for rs8170 in the entire BCAC data set, we focused on this SNP in the analyses of breast cancer subtypes. When considering ER status alone, rs8170 was associated with risk of ER-negative breast cancer [OR=1.09, 95% CI 1.05 – 1.14, p=6.69 × 10−5], but not with ER-positive breast cancer [OR=0.99, 95% CI 0.96 – 1.02, p=0.38] [pHet=1.61 × 10−5] (Table 2). A similar pattern was observed for PR status [PR-negative OR=1.05, 95% CI 1.01 – 1.10, p=7.39 × 10−3] [pHet=6.52 × 10−3] (Table 2). When considering both ER and PR status, rs8170 was associated only with tumors negative for both markers [OR=1.10, 95% CI 1.05 – 1.16, p=4.10 × 10−5] (Table 2). Incorporation of HER2 status demonstrated that the 19p13.1 locus was associated with risk of TN breast cancer [OR=1.21, 95% CI 1.13 – 1.31, p=2.97 × 10−7], but not any other combination of ER, PR and HER2 status [pHet=1.32 × 10−5]. In particular, rs8170 was not associated with risk of developing HER2-negative tumors that were ER-positive or PR-positive [OR=1.00, 95% CI 0.97 – 1.04, p=0.80], indicating that rs8170 is associated with TN rather than HER2-negative disease. The estimate of effect for rs8170 was stronger among TN breast cancers (OR=1.21) than all ER-negative breast cancers (OR=1.09). Analysis of rs8170 among cases only was consistent with the case-control analyses (Supplementary Table 6). Similar patterns by subtype were observed for rs8100241 and rs2363956 (Supplementary Table 7). Exclusion of the four case-only BCAC studies did not substantially alter these findings (Supplementary Table 8).
Table 2
Table 2
Risk of invasive breast cancer associated with rs8170 among white Europeans defined by ER, PR, and HER2 tumor status
We next investigated whether variants in the 19p13.1 locus were associated specifically with risk of TN disease by comparing TN cases (ER−, PR−, HER2−) to non-TN, ER-negative cases (ER−, PR+ or HER2+) in an analysis of ER-negative breast cancers with known ER, PR, and HER2 status (Table 3). Rs8170 was not associated with risk of ER-negative breast cancer when excluding TN cases [OR=0.98, 95% CI 0.89 – 1.07, p=0.63], but remained strongly associated with risk of TN breast cancer [OR=1.21, 95% CI 1.13 – 1.31, p=2.94 × 10−7, pHet=9.07 × 10−5]. Given that basal-like tumors account for approximately 80% of TN tumors (15), we also evaluated the influence of cytokeratin 5/6 (CK5/6) and epidermal growth factor receptor (EGFR) basal-tumor marker status on the 19p13.1 association with breast cancer risk. Due to limited data for these markers (Supplementary Table 3), we focused on rs8170 to maximize power to detect differences by basal status. Rs8170 was significantly associated with risk of basal-like TN tumors [OR=1.27, 95% CI 1.07 – 1.50, p=0.0069], but was not associated with risk of non-basal TN tumors [OR=1.03, 95%CI 0.79 – 1.34, p=0.83] [pHet=0.026] (Supplementary Table 9). Furthermore, rs8170 was not associated with either ER-positive basal tumors (n=301) [OR=0.90, 95% CI 0.73 – 1.10, p=0.30] or ER-negative, non-TN basal tumors (n=122) [OR=0.89, 95% CI 0.64 – 1.23, p=0.48] [pHet=0.80]. This suggests that the 19p13.1 locus is exclusively associated with TN, basal-like tumors. However, because of the small sample size and potential misclassification of CK5/6 and EGFR, these results need to be confirmed in larger studies of breast cancer subtypes.
Table 3
Table 3
Triple negative-specific risk associated with rs8170
We next extended our evaluation of 19p13.1 variants to non-overlapping subjects (1,350 TN cases, 3,852 controls) from the Triple Negative Breast Cancer Consortium (TNBCC) (Supplementary Table 1) (12). Among the TNBCC studies alone, rs8170 was associated with an increased risk of TN breast cancer [OR=1.26, 95% CI 1.13 – 1.40, p=3.02 × 10−5] (Table 3). Importantly, the combined rs8170 genotype data from BCAC and TNBCC (n=3,566 TN cases), yielded a genome wide significant association with risk of TN breast cancer [OR=1.25, 95% CI 1.18 – 1.33, p=4.24 × 10−13] (Table 3). There was no evidence for heterogeneity of the ORs by country for either TN or non-TN, ER-negative breast cancer in the combined analysis (Figure 1). The difference in effect estimates between TN and non-TN, ER-negative breast cancer was highly significant [pHet=2.51 × 10−6], indicating that rs8170 is a TN-specific risk variant. A similar pattern was observed for rs8100241, which was inversely associated only with TN disease [OR=0.81, 95% CI 0.76 – 0.86, p=1.91 × 10−12] and not with non-TN, ER-negative disease [OR=0.94, 95% CI 0.86 – 1.03, p=0.19] in the combined data set [pHet=3.30 × 10−3] (Supplementary Table 10).
Figure 1
Figure 1
19p13.1 (rs8170) association with risk of non-TN, ER-negative and TN breast cancer
To better understand the influence of 19p13.1 variants on risk of TN breast cancer, we included both rs8170 and rs8100241 in a multivariate model in the combined BCAC and TNBCC data set. Both rs8170 [OR=1.16, 95% CI 1.07 – 1.26, p=6.14 × 10−4] and rs8100241 [OR=0.85, 95% CI 0.79 – 0.91, p=5.10 × 10−6] remained significantly associated with risk of TN breast cancer with only slight attenuation of the ORs. However, when considering the association of one SNP stratified by the genotype of the other, we found that the effect of rs8170 was restricted to individuals with the rs8100241 “GA” genotype [OR=1.29, 95%CI 1.14 – 1.45, p=3.13 × 10−5] and that the effect of rs8100241 was restricted to individuals with the rs8170 “CC” genotype [OR=0.82, 95%CI 0.76 – 0.89, p=9.90 × 10−7] (Supplementary Table 11a). This is reflected by a significant interaction between these SNP [Interaction OR=1.21, 95% CI 1.06 – 1.37, p=0.0036] (Supplementary Table 11b). A haplotype analysis for these two SNPs found that the C-G and T-G haplotypes (rs8170-rs8100241) were both associated with risk of TN breast cancer compared to the C-A haplotype [C-G OR=1.17, 95% CI 1.09 – 1.25, p=1.00 × 10−5; T-G OR=1.35, 95% CI 1.25 – 1.46, p=2.51 × 10−14], while the T-A haplotype was not observed at all (Supplementary Table 12), suggesting that both SNPs tag the causal variant. No interactions were observed between these SNPs among other subtypes defined by any combination of ER, PR, and HER2 status.
Due to overlap between the BCAC samples in this analysis and a subset of those in SEARCH and the TNBCC, which were previously examined in an initial generalization of 19p13.1 SNP associations with BRCA1-related tumors (9), we performed a sensitivity analysis removing these studies from the ER and ER/PR/HER2 subtype analyses. The effect estimates in this sensitivity analysis were very similar to those from the complete BCAC analysis, with only slight attenuation of significance (Supplementary Table 13).
Here we report on the identification of the first TN breast cancer specific susceptibility locus at 19p13.1. We found that rs8170 was strongly associated with risk of TN breast cancer [OR=1.25, p=4.24 × 10−13], but was not associated with ER-positive [OR=0.99, p=0.38] or non-TN, ER-negative [OR=0.98, p=0.63] breast cancer. Further analyses based on basal tumor markers suggested that the 19p13.1 variants are associated specifically with basal-like TN tumors [OR=1.27, p=0.0069]. Ongoing histopathology studies in BCAC involving characterization of the CK5/6 and EGFR status of tumors may increase the numbers of TN-basal cases and allow re-evaluation of this finding in the future. We were well powered to detect an association between 19p13.1 variants and these breast cancer subtypes in more than 32,000 cases and 48,000 controls. Importantly, our ability to evaluate risk of breast cancer across histological subtypes in a single, large consortium strengthens the validity of the findings. Heterogeneity in hormone receptor and basal marker status across studies may influence our ability to detect associations with breast tumor subtypes at 19p13.1. However, in a sensitivity analysis including only cases from studies with the most stringent criteria for defining hormone receptor status (<1% of cells stained positive for ER and PR, HER2 0 or 1+ on IHC), the effect estimates were very similar to those from the complete analysis of the ER-negative, non-TN and TN subtypes. These findings have important implications for understanding genetic susceptibility to breast cancer, because they suggest that additional susceptibility variants for specific subtypes of breast cancer remain to be identified.
TN breast cancer accounts for approximately 15% of all breast cancer among women of European descent and differs substantially from other subtypes of breast cancer by expression and genomic profiles and by epidemiologic characteristics (15). Women with TN breast cancer are more likely to be younger, have an earlier age at menarche, higher body mass index during premenopausal years, higher parity, and a lower lifetime duration of breast feeding and in the US are more likely to be African American or Latina (1618), and TN tumors are associated with more aggressive disease and poorer survival (15, 19, 20). The biological and clinical distinctions between TN and other breast cancer subtypes are concordant with the identification of TN-specific genetic risk factors and provide additional evidence for a distinct TN tumor etiology. This highlights the importance of additional subtype-specific breast cancer studies, and studies of breast cancer in additional populations such as African Americans and Latinas, since it is not known whether similar associations with the SNPs described here exist in these populations.
The three 19p13.11 variants measured in this study are located in the genes C19orf62 and ANKLE1 and are approximately 13kb from the gene ABHD8. C19orf62, which encodes the MERIT40 protein, is currently hypothesized to be the most likely cancer susceptibility gene in this region due to the known interaction between MERIT40 and BRCA1. MERIT40 is integral to the localization of the BRCA1-A complex during DNA double-strand break repair, specifically through the recruitment and retention of the BRCA1-BARD1 ubiquitin ligase and the BRCC36 deubiquitination enzyme (2124). However, both ANKLE1 (ankyrin repeat and LEM domain containing 1) and ABHD8 (abhydrolase domain containing 8) encode proteins of uncharacterized functions, making conjecture about the involvement of these proteins in cancer-related processes difficult.
It is unknown whether a single causal variant or multiple rare variants underlie the 19p13.1 association, affecting TN risk through dysregulation of these or other nearby genes. Conversely, the causal variant at 19p13.1 may lie in a regulatory element that confers risk to TN disease through long-range effects on distant genes. Although the biology underlying this association is unknown, it is likely that the functional consequences of variants at 19p13.1 are to modify genes or proteins that cooperate with other factors in signaling pathways critical to the development of the TN phenotype. One can speculate that the causal 19p13.1 variants directly initiate and promote TN tumor development, or alternatively that the 19p13.1 causal variants act to change the morphology of an existing malignant breast lesion to a TN phenotype early in tumorigenesis. Re-sequencing and fine-mapping efforts in TN breast cancer cases will be important for identification of the causal variants in the 19p13.1 locus and the mechanism by which these variants specifically influence risk of TN breast cancer.
In conclusion, our study provides convincing evidence that the 19p13.1 locus is specifically associated with risk of TN disease, confirming that some breast cancer susceptibility loci differ by histological breast tumor subtype defined by ER, PR and HER2 status. This report provides further evidence that TN tumors and other subtypes likely arise through distinct etiologic pathways. Genetic and functional studies of TN breast cancer will be necessary to identify the mechanism underlying the 19p13.1 association and to identify additional TN-specific susceptibility loci.
Supplementary Material
Acknowledgments
Grant Support
This work was supported by the National Institutes of Health grant CA122340, a Specialized Program of Research Excellence (SPORE) in Breast Cancer (CA116201), the Komen Foundation for the Cure and the Breast Cancer Research Foundation (BCRF); BCAC is funded by CR-UK [C1287/A10118, C1287/A12014] and by the European Community’s Seventh Framework Programme under grant agreement n° 223175 (HEALTH-F2-2009-223175) (COGS), and by the European Union COST programme [BM0606]. D.F.E. is a Principal Research Fellow of Cancer Research UK; SBCS: Breast Cancer Campaign (2004Nov49 to AC) and Yorkshire Cancer Research Core Funding (Institute for Cancer Studies); ABCS: Dutch Cancer Society grant [NKI 2009-4363 and NKI 2007-3839 to MKS] and the Dutch National Genomics Initiative; ACP: Breast Cancer Research Trust, UK. ES is funded by National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Guy’s & St. Thomas’ NHS Foundation Trust in partnership with King’s College London. IT is funded by the Oxford Biomedical Research Centre; ABCFS, NC-BCFR and OFBCR: National Cancer Institute, National Institutes of Health (NIH) under RFA-CA-06-503 and through cooperative agreements with members of the Breast Cancer Family Registry (BCFR) and Principal Investigators, including Cancer Care Ontario (U01 CA69467), Northern California Cancer Center (U01 CA69417), University of Melbourne (U01 CA69638); ABCFS: National Health and Medical Research Council of Australia, the New South Wales Cancer Council, the Victorian Health Promotion Foundation (Australia) and the Victorian Breast Cancer Research Consortium. J.L.H. is a National Health and Medical Research Council (NHMRC) Australia Fellow and a Victorian Breast Cancer Research Consortium Group Leader. M.C.S. is a NHMRC Senior Research Fellow and a Victorian Breast Cancer Research Consortium Group Leader; CNIO-BCS: Genome Spain Foundation, the Red Temática de Investigación Cooperativa en Cáncer and grants from the Asociación Española Contra el Cáncer and the Fondo de Investigación Sanitario (PI081583 and PI081120); The California Teachers Study: California Breast Cancer Act of 1993, National Institutes of Health (R01 CA77398), the Lon V Smith Foundation [LVS39420]), and the California Breast Cancer Research Fund (contract 97-10500); UCIBCS: NIH [CA58860, CA92044] and the Lon V Smith Foundation [LVS39420]; ESTHER: Baden Württemberg Ministry of Science, Research and Arts, and the VERDI study supported by a grant from the German Cancer Aid (Deutsche Krebshilfe); GENICA: Federal Ministry of Education and Research (BMBF) Germany (01KW9975/5, 01KW9976/8, 01KW9977/0 and 01KW0114), the Robert Bosch Foundation, Stuttgart, Deutsches Krebsforschungszentrum (DKFZ) Heidelberg, Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, and the Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany: KBCP: Finnish Cancer Society, the Academy of Finland (grant number 127220), the special Government Funding (EVO) of Kuopio University Hospital (grant number 5654113 and 5501) and by the strategic funding of the University of Eastern Finland; OBCS: Finnish Cancer Foundation, the Academy of Finland, the University of Oulu, the Oulu University Hospital and Biocenter Oulu; RPCI: P30 grant to RPCI (CA016056-32); The Breakthrough Generations Study: Breakthrough Breast Cancer and the Institute of Cancer Research (ICR). ICR acknowledges NHS funding to the NIHR Biomedical Research Centre; PBCS: Intramural Research Funds of the National Cancer Institute, USA; HEBCS: Helsinki University Central Hospital Research Fund, Academy of Finland (132473), the Finnish Cancer Society, and the Sigrid Juselius Foundation; MARIE: Deutsche Krebshilfe e.V., grant number 70-2892-BR I, the Hamburg Cancer Society, the German Cancer Research Center (DKFZ) and the Federal Ministry of Education and Research (BMBF) Germany grant 01KH0402; GESBC: Deutsche Krebshilfe e. V. [70492] and the state of Baden-Württemberg through the Medical Faculty of the University of Ulm [P.685]; BSUCH: Dietmar Hopp Foundation, the German Cancer Research Center, DKFZ and the Helmholtz association; GC-HBOC: Deutsche Krebshilfe [107054], the Center of MolecularMedicine, Cologne, the German Cancer Research Center, DKFZ and the Helmholtz society; BBCS: Cancer Research UK, Breakthrough Breast Cancer and the National Cancer Research Network (NCRN); kConFab: National Breast Cancer Foundation, the National Health and Medical Research Council (NHMRC) and by the Queensland Cancer Fund, the Cancer Councils of New South Wales, Victoria, Tasmania and South Australia, the Cancer Foundation of Western Australia, and Cancer Australia #628333; LMBC: ‘Stichting tegen Kanker’ (232-2008 and 196-2010);MCCS: Australian National Health and Medical Research Council [grants #209057, 251533, 396414, 504711], Cancer Council Victoria, and VicHealth; ORIGO: Dutch Cancer Society; SEARCH: Cancer Research UK [C8197/A10123, C8197/A10123 and C490/A10124]. AMD was supported by Cancer Research UK grant [C8197/A10865] and by the Joseph Mitchell Fund; FCCC: National Institutes of Health (U01 CA69631, 5U01 CA113916 to A.K.G.), the Eileen Stein Jacoby Fund, The University of Kansas Cancer Center, and the Kansas Bioscience Authority Eminent Scholar Program. A.K.G. is the Chancellors Distinguished Chair in Biomedical Sciences endowed Professor.
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