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Geman D, Ochs M, Price ND, Tomasetti C, Younes L. An argument for mechanism-based statistical inference in cancer. Hum Genet 2015; 134:479-95. [PMID: 25381197 PMCID: PMC4612627 DOI: 10.1007/s00439-014-1501-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 10/14/2014] [Indexed: 01/07/2023]
Abstract
Cancer is perhaps the prototypical systems disease, and as such has been the focus of extensive study in quantitative systems biology. However, translating these programs into personalized clinical care remains elusive and incomplete. In this perspective, we argue that realizing this agenda—in particular, predicting disease phenotypes, progression and treatment response for individuals—requires going well beyond standard computational and bioinformatics tools and algorithms. It entails designing global mathematical models over network-scale configurations of genomic states and molecular concentrations, and learning the model parameters from limited available samples of high-dimensional and integrative omics data. As such, any plausible design should accommodate: biological mechanism, necessary for both feasible learning and interpretable decision making; stochasticity, to deal with uncertainty and observed variation at many scales; and a capacity for statistical inference at the patient level. This program, which requires a close, sustained collaboration between mathematicians and biologists, is illustrated in several contexts, including learning biomarkers, metabolism, cell signaling, network inference and tumorigenesis.
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Affiliation(s)
- Donald Geman
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, 21210, USA,
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202
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Delahaye-Sourdeix M, Oliver J, Timofeeva MN, Gaborieau V, Johansson M, Chabrier A, Wozniak MB, Brenner DR, Vallée MP, Anantharaman D, Lagiou P, Holcátová I, Richiardi L, Kjaerheim K, Agudo A, Castellsagué X, Macfarlane TV, Barzan L, Canova C, Thakker NS, Conway DI, Znaor A, Healy CM, Ahrens W, Zaridze D, Szeszenia-Dabrowska N, Lissowska J, Fabianova E, Mates IN, Bencko V, Foretova L, Janout V, Curado MP, Koifman S, Menezes A, Wünsch-Filho V, Eluf-Neto J, Boffetta P, Garrote LF, Serraino D, Lener M, Jaworowska E, Lubiński J, Boccia S, Rajkumar T, Samant TA, Mahimkar MB, Matsuo K, Franceschi S, Byrnes G, Brennan P, McKay JD. The 12p13.33/RAD52 locus and genetic susceptibility to squamous cell cancers of upper aerodigestive tract. PLoS One 2015; 10:e0117639. [PMID: 25793373 PMCID: PMC4368781 DOI: 10.1371/journal.pone.0117639] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/29/2014] [Indexed: 11/18/2022] Open
Abstract
Genetic variants located within the 12p13.33/RAD52 locus have been associated with lung squamous cell carcinoma (LUSC). Here, within 5,947 UADT cancers and 7,789 controls from 9 different studies, we found rs10849605, a common intronic variant in RAD52, to be also associated with upper aerodigestive tract (UADT) squamous cell carcinoma cases (OR = 1.09, 95% CI: 1.04-1.15, p = 6x10(-4)). We additionally identified rs10849605 as a RAD52 cis-eQTL inUADT(p = 1x10(-3)) and LUSC (p = 9x10(-4)) tumours, with the UADT/LUSC risk allele correlated with increased RAD52 expression levels. The 12p13.33 locus, encompassing rs10849605/RAD52, was identified as a significant somatic focal copy number amplification in UADT(n = 374, q-value = 0.075) and LUSC (n = 464, q-value = 0.007) tumors and correlated with higher RAD52 tumor expression levels (p = 6x10(-48) and p = 3x10(-29) in UADT and LUSC, respectively). In combination, these results implicate increased RAD52 expression in both genetic susceptibility and tumorigenesis of UADT and LUSC tumors.
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Affiliation(s)
- Manon Delahaye-Sourdeix
- Genetic Cancer Susceptibility group (GCS), International Agency for Research on Cancer (IARC), Lyon, France
| | - Javier Oliver
- Genetic Cancer Susceptibility group (GCS), International Agency for Research on Cancer (IARC), Lyon, France
| | - Maria N. Timofeeva
- Genetic Epidemiology group (GEP), International Agency for Research on Cancer (IARC), Lyon, France
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council (MRC) Human Genetics Unit, Edinburgh, United Kingdom
| | - Valérie Gaborieau
- Genetic Epidemiology group (GEP), International Agency for Research on Cancer (IARC), Lyon, France
| | - Mattias Johansson
- Genetic Epidemiology group (GEP), International Agency for Research on Cancer (IARC), Lyon, France
| | - Amélie Chabrier
- Genetic Cancer Susceptibility group (GCS), International Agency for Research on Cancer (IARC), Lyon, France
| | - Magdalena B. Wozniak
- Genetic Epidemiology group (GEP), International Agency for Research on Cancer (IARC), Lyon, France
| | - Darren R. Brenner
- Genetic Epidemiology group (GEP), International Agency for Research on Cancer (IARC), Lyon, France
| | - Maxime P. Vallée
- Genetic Cancer Susceptibility group (GCS), International Agency for Research on Cancer (IARC), Lyon, France
| | - Devasena Anantharaman
- Genetic Epidemiology group (GEP), International Agency for Research on Cancer (IARC), Lyon, France
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, University of Athens School of Medicine, Athens, Greece
| | - Ivana Holcátová
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lorenzo Richiardi
- University of Turin, Department of Medical Sciences, Unit of Cancer Epidemiology, Turin, Italy
| | | | - Antonio Agudo
- Catalan Institute of Oncology-ICO, IDIBELL. L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Castellsagué
- Catalan Institute of Oncology-ICO, IDIBELL. L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | | | - Cristina Canova
- Department of Environmental Medicine and Public Health, University of Padova, Padova, Italy
- MRC-HPA Centre for Environment and Health, Respiratory Epidemiology and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Nalin S. Thakker
- University of Manchester, School of Dentistry, Manchester, United Kingdom
| | - David I. Conway
- University of Glasgow Dental School, Glasgow, Scotland, United Kingdom
| | - Ariana Znaor
- Croatian National Cancer Registry, Croatian National Institute of Public Health, Zagreb, Croatia
| | | | - Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology—BIPS, Bremen, Germany
- Faculty of Mathematics and Computer Science, University of Bremen, Bremen, Germany
| | - David Zaridze
- Institute of Carcinogenesis, Cancer Research Centre, Moscow, Russian Federation
| | | | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | | | - Ioan Nicolae Mates
- Saint Mary General and Esophageal Surgery Clinic, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Vladimir Bencko
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute and Masaryk University, Brno, Czech Republic
| | | | | | - Sergio Koifman
- National School of Public Health/FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Menezes
- Universidade Federal de Pelotas, Pelotas, Brazil
| | | | | | - Paolo Boffetta
- The Tisch Cancer Institute Mount Sinai School of Medicine, New York, NY, United States of America
| | | | - Diego Serraino
- Centro di Riferimento Oncologico, IRCSS, Unit of Epidemiology and Biostatistics, Aviano, Italy
| | - Marcin Lener
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Ewa Jaworowska
- Department of Otolaryngology and Laryngological Oncology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Stefania Boccia
- Institute of Public Health, Section of Hygiene, Faculty of Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Tanuja A. Samant
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Manoj B. Mahimkar
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Keitaro Matsuo
- Department of Health Promotion, Division of Oral Pathology, Kyushu Dental University, Kitakyushu, Japan
| | - Silvia Franceschi
- Infections and Cancer Epidemiology group (ICE), International Agency for Research on Cancer (IARC), Lyon, France
| | - Graham Byrnes
- Biostatistics group (BST), International Agency for Research on Cancer (IARC), Lyon, France
| | - Paul Brennan
- Genetic Epidemiology group (GEP), International Agency for Research on Cancer (IARC), Lyon, France
| | - James D. McKay
- Genetic Cancer Susceptibility group (GCS), International Agency for Research on Cancer (IARC), Lyon, France
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203
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Quitadamo A, Tian L, Hall B, Shi X. An integrated network of microRNA and gene expression in ovarian cancer. BMC Bioinformatics 2015; 16 Suppl 5:S5. [PMID: 25860109 PMCID: PMC4402579 DOI: 10.1186/1471-2105-16-s5-s5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Ovarian cancer is a deadly female reproductive cancer. Understanding the biological mechanisms underlying ovarian cancer could help lead to quicker and more accurate diagnosis and more effective treatments. Both changes in microRNA(miRNA) expression and miRNA/mRNA dysregulation have been associated with ovarian cancer. With the availability of whole-genome miRNA and mRNA sequencing we now have new potentials to study these associations. In this study, we performed a comprehensive analysis of miRNA and mRNA expression in ovarian cancer using an integrative network approach combined with association analysis. Results We developed an integrative approach to construct a network that illustrates the complex interplay among miRNA and gene expression from a systems perspective. Our method is composed of expanding networks from eQTL associations, building network associations in eQTL analysis, and then combine the networks into an integrated network. This integrated network takes account of miRNA expression quantitative trait loci (eQTL) associations, miRNAs and their targets, protein-protein interactions, co-expressions among miRNAs and genes respectively. Applied to the ovarian cancer data set from The Cancer Genome Atlas (TCGA), we created an integrated network with 167 nodes containing 108 miRNA-target interactions and 145 from protein-protein interactions, starting from 44 initial eQTLs. This integrated network encompassed 26 genes and 14 miRNAs associated with cancer. In particular, 11 genes and 12 miRNAs in the integrated network are associated with ovarian cancer. Conclusion We demonstrated an integrated network approach that integrates multiple data sources at a systems level. We applied this approach to the TCGA ovarian cancer dataset, and constructed a network that provided a more inclusive view of miRNA and gene expression in ovarian cancer. This network included four separate types of interactions among miRNAs and genes. Simply analyzing each interaction component in isolation, such as the eQTL associations, the miRNA-target interactions or the protein-protein interactions, would create a much more limited network than the integrated one.
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204
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Garritano S, Romanel A, Ciribilli Y, Bisio A, Gavoci A, Inga A, Demichelis F. In-silico identification and functional validation of allele-dependent AR enhancers. Oncotarget 2015; 6:4816-28. [PMID: 25693204 PMCID: PMC4467117 DOI: 10.18632/oncotarget.3019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/30/2014] [Indexed: 12/13/2022] Open
Abstract
Androgen Receptor (AR) and Estrogen Receptors (ERs) are key nuclear receptors that can cooperate in orchestrating gene expression programs in multiple tissues and diseases, targeting binding elements in promoters and distant enhancers. We report the unbiased identification of enhancer elements bound by AR and ER-α whose activity can be allele-specific depending on the status of nearby Single Nucleotide Polymorphisms (SNP). ENCODE data were computationally mined to nominate genomic loci with: (i) chromatin signature of enhancer activity from activation histone marks, (ii) binding evidence by AR and ER-α, (iii) presence of a SNP. Forty-one loci were identified and two, on 1q21.3 and 13q34, selected for characterization by gene reporter, Chromatin immunoprecipitation (ChIP) and RT-qPCR assays in breast (MCF7) and prostate (PC-3) cancer-derived cell lines. We observed allele-specific enhancer activity, responsiveness to ligand-bound AR, and potentially influence on the transcription of closely located genes (RAB20, ING1, ARHGEF7, ADAM15). The 1q21.3 variant, rs2242193, showed impact on AR binding in MCF7 cells that are heterozygous for the SNP. Our unbiased genome-wide search proved to be an efficient methodology to discover new functional polymorphic regulatory regions (PRR) potentially acting as risk modifiers in hormone-driven cancers and overall nominated SNPs in PRR across 136 transcription factors.
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MESH Headings
- Alleles
- Blotting, Western
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Chromatin Immunoprecipitation
- Computer Simulation
- Enhancer Elements, Genetic/genetics
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Genome, Human
- Humans
- Male
- Polymorphism, Single Nucleotide/genetics
- Promoter Regions, Genetic/genetics
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Tumor Cells, Cultured
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Affiliation(s)
- Sonia Garritano
- Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, Italy
| | - Alessandro Romanel
- Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, Italy
| | - Yari Ciribilli
- Laboratory of Transcriptional Networks, CIBIO, Centre for Integrative Biology, University of Trento, Italy
| | - Alessandra Bisio
- Laboratory of Transcriptional Networks, CIBIO, Centre for Integrative Biology, University of Trento, Italy
| | - Antoneta Gavoci
- Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, CIBIO, Centre for Integrative Biology, University of Trento, Italy
| | - Francesca Demichelis
- Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, Italy
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, USA
- Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY, USA
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205
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Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015; 16:197-212. [DOI: 10.1038/nrg3891] [Citation(s) in RCA: 684] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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206
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Singh PK, Preus L, Hu Q, Yan L, Long MD, Morrison CD, Nesline M, Johnson CS, Koochekpour S, Kohli M, Liu S, Trump DL, Sucheston-Campbell LE, Campbell MJ. Serum microRNA expression patterns that predict early treatment failure in prostate cancer patients. Oncotarget 2015; 5:824-40. [PMID: 24583788 PMCID: PMC3996656 DOI: 10.18632/oncotarget.1776] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We aimed to identify microRNA (miRNA) expression patterns in the serum of prostate cancer (CaP) patients that predict the risk of early treatment failure following radical prostatectomy (RP). Microarray and Q-RT-PCR analyses identified 43 miRNAs as differentiating disease stages within 14 prostate cell lines and reflectedpublically available patient data. 34 of these miRNA were detectable in the serum of CaP patients. Association with time to biochemical progression was examined in a cohort of CaP patients following RP. A greater than two-fold increase in hazard of biochemical progression associated with altered expression of miR-103, miR-125b and miR-222 (p <.0008) in the serum of CaP patients. Prediction models based on penalized regression analyses showed that the levels of the miRNAs and PSA together were better at detecting false positives than models without miRNAs, for similar level of sensitivity. Analyses of publically available data revealed significant and reciprocal relationships between changes in CpG methylation and miRNA expression patterns suggesting a role for CpG methylation to regulate miRNA. Exploratory validation supported roles for miR-222 and miR-125b to predict progression risk in CaP. The current study established that expression patterns of serum-detectable miRNAs taken at the time of RP are prognostic for men who are at risk of experiencing subsequent early biochemical progression. These non-invasive approaches could be used to augment treatment decisions.
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Affiliation(s)
- Prashant K Singh
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY
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207
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Pierce BL, Tong L, Chen LS, Rahaman R, Argos M, Jasmine F, Roy S, Paul-Brutus R, Westra HJ, Franke L, Esko T, Zaman R, Islam T, Rahman M, Baron JA, Kibriya MG, Ahsan H. Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians. PLoS Genet 2014; 10:e1004818. [PMID: 25474530 PMCID: PMC4256471 DOI: 10.1371/journal.pgen.1004818] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 10/13/2014] [Indexed: 11/21/2022] Open
Abstract
A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine if observed trans-eQTL associations are mediated by expression of transcripts in cis with the SNPs showing trans-association, using Sobel tests of mediation. We observed 434 independent trans-eQTL associations at a false-discovery rate of 0.05, and 189 of these trans-eQTLs were also cis-eQTLs (enrichment P<0.0001). Among these 189 trans-eQTL associations, 39 were significantly attenuated after adjusting for a cis-mediator based on Sobel P<10-5. We attempted to replicate 21 of these mediation signals in two European cohorts, and while only 7 trans-eQTL associations were present in one or both cohorts, 6 showed evidence of cis-mediation. Analyses of simulated data show that complete mediation will be observed as partial mediation in the presence of mediator measurement error or imperfect LD between measured and causal variants. Our data demonstrates that trans-associations can become significantly stronger or switch directions after adjusting for a potential mediator. Using simulated data, we demonstrate that this phenomenon is expected in the presence of strong cis-trans confounding and when the measured cis-transcript is correlated with the true (unmeasured) mediator. In conclusion, by applying mediation analysis to eQTL data, we show that a substantial fraction of observed trans-eQTL associations can be explained by cis-mediation. Future studies should focus on understanding the mechanisms underlying widespread cis-mediation and their relevance to disease biology, as well as using mediation analysis to improve eQTL discovery. Expression quantitative trait locus (eQTL) studies have demonstrated that human genes can be regulated by genetic variation residing close to the gene (cis-eQTLs) or in a distant region or on a different chromosome (trans-eQTLs). While cis-eQTL variants are likely to affect transcription factor binding or chromatin structure, our understanding of the mechanisms underlying trans-eQTLs is incomplete. We hypothesize that a substantial fraction of trans-eQTLs influence expression of distant genes through mediation by expression levels of a cis-transcript. In this paper, we use genome-wide SNPs and expression data for 1,799 South Asians to identify cis- and trans-eQTLs and to test our hypothesis using Sobel tests of mediation. Among 189 observed trans-eQTL associations, we provide evidence of cis-mediation for 39, 6 of which show mediation in an independent European cohort. We used simulated data to demonstrate that complete mediation will be observed as partial mediation in the presence of mediator measurement error or imperfect LD between measured and causal variants. We also demonstrate how unobserved confounding variables and incorrect mediator selection can bias mediation estimates. In conclusion, we have identified cis-mediators for many trans-eQTLs and described a mediation analysis approach that can be used to validate, characterize, and enhance discovery of trans-eQTLs.
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Affiliation(s)
- Brandon L. Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
- Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (BLP); (HA)
| | - Lin Tong
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Lin S. Chen
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Ronald Rahaman
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Maria Argos
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Shantanu Roy
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Rachelle Paul-Brutus
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Harm-Jan Westra
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Rakibuz Zaman
- UChicago Research Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Tariqul Islam
- UChicago Research Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Mahfuzar Rahman
- UChicago Research Bangladesh, Mohakhali, Dhaka, Bangladesh
- Research and Evaluation Division, BRAC, Dhaka, Bangladhesh
| | - John A. Baron
- University of North Carolina, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, United States of America
| | - Muhammad G. Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, Illinois, United States of America
- Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, United States of America
- Department of Medicine The University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (BLP); (HA)
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208
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Huang YT, Hsu T, Christiani DC. TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile. Cancer Inform 2014; 13:15-23. [PMID: 25452685 PMCID: PMC4218657 DOI: 10.4137/cin.s13978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 11/30/2022] Open
Abstract
The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. We proposed a novel method to analyze multiple copy numbers of genes within a pathway, termed Test for the Effect of a Gene Set with Copy Number data (TEGS-CN). TEGS-CN was adapted from TEGS, a method that we previously developed for gene expression data using a variance component score test. With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X2 distributions that can be obtained using permutation with scaled X2 approximation. We conducted simulation studies to evaluate the size and the power of TEGS-CN and to compare its performance with TEGS. We analyzed a genome-wide copy number data from 264 patients of non-small-cell lung cancer. With the Molecular Signatures Database (MSigDB) pathway database, the genome-wide copy number data can be classified into 1814 biological pathways or gene sets. We investigated associations of the copy number profile of the 1814 gene sets with pack-years of cigarette smoking. Our analysis revealed five pathways with significant P values after Bonferroni adjustment (<2.8 × 10−5), including the PTEN pathway (7.8 × 10−7), the gene set up-regulated under heat shock (3.6 × 10−6), the gene sets involved in the immune profile for rejection of kidney transplantation (9.2 × 10−6) and for transcriptional control of leukocytes (2.2 × 10−5), and the ganglioside biosynthesis pathway (2.7 × 10−5). In conclusion, we present a new method for pathway analyses of copy number data, and causal mechanisms of the five pathways require further study.
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Affiliation(s)
- Yen-Tsung Huang
- Department of Epidemiology, Brown University, Providence, RI
| | - Thomas Hsu
- Program in Biology, Brown University, Providence, RI
| | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard School of Public Health, Boston, MA. ; Massachusetts General Hospital/Harvard Medical School, Boston, MA
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Purrington KS, Slettedahl S, Bolla MK, Michailidou K, Czene K, Nevanlinna H, Bojesen SE, Andrulis IL, Cox A, Hall P, Carpenter J, Yannoukakos D, Haiman CA, Fasching PA, Mannermaa A, Winqvist R, Brenner H, Lindblom A, Chenevix-Trench G, Benitez J, Swerdlow A, Kristensen V, Guénel P, Meindl A, Darabi H, Eriksson M, Fagerholm R, Aittomäki K, Blomqvist C, Nordestgaard BG, Nielsen SF, Flyger H, Wang X, Olswold C, Olson JE, Mulligan AM, Knight JA, Tchatchou S, Reed MWR, Cross SS, Liu J, Li J, Humphreys K, Clarke C, Scott R, Fostira F, Fountzilas G, Konstantopoulou I, Henderson BE, Schumacher F, Le Marchand L, Ekici AB, Hartmann A, Beckmann MW, Hartikainen JM, Kosma VM, Kataja V, Jukkola-Vuorinen A, Pylkäs K, Kauppila S, Dieffenbach AK, Stegmaier C, Arndt V, Margolin S, Balleine R, Arias Perez JI, Pilar Zamora M, Menéndez P, Ashworth A, Jones M, Orr N, Arveux P, Kerbrat P, Truong T, Bugert P, Toland AE, Ambrosone CB, Labrèche F, Goldberg MS, Dumont M, Ziogas A, Lee E, Dite GS, Apicella C, Southey MC, Long J, Shrubsole M, Deming-Halverson S, Ficarazzi F, Barile M, Peterlongo P, Durda K, Jaworska-Bieniek K, Tollenaar RAEM, Seynaeve C, Brüning T, Ko YD, Van Deurzen CHM, Martens JWM, Kriege M, Figueroa JD, Chanock SJ, Lissowska J, Tomlinson I, Kerin MJ, Miller N, Schneeweiss A, Tapper WJ, Gerty SM, Durcan L, Mclean C, Milne RL, Baglietto L, dos Santos Silva I, Fletcher O, Johnson N, Van'T Veer LJ, Cornelissen S, Försti A, Torres D, Rüdiger T, Rudolph A, Flesch-Janys D, Nickels S, Weltens C, Floris G, Moisse M, Dennis J, Wang Q, Dunning AM, Shah M, Brown J, Simard J, Anton-Culver H, Neuhausen SL, Hopper JL, Bogdanova N, Dörk T, Zheng W, Radice P, Jakubowska A, Lubinski J, Devillee P, Brauch H, Hooning M, García-Closas M, Sawyer E, Burwinkel B, Marmee F, Eccles DM, Giles GG, Peto J, Schmidt M, Broeks A, Hamann U, Chang-Claude J, Lambrechts D, Pharoah PDP, Easton D, Pankratz VS, Slager S, Vachon CM, Couch FJ. Genetic variation in mitotic regulatory pathway genes is associated with breast tumor grade. Hum Mol Genet 2014; 23:6034-46. [PMID: 24927736 PMCID: PMC4204763 DOI: 10.1093/hmg/ddu300] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 05/20/2014] [Accepted: 06/10/2014] [Indexed: 01/01/2023] Open
Abstract
Mitotic index is an important component of histologic grade and has an etiologic role in breast tumorigenesis. Several small candidate gene studies have reported associations between variation in mitotic genes and breast cancer risk. We measured associations between 2156 single nucleotide polymorphisms (SNPs) from 194 mitotic genes and breast cancer risk, overall and by histologic grade, in the Breast Cancer Association Consortium (BCAC) iCOGS study (n = 39 067 cases; n = 42 106 controls). SNPs in TACC2 [rs17550038: odds ratio (OR) = 1.24, 95% confidence interval (CI) 1.16-1.33, P = 4.2 × 10(-10)) and EIF3H (rs799890: OR = 1.07, 95% CI 1.04-1.11, P = 8.7 × 10(-6)) were significantly associated with risk of low-grade breast cancer. The TACC2 signal was retained (rs17550038: OR = 1.15, 95% CI 1.07-1.23, P = 7.9 × 10(-5)) after adjustment for breast cancer risk SNPs in the nearby FGFR2 gene, suggesting that TACC2 is a novel, independent genome-wide significant genetic risk locus for low-grade breast cancer. While no SNPs were individually associated with high-grade disease, a pathway-level gene set analysis showed that variation across the 194 mitotic genes was associated with high-grade breast cancer risk (P = 2.1 × 10(-3)). These observations will provide insight into the contribution of mitotic defects to histological grade and the etiology of breast cancer.
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Affiliation(s)
- Kristen S Purrington
- Department of Health Sciences Research, Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, USA
| | | | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics
| | | | - Stig E Bojesen
- Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Irene L Andrulis
- Ontario Cancer Genetics Network, Department of Molecular Genetics
| | - Angela Cox
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics
| | | | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Peter A Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, USA
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | | | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain, Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Division of Breast Cancer Research, Institute of Cancer Research, Sutton, UK
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway, Faculty of Medicine (Faculty Division Ahus), University of Oslo (UiO), Oslo, Norway
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France, University Paris-Sud, UMRS 1018, Villejuif, France
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics
| | | | - Rainer Fagerholm
- Department of Obstetrics and Gynecology, Oncology and Clinical Genetics
| | | | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA
| | | | | | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Julia A Knight
- Prosserman Centre for Health Research, Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Sandrine Tchatchou
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Malcolm W R Reed
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | | | - Christine Clarke
- Westmead Institute for Cancer Research, Sydney Medical School Westmead, University of Sydney at the Westmead Millennium Institute, Westmead, Australia
| | - Rodney Scott
- Division of Genetics, Hunter Area Pathology Service and University of Newcastle, Newcastle, Australia
| | - Florentia Fostira
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - George Fountzilas
- Department of Medical Oncology, "Papageorgiou" Hospital, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, USA
| | | | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | | | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Imaging Center, Department of Clinical Pathology
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Oncology, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland, Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | | | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Saila Kauppila
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Aida Karina Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research
| | - Sara Margolin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rosemary Balleine
- Westmead Millenium Institute for Medical Research, Sydney, Australia
| | | | - M Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
| | | | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre and Division of Breast Cancer Research
| | | | - Nick Orr
- Breakthrough Breast Cancer Research Centre and Division of Breast Cancer Research
| | - Patrick Arveux
- Center Georges-Francois Leclerc, Registry of Gynecologic Tumors, Dijon, France
| | - Pierre Kerbrat
- Centre Eugène Marquis, Department of Medical Oncology, Rennes, France
| | - Thérèse Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France, University Paris-Sud, UMRS 1018, Villejuif, France
| | - Peter Bugert
- German Red Cross Blood Service of Baden-Württemberg-Hessen, Mannheim, Germany, Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, Heidelberg University, Heidelberg, Germany
| | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | | | - France Labrèche
- Department of Environmental & Occupational Health and of Social & Preventive Medicine, School of Public Health, Université de Montréal, Montreal, Canada
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montreal, Canada, Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Canada
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, USA
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gillian S Dite
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | | | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Martha Shrubsole
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Sandra Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Filomena Ficarazzi
- Cogentech Cancer Genetic Test Laboratory, Milan, Italy, IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Caroline Seynaeve
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC-Daniel den Hoed Cancer Centrer, Rotterdam, The Netherlands
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | | | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mieke Kriege
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Michael J Kerin
- Clinical Science Institute, University Hospital Galway, Galway, Ireland
| | - Nicola Miller
- Clinical Science Institute, University Hospital Galway, Galway, Ireland
| | - Andreas Schneeweiss
- Department of Obstetrics and Gynecology, National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | | | - Susan M Gerty
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lorraine Durcan
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Catriona Mclean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Roger L Milne
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Laura Baglietto
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Isabel dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Laura J Van'T Veer
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Sten Cornelissen
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, Center for Primary Health Care Research, University of Lund, Malmö, Sweden
| | - Diana Torres
- Molecular Genetics of Breast Cancer, Institute of Human Genetics, Pontificia University Javeriana, Bogota, Colombia
| | - Thomas Rüdiger
- Institute of Pathology, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Matthieu Moisse
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium, Vesalius Research Center (VRC), VIB, Leuven, Belgium
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Judith Brown
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, USA
| | | | - John L Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health
| | | | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy and
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Peter Devillee
- Department of Human Genetics & Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, University of Tübingen, Tübingen, Germany
| | - Maartje Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Elinor Sawyer
- Division of Cancer Studies, Kings College London, Guy's Hospital, London, UK
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederick Marmee
- Department of Obstetrics and Gynecology, National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Graham G Giles
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia, Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Marjanka Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | | | | | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium, Vesalius Research Center (VRC), VIB, Leuven, Belgium
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | | | | | - Fergus J Couch
- Department of Health Sciences Research, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA,
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Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nat Genet 2014; 46:1258-63. [PMID: 25383969 DOI: 10.1038/ng.3141] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/15/2014] [Indexed: 02/07/2023]
Abstract
Somatic mutations in noncoding sequences are poorly explored in cancer, a rare exception being the recent identification of activating mutations in TERT regulatory DNA. Although this finding is suggestive of a general mechanism for oncogene activation, this hypothesis remains untested. Here we map somatic mutations in 505 tumor genomes across 14 cancer types and systematically screen for associations between mutations in regulatory regions and RNA-level changes. We identify recurrent promoter mutations in several genes but find that TERT mutations are exceptional in showing a strong and genome-wide significant association with increased expression. Detailed analysis of TERT across cancers shows that the strength of this association is highly variable and is strongest in copy number-stable cancers such as thyroid carcinoma. We additionally propose that TERT promoter mutations control expression of the nearby gene CLPTM1L. Our analysis provides a detailed pan-cancer view of TERT transcriptional activation but finds no clear evidence for frequent oncogenic promoter mutations beyond TERT.
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211
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Dryden NH, Broome LR, Dudbridge F, Johnson N, Orr N, Schoenfelder S, Nagano T, Andrews S, Wingett S, Kozarewa I, Assiotis I, Fenwick K, Maguire SL, Campbell J, Natrajan R, Lambros M, Perrakis E, Ashworth A, Fraser P, Fletcher O. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res 2014; 24:1854-68. [PMID: 25122612 PMCID: PMC4216926 DOI: 10.1101/gr.175034.114] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/06/2014] [Indexed: 01/17/2023]
Abstract
Genome-wide association studies have identified more than 70 common variants that are associated with breast cancer risk. Most of these variants map to non-protein-coding regions and several map to gene deserts, regions of several hundred kilobases lacking protein-coding genes. We hypothesized that gene deserts harbor long-range regulatory elements that can physically interact with target genes to influence their expression. To test this, we developed Capture Hi-C (CHi-C), which, by incorporating a sequence capture step into a Hi-C protocol, allows high-resolution analysis of targeted regions of the genome. We used CHi-C to investigate long-range interactions at three breast cancer gene deserts mapping to 2q35, 8q24.21, and 9q31.2. We identified interaction peaks between putative regulatory elements ("bait fragments") within the captured regions and "targets" that included both protein-coding genes and long noncoding (lnc) RNAs over distances of 6.6 kb to 2.6 Mb. Target protein-coding genes were IGFBP5, KLF4, NSMCE2, and MYC; and target lncRNAs included DIRC3, PVT1, and CCDC26. For one gene desert, we were able to define two SNPs (rs12613955 and rs4442975) that were highly correlated with the published risk variant and that mapped within the bait end of an interaction peak. In vivo ChIP-qPCR data show that one of these, rs4442975, affects the binding of FOXA1 and implicate this SNP as a putative functional variant.
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MESH Headings
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Cell Line, Tumor
- Chromatin Immunoprecipitation
- Chromosome Mapping
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 8/genetics
- Chromosomes, Human, Pair 9/genetics
- Genetic Predisposition to Disease/genetics
- Genome, Human/genetics
- Genome-Wide Association Study/methods
- Hepatocyte Nuclear Factor 3-alpha/genetics
- Hepatocyte Nuclear Factor 3-alpha/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Kruppel-Like Factor 4
- MCF-7 Cells
- Oligonucleotide Array Sequence Analysis
- Polymorphism, Single Nucleotide
- Protein Binding
- Protein Interaction Mapping
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Real-Time Polymerase Chain Reaction
- Regulatory Sequences, Nucleic Acid/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
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Affiliation(s)
- Nicola H Dryden
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Laura R Broome
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Takashi Nagano
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Simon Andrews
- Babraham Bioinformatics, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Steven Wingett
- Babraham Bioinformatics, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Iwanka Kozarewa
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Ioannis Assiotis
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Kerry Fenwick
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Sarah L Maguire
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - James Campbell
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Rachael Natrajan
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Maryou Lambros
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Eleni Perrakis
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
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Postmus I, Trompet S, Deshmukh HA, Barnes MR, Li X, Warren HR, Chasman DI, Zhou K, Arsenault BJ, Donnelly LA, Wiggins KL, Avery CL, Griffin P, Feng Q, Taylor KD, Li G, Evans DS, Smith AV, de Keyser CE, Johnson AD, de Craen AJM, Stott DJ, Buckley BM, Ford I, Westendorp RGJ, Eline Slagboom P, Sattar N, Munroe PB, Sever P, Poulter N, Stanton A, Shields DC, O’Brien E, Shaw-Hawkins S, Ida Chen YD, Nickerson DA, Smith JD, Pierre Dubé M, Matthijs Boekholdt S, Kees Hovingh G, Kastelein JJP, McKeigue PM, Betteridge J, Neil A, Durrington PN, Doney A, Carr F, Morris A, McCarthy MI, Groop L, Ahlqvist E, Bis JC, Rice K, Smith NL, Lumley T, Whitsel EA, Stürmer T, Boerwinkle E, Ngwa JS, O’Donnell CJ, Vasan RS, Wei WQ, Wilke RA, Liu CT, Sun F, Guo X, Heckbert SR, Post W, Sotoodehnia N, Arnold AM, Stafford JM, Ding J, Herrington DM, Kritchevsky SB, Eiriksdottir G, Launer LJ, Harris TB, Chu AY, Giulianini F, MacFadyen JG, Barratt BJ, Nyberg F, Stricker BH, Uitterlinden AG, Hofman A, Rivadeneira F, Emilsson V, Franco OH, Ridker PM, Gudnason V, Liu Y, Denny JC, Ballantyne CM, Rotter JI, Adrienne Cupples L, Psaty BM, Palmer CNA, Tardif JC, Colhoun HM, Hitman G, Krauss RM, Wouter Jukema J, Caulfield MJ. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins. Nat Commun 2014; 5:5068. [PMID: 25350695 PMCID: PMC4220464 DOI: 10.1038/ncomms6068] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 08/22/2014] [Indexed: 11/17/2022] Open
Abstract
Statins effectively lower LDL cholesterol levels in large studies and the observed interindividual response variability may be partially explained by genetic variation. Here we perform a pharmacogenetic meta-analysis of genome-wide association studies (GWAS) in studies addressing the LDL cholesterol response to statins, including up to 18,596 statin-treated subjects. We validate the most promising signals in a further 22,318 statin recipients and identify two loci, SORT1/CELSR2/PSRC1 and SLCO1B1, not previously identified in GWAS. Moreover, we confirm the previously described associations with APOE and LPA. Our findings advance the understanding of the pharmacogenetic architecture of statin response.
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Affiliation(s)
- Iris Postmus
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
- The Netherlands Consortium for Healthy Ageing, Leiden 2300 RC, The Netherlands
| | - Stella Trompet
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Harshal A. Deshmukh
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Michael R. Barnes
- Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, London EC1M6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London EC1M 6BQ, UK
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Helen R. Warren
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, London EC1M6BQ, UK
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215-1204, USA
- Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Kaixin Zhou
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Benoit J. Arsenault
- Montreal Heart Institute, Universite de Montreal, Montreal H1T 1C8, Quebec, Canada
| | - Louise A. Donnelly
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 98101 Seattle, Washington, USA
| | - Christy L. Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Paula Griffin
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02215, USA
| | - QiPing Feng
- Department of Clinical Pharmacology, Vanderbilt University, Nashville, Tennessee 37240, USA
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Guo Li
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 98101 Seattle, Washington, USA
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, California 94107, USA
| | - Albert V. Smith
- Icelandic Heart Association, IS-201 Kopavogur, Iceland
- University of Iceland, IS-101 Reykjavik, Iceland
| | - Catherine E. de Keyser
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Health Care Inspectorate, 2595 AN The Hague, The Netherlands
| | - Andrew D. Johnson
- Framingham Heart Study (FHS) of the National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics, Framingham, Massachusetts 01702, USA
| | - Anton J. M. de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
- The Netherlands Consortium for Healthy Ageing, Leiden 2300 RC, The Netherlands
| | - David J. Stott
- Faculty of Medicine, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G31 2ER, UK
| | - Brendan M. Buckley
- Department of Pharmacology and Therapeutics, University College Cork, Cork 30, Ireland
| | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rudi G. J. Westendorp
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
- The Netherlands Consortium for Healthy Ageing, Leiden 2300 RC, The Netherlands
- Leyden Academy of Vitality and Ageing, 2333 AA Leiden, The Netherlands
| | - P. Eline Slagboom
- The Netherlands Consortium for Healthy Ageing, Leiden 2300 RC, The Netherlands
- Department of Molecular Epidemiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Naveed Sattar
- Faculty of Medicine, BHF Glasgow Cardiovascular Research Centre, Glasgow G12 8QQ, UK
| | - Patricia B. Munroe
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, London EC1M6BQ, UK
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College, London SW7 2AZ, UK
| | - Neil Poulter
- International Centre for Circulatory Health, Imperial College, London SW7 2AZ, UK
| | - Alice Stanton
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Beaumont Hospital, Dublin 9, Ireland
| | - Denis C. Shields
- The Conway Institute, University College Dublin, Dublin 4, Ireland
- School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Eoin O’Brien
- The Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sue Shaw-Hawkins
- Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, London EC1M6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London EC1M 6BQ, UK
| | - Y.-D. Ida Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98101, USA
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington 98101, USA
| | - Marie Pierre Dubé
- Montreal Heart Institute, Universite de Montreal, Montreal H1T 1C8, Quebec, Canada
| | - S. Matthijs Boekholdt
- Department of Cardiology, Academic Medical Center, 1100 DD Amsterdam, The Netherlands
| | - G. Kees Hovingh
- Department of Vascular Medicine, Academic Medical Center, 1100 DD Amsterdam, The Netherlands
| | - John J. P. Kastelein
- Department of Vascular Medicine, Academic Medical Center, 1100 DD Amsterdam, The Netherlands
| | | | | | | | - Paul N. Durrington
- Cardiovascular Research Group, School of Biosciences, University of Manchester, Manchester M13 9NT, UK
| | - Alex Doney
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Fiona Carr
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Andrew Morris
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Old Road, Headington, Oxford OX3 7LJ, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Old Road, Headington, Oxford OX3 7LJ, UK
| | - Leif Groop
- Department of Clinical Sciences/Diabetes & Endocrinology, Lund University, Malmo 205 02, Sweden
| | - Emma Ahlqvist
- Department of Clinical Sciences/Diabetes & Endocrinology, Lund University, Malmo 205 02, Sweden
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 98101 Seattle, Washington, USA
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, 98115 Seattle, Washington, USA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, Washington 98101, USA
| | - Thomas Lumley
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 98101 Seattle, Washington, USA
- Department of Statistic, University of Auckland, Auckland 1142, New Zealand
| | - Eric A. Whitsel
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Til Stürmer
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Julius S. Ngwa
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02215, USA
| | - Christopher J. O’Donnell
- NHLBI Framingham Heart Study, Framingham, Massachusetts 01701, USA
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Ramachandran S. Vasan
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, and the Framingham Heart Study, Framingham, Massachusetts 01701, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37240, USA
| | - Russell A. Wilke
- Department of Internal Medicine, Center for IMAGENETICS, Sanford Healthcare, Fargo, North Dakota, 58104 USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02215, USA
| | - Fangui Sun
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02215, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington 98101, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98101, USA
| | - Wendy Post
- Department of Cardiology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 98101 Seattle, Washington, USA
- Division of Cardiology, Harborview Medical Center, University of Washington, Seattle 98101, Washington, USA
| | - Alice M. Arnold
- Department of Biostatistics, University of Washington, 98115 Seattle, Washington, USA
| | - Jeanette M. Stafford
- Division of Public Health Sciences, Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Jingzhong Ding
- Division of Public Health Sciences, Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - David M. Herrington
- Department of Internal Medicine, Section on Cardiology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Stephen B. Kritchevsky
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | | | - Leonore J. Launer
- Laboratory of Epidemiology, Demography, Biometry, National Institute on Aging, National Institutes of Health, 7201 Wisconsin Avenue, Bethesda, Maryland 20892, USA
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, Biometry, National Institute on Aging, National Institutes of Health, 7201 Wisconsin Avenue, Bethesda, Maryland 20892, USA
| | - Audrey Y. Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215-1204, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215-1204, USA
| | - Jean G. MacFadyen
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215-1204, USA
| | - Bryan J. Barratt
- Personalised Healthcare and Biomarkers, AstraZeneca, Alderley Park SK10 4TG, UK
| | - Fredrik Nyberg
- AstraZeneca Research and Development, 481 83 Mölndal, Sweden
- Unit of Occupational and Environmental Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Bruno H. Stricker
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Health Care Inspectorate, 2595 AN The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - André G. Uitterlinden
- The Netherlands Consortium for Healthy Ageing, Leiden 2300 RC, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Albert Hofman
- The Netherlands Consortium for Healthy Ageing, Leiden 2300 RC, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | | | - Oscar H. Franco
- Department of Epidemiology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02215-1204, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, IS-201 Kopavogur, Iceland
- University of Iceland, IS-101 Reykjavik, Iceland
| | - Yongmei Liu
- Division of Public Health Sciences, Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37240, USA
- Department of Medicine, Vanderbilt University, Vanderbilt, Tennessee 37240, USA
| | | | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02215, USA
- NHLBI Framingham Heart Study, Framingham, Massachusetts 01701, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 98101 Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington 98101, USA
- Department of Health Services, University of Washington, Seattle, Washington 98101, USA
| | - Colin N. A. Palmer
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Jean-Claude Tardif
- Montreal Heart Institute, Universite de Montreal, Montreal H1T 1C8, Quebec, Canada
| | - Helen M. Colhoun
- Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
- Department of Public Health, University of Dundee, Dundee DD1 9SY, UK
| | - Graham Hitman
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Ronald M. Krauss
- Children’s Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
- Durrer Center for Cardiogenetic Research, 1105 AZ Amsterdam, The Netherlands
- Interuniversity Cardiology Institute of the Netherlands, 3511 GC Utrecht, The Netherlands
| | - Mark J. Caulfield
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, London EC1M6BQ, UK
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Perry JRB, Day F, Elks CE, Sulem P, Thompson DJ, Ferreira T, He C, Chasman DI, Esko T, Thorleifsson G, Albrecht E, Ang WQ, Corre T, Cousminer DL, Feenstra B, Franceschini N, Ganna A, Johnson AD, Kjellqvist S, Lunetta KL, McMahon G, Nolte IM, Paternoster L, Porcu E, Smith AV, Stolk L, Teumer A, Tšernikova N, Tikkanen E, Ulivi S, Wagner EK, Amin N, Bierut LJ, Byrne EM, Hottenga JJ, Koller DL, Mangino M, Pers TH, Yerges-Armstrong LM, Zhao JH, Andrulis IL, Anton-Culver H, Atsma F, Bandinelli S, Beckmann MW, Benitez J, Blomqvist C, Bojesen SE, Bolla MK, Bonanni B, Brauch H, Brenner H, Buring JE, Chang-Claude J, Chanock S, Chen J, Chenevix-Trench G, Collée JM, Couch FJ, Couper D, Coveillo AD, Cox A, Czene K, D’adamo AP, Smith GD, De Vivo I, Demerath EW, Dennis J, Devilee P, Dieffenbach AK, Dunning AM, Eiriksdottir G, Eriksson JG, Fasching PA, Ferrucci L, Flesch-Janys D, Flyger H, Foroud T, Franke L, Garcia ME, García-Closas M, Geller F, de Geus EEJ, Giles GG, Gudbjartsson DF, Gudnason V, Guénel P, Guo S, Hall P, Hamann U, Haring R, Hartman CA, Heath AC, Hofman A, Hooning MJ, Hopper JL, Hu FB, Hunter DJ, Karasik D, Kiel DP, Knight JA, Kosma VM, Kutalik Z, Lai S, Lambrechts D, Lindblom A, Mägi R, Magnusson PK, Mannermaa A, Martin NG, Masson G, McArdle PF, McArdle WL, Melbye M, Michailidou K, Mihailov E, Milani L, Milne RL, Nevanlinna H, Neven P, Nohr EA, Oldehinkel AJ, Oostra BA, Palotie A, Peacock M, Pedersen NL, Peterlongo P, Peto J, Pharoah PDP, Postma DS, Pouta A, Pylkäs K, Radice P, Ring S, Rivadeneira F, Robino A, Rose LM, Rudolph A, Salomaa V, Sanna S, Schlessinger D, Schmidt MK, Southey MC, Sovio U, Stampfer MJ, Stöckl D, Storniolo AM, Timpson NJ, Tyrer J, Visser JA, Vollenweider P, Völzke H, Waeber G, Waldenberger M, Wallaschofski H, Wang Q, Willemsen G, Winqvist R, Wolffenbuttel BHR, Wright MJ, Boomsma DI, Econs MJ, Khaw KT, Loos RJF, McCarthy MI, Montgomery GW, Rice JP, Streeten EA, Thorsteinsdottir U, van Duijn CM, Alizadeh BZ, Bergmann S, Boerwinkle E, Boyd HA, Crisponi L, Gasparini P, Gieger C, Harris TB, Ingelsson E, Järvelin MR, Kraft P, Lawlor D, Metspalu A, Pennell CE, Ridker PM, Snieder H, Sørensen TIA, Spector TD, Strachan DP, Uitterlinden AG, Wareham NJ, Widen E, Zygmunt M, Murray A, Easton DF, Stefansson K, Murabito JM, Ong KK. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Nature 2014; 514:92-97. [PMID: 25231870 PMCID: PMC4185210 DOI: 10.1038/nature13545] [Citation(s) in RCA: 386] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/30/2014] [Indexed: 02/02/2023]
Abstract
Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P < 5 × 10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and γ-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition.
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Affiliation(s)
- John RB Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- University of Exeter Medical School, University of Exeter, Exeter, UK EX1 2LU
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Felix Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Cathy E Elks
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | | | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chunyan He
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN 46202, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children’s Hospital, Boston, MA 02115, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140 Cambridge 02142, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Wei Q Ang
- School of Women’s and Infants’ Health, The University of Western Australia
| | - Tanguy Corre
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Diana L Cousminer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - Andrea Ganna
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Andrew D Johnson
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, MA
| | - Sanela Kjellqvist
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Kathryn L Lunetta
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, MA
- Boston University School of Public Health, Department of Biostatistics. Boston, MA
| | - George McMahon
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Eleonora Porcu
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy
- University of Sassari, Dept. Of Biomedical Sciences, Sassari, Italy
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Natalia Tšernikova
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Department of Biotechnology, University of Tartu, Tartu, 51010, Estonia
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
- Hjelt Institute, University of Helsinki, Finland
| | - Sheila Ulivi
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo” – Trieste, Italy
| | - Erin K Wagner
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, IN 46202, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Najaf Amin
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Laura J Bierut
- Dept. of Psychiatry, Washington University, St. Louis, MO 63110
| | - Enda M Byrne
- The University of Queensland, Queensland Brain Institute, St.Lucia, QLD, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Daniel L Koller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Tune H Pers
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children’s Hospital, Boston, MA 02115, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140 Cambridge 02142, MA, USA
- Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, US
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical 142 University of Denmark, Lyngby 2800, Denmark
| | - Laura M Yerges-Armstrong
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition - University of Maryland School of Medicine, USA. Baltimore, MD 21201
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Irene L Andrulis
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, California, USA
| | | | - Stefania Bandinelli
- Tuscany Regional Health Agency, Florence, Italy, I.O.T. and Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
- Geriatric Unit, Azienda Sanitaria di Firenze, Florence, Italy
| | - Matthias W Beckmann
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan, Italy
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart
- University of Tübingen, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jinhui Chen
- Departments of Anatomy and Neurological Surgery, Indiana University school of Medicine, Indianapolis, IN 46202, USA
- Stark Neuroscience Research Center, Indiana University school of Medicine, Indianapolis, IN 46202, USA
| | | | - J. Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - David Couper
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
| | - Andrea D Coveillo
- Boston University School of Medicine, Department of Medicine, Sections of Preventive Medicine and Endocrinology, Boston, MA
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Adamo Pio D’adamo
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo” – Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, Italy
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minn., USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Peter Devilee
- Department of Human Genetics & Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Aida K Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, UK
| | | | - Johan G Eriksson
- National Institute for Health and Welfare, Finland
- Department of General Practice and Primary health Care, University of Helsinki, Finland
- Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland
- Folkhalsan Research Centre, Helsinki, Finland
| | - Peter A Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Research Branch, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland, United States of America
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Melissa E Garcia
- National Insitute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Montserrat García-Closas
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Eco EJ de Geus
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
- EMGO + Institute for Health and Care Research, VU University Medical Centre, Van der Boechorststraat 7, 1081 Bt, Amsterdam, The Netherlands
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Daniel F Gudbjartsson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Suiqun Guo
- Department of Obstetrics and Gynecology, Southern Medical University, Guangzhou, China
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Robin Haring
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Catharina A Hartman
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Andrew C Heath
- Washington University, Department of Psychiatry, St.Louis, Missouri, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdan, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Frank B Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
| | - David J Hunter
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, 140 Cambridge 02142, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David Karasik
- Harvard Medical School, Boston, MA 02115
- Hebrew SeniorLife Institute for Aging Research, Boston, MA
| | - Douglas P Kiel
- Hebrew SeniorLife Institute for Aging Research, Boston, MA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Veli-Matti Kosma
- School of Medicine, 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
| | - Zoltan Kutalik
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandra Lai
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Patrik K Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Arto Mannermaa
- School of Medicine, 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
| | - Nicholas G Martin
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Patrick F McArdle
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition - University of Maryland School of Medicine, USA. Baltimore, MD 21201
| | - Wendy L McArdle
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
- Department of Medicine, Stanford School of Medicine, Stanford, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Department of Biotechnology, University of Tartu, Tartu, 51010, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Patrick Neven
- KULeuven (University of Leuven), Department of Oncology, Multidisciplinary Breast Center, University Hospitals Leuven, Belgium
| | - Ellen A Nohr
- Research Unit of Obstetrics & Gynecology, Institute of Clinical Research, University of Southern denmark, DK
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ben A Oostra
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Munro Peacock
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Paul DP Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, UK
| | - Dirkje S Postma
- University Groningen, University Medical Center Groningen, Department Pulmonary Medicine and Tuberculosis, GRIAC Research Institute, Groningen, The Netherlands
| | - Anneli Pouta
- National Institute for Health and Welfare, Finland
- Department of Obstetrics and Gynecology, Oulu University Hospital, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdan, the Netherlands
| | - Antonietta Robino
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo” – Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, Italy
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Serena Sanna
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy
| | - David Schlessinger
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Mellissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Ulla Sovio
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, United Kingdom
| | - Meir J Stampfer
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
| | - Doris Stöckl
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Obstetrics and Gynaecology, Campus Grosshadern, Ludwig-Maximilians- University, Munich, Germany
| | - Anna M Storniolo
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Jonathan Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, UK
| | - Jenny A Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Peter Vollenweider
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
| | - Gerard Waeber
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Henri Wallaschofski
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu University Hospital/NordLab Oulu, Oulu, Finland
| | - Bruce HR Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Margaret J Wright
- Queensland Insitute of Medical Research, Brisbane, Queensland, Australia
| | - Australian Ovarian Cancer Study
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - The GENICA Network
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart
- University of Tübingen, Germany
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
- Institute of Pathology, Medical Faculty of the University of Bonn, Bonn, Germany
- Institute of Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - kConFab
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Michael J Econs
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana USA
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ruth JF Loos
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Genetics of Obesity and Related Metabolic Traits Program, The Charles Bronfman Institute for Personalized Medicine, The Mindich Child Health and Development Institute, Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1003, New York, NY 10029, USA
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
| | - Grant W Montgomery
- Queensland Insitute of Medical Research, Brisbane, Queensland, Australia
| | - John P Rice
- Dept. of Psychiatry, Washington University, St. Louis, MO 63110
| | - Elizabeth A Streeten
- Program in Personalized and Genomic Medicine, and Department of Medicine, Division of Endocrinology, Diabetes and Nutrition - University of Maryland School of Medicine, USA. Baltimore, MD 21201
- Geriatric Research and Education Clinical Center (GRECC) - Veterans Administration Medical Center, USA. Baltimore, MD 21201
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Cornelia M van Duijn
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
- Genetic Epidemiology Unit Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- Centre of Medical Systems Biology, Leiden, the Netherlands
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sven Bergmann
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eric Boerwinkle
- Human Genetics Center and Div. of Epidemiology, University of Houston, TX
| | - Heather A Boyd
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Laura Crisponi
- Institute of Genetics and Biomedical Research, National Research Council, Cagliari, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo” – Trieste, Italy
- Department of Clinical Medical Sciences, Surgical and Health, University of Trieste, Italy
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Tamara B Harris
- National Insitute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, UK
- Institute of Health Sciences, P.O.Box 5000, FI-90014 University of Oulu, Finland
- Biocenter Oulu, P.O.Box 5000, Aapistie 5A, FI-90014 University of Oulu, Finland
- Department of Children and Young People and Families, National Institute for Health and Welfare, Aapistie 1, Box 310, FI-90101 Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, P.O.Box 20, FI-90220 Oulu, 90029 OYS, Finland
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Debbie Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Department of Biotechnology, University of Tartu, Tartu, 51010, Estonia
| | - Craig E Pennell
- School of Women’s and Infants’ Health, The University of Western Australia
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA 02215
- Harvard Medical School, Boston, MA 02115
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Thorkild IA Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, The Capital Region, Copenhagen, Denmark
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - David P Strachan
- Division of Population Health Sciences and Education, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdan, the Netherlands
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Marek Zygmunt
- Department of Obstetrics and Gynecology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Anna Murray
- University of Exeter Medical School, University of Exeter, Exeter, UK EX1 2LU
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, UK
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Joanne M Murabito
- NHLBI’s and Boston University’s Framingham Heart Study, Framingham, MA
- Boston University School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA
| | - Ken K Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285 Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Department of Paediatrics,University of Cambridge,Cambridge,UK
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Al Olama AA, Kote-Jarai Z, Berndt SI, Conti DV, Schumacher F, Han Y, Benlloch S, Hazelett DJ, Wang Z, Saunders E, Leongamornlert D, Lindstrom S, Jugurnauth-Little S, Dadaev T, Tymrakiewicz M, Stram DO, Rand K, Wan P, Stram A, Sheng X, Pooler LC, Park K, Xia L, Tyrer J, Kolonel LN, Le Marchand L, Hoover RN, Machiela MJ, Yeager M, Burdette L, Chung CC, Hutchinson A, Yu K, Goh C, Ahmed M, Govindasami K, Guy M, Tammela TLJ, Auvinen A, Wahlfors T, Schleutker J, Visakorpi T, Leinonen KA, Xu J, Aly M, Donovan J, Travis RC, Key TJ, Siddiq A, Canzian F, Khaw KT, Takahashi A, Kubo M, Pharoah P, Pashayan N, Weischer M, Nordestgaard BG, Nielsen SF, Klarskov P, Røder MA, Iversen P, Thibodeau SN, McDonnell SK, Schaid DJ, Stanford JL, Kolb S, Holt S, Knudsen B, Coll AH, Gapstur SM, Diver WR, Stevens VL, Maier C, Luedeke M, Herkommer K, Rinckleb AE, Strom SS, Pettaway C, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, Cannon-Albright L, Cybulski C, Wokołorczyk D, Kluźniak W, Park J, Sellers T, Lin HY, Isaacs WB, Partin AW, Brenner H, Dieffenbach AK, Stegmaier C, Chen C, Giovannucci EL, Ma J, Stampfer M, Penney KL, Mucci L, John EM, Ingles SA, Kittles RA, Murphy AB, Pandha H, Michael A, Kierzek AM, Blot W, Signorello LB, Zheng W, Albanes D, Virtamo J, Weinstein S, Nemesure B, Carpten J, Leske C, Wu SY, Hennis A, Kibel AS, Rybicki BA, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Zheng SL, Batra J, Clements J, Spurdle A, Teixeira MR, Paulo P, Maia S, Slavov C, Kaneva R, Mitev V, Witte JS, Casey G, Gillanders EM, Seminara D, Riboli E, Hamdy FC, Coetzee GA, Li Q, Freedman ML, Hunter DJ, Muir K, Gronberg H, Neal DE, Southey M, Giles GG, Severi G, Cook MB, Nakagawa H, Wiklund F, Kraft P, Chanock SJ, Henderson BE, Easton DF, Eeles RA, Haiman CA. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. Nat Genet 2014; 46:1103-9. [PMID: 25217961 PMCID: PMC4383163 DOI: 10.1038/ng.3094] [Citation(s) in RCA: 344] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/19/2014] [Indexed: 02/02/2023]
Abstract
Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of > 10 million SNPs in 43,303 prostate cancer cases and 43,737 controls from studies in populations of European, African, Japanese and Latino ancestry. Twenty-three new susceptibility loci were identified at association P < 5 × 10(-8); 15 variants were identified among men of European ancestry, 7 were identified in multi-ancestry analyses and 1 was associated with early-onset prostate cancer. These 23 variants, in combination with known prostate cancer risk variants, explain 33% of the familial risk for this disease in European-ancestry populations. These findings provide new regions for investigation into the pathogenesis of prostate cancer and demonstrate the usefulness of combining ancestrally diverse populations to discover risk loci for disease.
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Affiliation(s)
- Ali Amin Al Olama
- 1] Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. [2]
| | | | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - David V Conti
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Fredrick Schumacher
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Ying Han
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dennis J Hazelett
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Zhaoming Wang
- 1] Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA. [2] Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick, Maryland, USA
| | | | | | - Sara Lindstrom
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | | | | | | | - Daniel O Stram
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Kristin Rand
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Peggy Wan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Loreall C Pooler
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Karen Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Lucy Xia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jonathan Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Merideth Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Chee Goh
- Institute of Cancer Research, London, UK
| | | | | | | | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | - Anssi Auvinen
- Department of Epidemiology, School of Health Sciences, University of Tampere, Tampere, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Johanna Schleutker
- 1] BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland. [2] Department of Medical Biochemistry, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tapio Visakorpi
- Institute of Biomedical Technology/BioMediTech, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Katri A Leinonen
- Institute of Biomedical Technology/BioMediTech, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Markus Aly
- 1] Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden. [2] Department of Clinical Sciences at Danderyds Hospital, Stockholm, Sweden
| | - Jenny Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tim J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Borge G Nordestgaard
- 1] Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark. [2] Faculty of Healthy and Medical Sciences, University of Copenhagen, Herlev, Denmark
| | - Sune F Nielsen
- 1] Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark. [2] Faculty of Healthy and Medical Sciences, University of Copenhagen, Herlev, Denmark
| | - Peter Klarskov
- Department of Urology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Martin Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter Iversen
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | | | - Janet L Stanford
- 1] Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA. [2] Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sarah Holt
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Beatrice Knudsen
- Translational Pathology, Cedars-Sinai, Los Angeles, California, USA
| | | | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | | | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, Ulm, Germany
| | - Kathleen Herkommer
- Department of Urology, Klinikum Rechts der Isar der Technischen Universität München, Munich, Germany
| | | | - Sara S Strom
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Curtis Pettaway
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Edward D Yeboah
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | - Yao Tettey
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | - Richard B Biritwum
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | - Andrew A Adjei
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | - Evelyn Tay
- 1] University of Ghana Medical School, Accra, Ghana. [2] Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Anand P Chokkalingam
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Lisa Cannon-Albright
- 1] Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA. [2] George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokołorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Kluźniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jong Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Thomas Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Hui-Yi Lin
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, Maryland, USA
| | - Alan W Partin
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, Maryland, USA
| | - Hermann Brenner
- 1] Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] German Cancer Consortium, Heidelberg, Germany
| | - Aida Karina Dieffenbach
- 1] Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] German Cancer Consortium, Heidelberg, Germany
| | | | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Edward L Giovannucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Jing Ma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Meir Stampfer
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA. [3] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathryn L Penney
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lorelei Mucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Esther M John
- 1] Cancer Prevention Institute of California, Fremont, California, USA. [2] Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Sue A Ingles
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Rick A Kittles
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, Illinois, USA
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Agnieszka Michael
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Andrzej M Kierzek
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - William Blot
- 1] International Epidemiology Institute, Rockville, Maryland, USA. [2] Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lisa B Signorello
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Demetrius Albanes
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Stephanie Weinstein
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York, USA
| | - John Carpten
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Cristina Leske
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Suh-Yuh Wu
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Anselm Hennis
- 1] Department of Preventive Medicine, Stony Brook University, Stony Brook, New York, USA. [2] Chronic Disease Research Centre, University of the West Indies, Bridgetown, Barbados
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan, USA
| | | | - Ann W Hsing
- 1] Cancer Prevention Institute of California, Fremont, California, USA. [2] Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Lisa Chu
- 1] Cancer Prevention Institute of California, Fremont, California, USA. [2] Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Phyllis J Goodman
- Southwest Oncology Group Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eric A Klein
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - S Lilly Zheng
- Center for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia
| | - Judith Clements
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia
| | - Amanda Spurdle
- Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Manuel R Teixeira
- 1] Department of Genetics, Portuguese Oncology Institute, Porto, Portugal. [2] Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Sofia Maia
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Chavdar Slavov
- Department of Urology, Medical University-Sofia, Sofia, Bulgaria
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University-Sofia, Sofia, Bulgaria
| | - John S Witte
- 1] Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA. [2] Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Graham Casey
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Elizabeth M Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland, USA
| | - Daniella Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland, USA
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Gerhard A Coetzee
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Qiyuan Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Kenneth Muir
- 1] Institute of Population Health, University of Manchester, Manchester, UK. [2] Warwick Medical School, University of Warwick, Coventry, UK
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - David E Neal
- 1] Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK. [2] Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- 1] Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. [2] Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Gianluca Severi
- 1] Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia. [2] Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia. [3] Human Genetics Foundation, Torino, Italy
| | - Michael B Cook
- 1] Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA. [2]
| | - Hidewaki Nakagawa
- 1] Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan. [2]
| | - Fredrik Wiklund
- 1] Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden. [2]
| | - Peter Kraft
- 1] Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA. [3]
| | - Stephen J Chanock
- 1] Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland, USA. [2]
| | - Brian E Henderson
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA. [3]
| | - Douglas F Easton
- 1] Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. [2]
| | - Rosalind A Eeles
- 1] Institute of Cancer Research, London, UK. [2] Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, UK. [3]
| | - Christopher A Haiman
- 1] Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [2] Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA. [3]
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215
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Li Q, Stram A, Chen C, Kar S, Gayther S, Pharoah P, Haiman C, Stranger B, Kraft P, Freedman ML. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types. Hum Mol Genet 2014; 23:5294-302. [PMID: 24907074 PMCID: PMC4215106 DOI: 10.1093/hmg/ddu228] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/17/2014] [Accepted: 05/06/2014] [Indexed: 11/13/2022] Open
Abstract
The majority of trait-associated loci discovered through genome-wide association studies are located outside of known protein coding regions. Consequently, it is difficult to ascertain the mechanism underlying these variants and to pinpoint the causal alleles. Expression quantitative trait loci (eQTLs) provide an organizing principle to address both of these issues. eQTLs are genetic loci that correlate with RNA transcript levels. Large-scale data sets such as the Cancer Genome Atlas (TCGA) provide an ideal opportunity to systematically evaluate eQTLs as they have generated multiple data types on hundreds of samples. We evaluated the determinants of gene expression (germline variants and somatic copy number and methylation) and performed cis-eQTL analyses for mRNA expression and miRNA expression in five tumor types (breast, colon, kidney, lung and prostate). We next tested 149 known cancer risk loci for eQTL effects, and observed that 42 (28.2%) were significantly associated with at least one transcript. Lastly, we described a fine-mapping strategy for these 42 eQTL target-gene associations based on an integrated strategy that combines the eQTL level of significance and the regulatory potential as measured by DNaseI hypersensitivity. For each of the risk loci, our analyses suggested 1 to 81 candidate causal variants that may be prioritized for downstream functional analysis. In summary, our study provided a comprehensive landscape of the genetic determinants of gene expression in different tumor types and ranked the genes and loci for further functional assessment of known cancer risk loci.
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Affiliation(s)
- Qiyuan Li
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA, USA Medical College of Xiamen University, Xiamen, China Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA, USA
| | | | - Constance Chen
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Siddhartha Kar
- Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Simon Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Log Angeles, CA, USA
| | - Paul Pharoah
- Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | | | - Barbara Stranger
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA, USA Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA, USA
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216
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths in the United States. Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with increased risk for CRC. A molecular understanding of the functional consequences of this genetic variation has been complicated because each GWAS SNP is a surrogate for hundreds of other SNPs, most of which are located in non-coding regions. Here we use genomic and epigenomic information to test the hypothesis that the GWAS SNPs and/or correlated SNPs are in elements that regulate gene expression, and identify 23 promoters and 28 enhancers. Using gene expression data from normal and tumour cells, we identify 66 putative target genes of the risk-associated enhancers (10 of which were also identified by promoter SNPs). Employing CRISPR nucleases, we delete one risk-associated enhancer and identify genes showing altered expression. We suggest that similar studies be performed to characterize all CRC risk-associated enhancers. Previous studies identified genetic variants associated with colorectal cancer (CRC), but the functional consequences of these genetic risk factors remain poorly understood. Here, the authors report that CRC risk variants reside in promoters and enhancers and could increase colon cancer risk through gene expression regulation.
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217
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Li WQ, Pfeiffer RM, Hyland PL, Shi J, Gu F, Wang Z, Bhattacharjee S, Luo J, Xiong X, Yeager M, Deng X, Hu N, Taylor PR, Albanes D, Caporaso NE, Gapstur SM, Amundadottir L, Chanock SJ, Chatterjee N, Landi MT, Tucker MA, Goldstein AM, Yang XR. Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. Carcinogenesis 2014; 35:2698-705. [PMID: 25239644 DOI: 10.1093/carcin/bgu203] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The chromosome 9p21 region has been implicated in the pathogenesis of multiple cancers. We analyzed 9p21 single nucleotide polymorphisms (SNPs) from eight genome-wide association studies (GWAS) with data deposited in dbGaP, including studies of esophageal squamous cell carcinoma (ESCC), gastric cancer (GC), pancreatic cancer, renal cell carcinoma (RCC), lung cancer (LC), breast cancer (BrC), bladder cancer (BC) and prostate cancer (PrC). The number of subjects ranged from 2252 (PrC) to 7619 (LC). SNP-level analyses for each cancer were conducted by logistic regression or random-effects meta-analysis. A subset-based statistical approach (ASSET) was performed to combine SNP-level P values across multiple cancers. We calculated gene-level P values using the adaptive rank truncated product method. We identified that rs1063192 and rs2157719 in the CDKN2A/2B region were significantly associated with ESCC and rs2764736 (3' of TUSC1) was associated with BC (P ≤ 2.59 × 10(-6)). ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2A intronic) with ESCC, GC and BC (P = 3.96 × 10(-) (4)); rs10811474 (3' of IFNW1) with RCC and BrC (P = 0.001); rs12683422 (LINGO2 intronic) with RCC and BC (P = 5.93 × 10(-) (4)) and rs10511729 (3' of ELAVL2) with LC and BrC (P = 8.63 × 10(-) (4)). At gene level, CDKN2B, CDKN2A and CDKN2B-AS1 were significantly associated with ESCC (P ≤ 4.70 × 10(-) (5)). Rs10511729 and rs10811474 were associated with cis-expression of 9p21 genes in corresponding cancer tissues in the expression quantitative trait loci analysis. In conclusion, we identified several genetic variants in the 9p21 region associated with the risk of multiple cancers, suggesting that this region may contribute to a shared susceptibility across different cancer types.
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Affiliation(s)
- Wen-Qing Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, RI, USA,
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Fangyi Gu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | | | - Jun Luo
- Information Management Services, Inc., Calverton, MD, USA and
| | - Xiaoqin Xiong
- Information Management Services, Inc., Calverton, MD, USA and
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Xiang Deng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
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218
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Zhang J, Jiang K, Shen Z, Gao Z, Lv L, Ye Y, Wang S. Expression QTL-based analyses reveal the mechanisms underlying colorectal cancer predisposition. Tumour Biol 2014; 35:12607-11. [PMID: 25201067 DOI: 10.1007/s13277-014-2583-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/29/2014] [Indexed: 11/25/2022] Open
Abstract
Genome-wide association studies have identified many risk loci associated with colorectal cancer. Strategies integrating biological data sets with GWAS results will provide insights into the roles of risk single-nucleotide polymorphisms. We performed expression quantitative trait locus-based analyses using the information provided in The Cancer Genome Atlas. Analysis of the cis-expression quantitative trait loci (eQTLs) of 18 previously reported colorectal cancer risk loci resulted in the discovery of five variants that were significantly associated with gene expressions. Analysis of the trans-eQTLs identified three risk loci that affect the expression levels of a neighboring transcription factor, MYC. These findings provide a more comprehensive picture of gene expression determinants in colorectal cancer and insights into the underlying biology of risk loci.
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Affiliation(s)
- Jizhun Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, No.11 Xizhimen South St, Xicheng District, Beijing, 100044, People's Republic of China
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219
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Du M, Yuan T, Schilter KF, Dittmar RL, Mackinnon A, Huang X, Tschannen M, Worthey E, Jacob H, Xia S, Gao J, Tillmans L, Lu Y, Liu P, Thibodeau SN, Wang L. Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. Hum Mol Genet 2014; 24:154-66. [PMID: 25149474 DOI: 10.1093/hmg/ddu426] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chromosome 8q24 locus contains regulatory variants that modulate genetic risk to various cancers including prostate cancer (PC). However, the biological mechanism underlying this regulation is not well understood. Here, we developed a chromosome conformation capture (3C)-based multi-target sequencing technology and systematically examined three PC risk regions at the 8q24 locus and their potential regulatory targets across human genome in six cell lines. We observed frequent physical contacts of this risk locus with multiple genomic regions, in particular, inter-chromosomal interaction with CD96 at 3q13 and intra-chromosomal interaction with MYC at 8q24. We identified at least five interaction hot spots within the predicted functional regulatory elements at the 8q24 risk locus. We also found intra-chromosomal interaction genes PVT1, FAM84B and GSDMC and inter-chromosomal interaction gene CXorf36 in most of the six cell lines. Other gene regions appeared to be cell line-specific, such as RRP12 in LNCaP, USP14 in DU-145 and SMIN3 in lymphoblastoid cell line. We further found that the 8q24 functional domains more likely interacted with genomic regions containing genes enriched in critical pathways such as Wnt signaling and promoter motifs such as E2F1 and TCF3. This result suggests that the risk locus may function as a regulatory hub by physical interactions with multiple genes important for prostate carcinogenesis. Further understanding genetic effect and biological mechanism of these chromatin interactions will shed light on the newly discovered regulatory role of the risk locus in PC etiology and progression.
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Affiliation(s)
- Meijun Du
- Department of Pathology and Cancer Center
| | | | | | | | | | | | | | | | | | - Shu Xia
- Department of Pathology and Cancer Center Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jianzhong Gao
- Beijing 3H Medical Technology Co. Ltd., Beijing 100176, China and
| | - Lori Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yan Lu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Pengyuan Liu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liang Wang
- Department of Pathology and Cancer Center
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220
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Chen QR, Hu Y, Yan C, Buetow K, Meerzaman D. Systematic genetic analysis identifies Cis-eQTL target genes associated with glioblastoma patient survival. PLoS One 2014; 9:e105393. [PMID: 25133526 PMCID: PMC4136869 DOI: 10.1371/journal.pone.0105393] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/19/2014] [Indexed: 01/23/2023] Open
Abstract
Prior expression quantitative trait locus (eQTL) studies have demonstrated heritable variation determining differences in gene expression. The majority of eQTL studies were based on cell lines and normal tissues. We performed cis-eQTL analysis using glioblastoma multiforme (GBM) data sets obtained from The Cancer Genome Atlas (TCGA) to systematically investigate germline variation's contribution to tumor gene expression levels. We identified 985 significant cis-eQTL associations (FDR<0.05) mapped to 978 SNP loci and 159 unique genes. Approximately 57% of these eQTLs have been previously linked to the gene expression in cell lines and normal tissues; 43% of these share cis associations known to be associated with functional annotations. About 25% of these cis-eQTL associations are also common to those identified in Breast Cancer from a recent study. Further investigation of the relationship between gene expression and patient clinical information identified 13 eQTL genes whose expression level significantly correlates with GBM patient survival (p<0.05). Most of these genes are also differentially expressed in tumor samples and organ-specific controls (p<0.05). Our results demonstrated a significant relationship of germline variation with gene expression levels in GBM. The identification of eQTLs-based expression associated survival might be important to the understanding of genetic contribution to GBM cancer prognosis.
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Affiliation(s)
- Qing-Rong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kenneth Buetow
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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221
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Lee M, Dworkin AM, Lichtenberg J, Patel SJ, Trivedi NS, Gildea D, Bodine DM, Crawford NPS. Metastasis-associated protein ribosomal RNA processing 1 homolog B (RRP1B) modulates metastasis through regulation of histone methylation. Mol Cancer Res 2014; 12:1818-28. [PMID: 25092915 DOI: 10.1158/1541-7786.mcr-14-0167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
UNLABELLED Overexpression of ribosomal RNA processing 1 homolog B (RRP1B) induces a transcriptional profile that accurately predicts patient outcome in breast cancer. However, the mechanism by which RRP1B modulates transcription is unclear. Here, the chromatin-binding properties of RRP1B were examined to define how it regulates metastasis-associated transcription. To identify genome-wide RRP1B-binding sites, high-throughput ChIP-seq was performed in the human breast cancer cell line MDA-MB-231 and HeLa cells using antibodies against endogenous RRP1B. Global changes in repressive marks such as histone H3 lysine 9 trimethylation (H3K9me3) were also examined by ChIP-seq. Analysis of these samples identified 339 binding regions in MDA-MB-231 cells and 689 RRP1B-binding regions in HeLa cells. Among these, 136 regions were common to both cell lines. Gene expression analyses of these RRP1B-binding regions revealed that transcriptional repression is the primary result of RRP1B binding to chromatin. ChIP-reChIP assays demonstrated that RRP1B co-occupies loci with decreased gene expression with the heterochromatin-associated proteins, tripartite motif-containing protein 28 (TRIM28/KAP1), and heterochromatin protein 1-α (CBX5/HP1α). RRP1B occupancy at these loci was also associated with higher H3K9me3 levels, indicative of heterochromatinization mediated by the TRIM28/HP1α complex. In addition, RRP1B upregulation, which is associated with metastasis suppression, induced global changes in histone methylation. IMPLICATIONS RRP1B, a breast cancer metastasis suppressor, regulates gene expression through heterochromatinization and transcriptional repression, which helps our understanding of mechanisms that drive prognostic gene expression in human breast cancer.
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Affiliation(s)
- Minnkyong Lee
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Amy M Dworkin
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Jens Lichtenberg
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Shashank J Patel
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Niraj S Trivedi
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Derek Gildea
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - David M Bodine
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Nigel P S Crawford
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland.
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223
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Ganesh S, Chasman D, Larson M, Guo X, Verwoert G, Bis J, Gu X, Smith A, Yang ML, Zhang Y, Ehret G, Rose L, Hwang SJ, Papanicolau G, Sijbrands E, Rice K, Eiriksdottir G, Pihur V, Ridker P, Vasan R, Newton-Cheh C, Raffel LJ, Amin N, Rotter JI, Liu K, Launer LJ, Xu M, Caulfield M, Morrison AC, Johnson AD, Vaidya D, Dehghan A, Li G, Bouchard C, Harris TB, Zhang H, Boerwinkle E, Siscovick DS, Gao W, Uitterlinden AG, Rivadeneira F, Hofman A, Willer CJ, Franco OH, Huo Y, Witteman JC, Munroe PB, Gudnason V, Palmas W, van Duijn C, Fornage M, Levy D, Psaty BM, Chakravarti A, Newton-Cheh C, Johnson T, Gateva V, Tobin M, Bochud M, Coin L, Najjar S, Zhao J, Heath S, Eyheramendy S, Papadakis K, Voight B, Scott L, Zhang F, Farrall M, Tanaka T, Wallace C, Chambers J, Khaw KT, Nilsson P, van der Harst P, Polidoro S, Grobbee D, Onland-Moret N, Bots M, Wain L, Elliott K, Teumer A, Luan J, Lucas G, Kuusisto J, Burton P, Hadley D, McArdle W, Brown M, Dominiczak A, Newhouse S, Samani N, Webster J, Zeggini E, Beckmann J, Bergmann S, Lim N, Song K, Vollenweider P, Waeber G, Waterworth D, Yuan X, Groop L, Orho-Melander M, Allione A, Di Gregorio A, Guarrera S, Panico S, Ricceri F, Romanazzi V, Sacerdote C, Vineis P, Barroso I, Sandhu M, Luben R, Crawford G, Jousilahti P, Perola M, Boehnke M, Bonnycastle L, Collins F, Jackson A, Mohlke K, Stringham H, Valle T, Willer C, Bergman R, Morken M, Döring A, Gieger C, Illig T, Meitinger T, Org E, Pfeufer A, Wichmann H, Kathiresan S, Marrugat J, O’Donnell C, Schwartz S, Siscovick D, Subirana I, Freimer N, Hartikainen AL, McCarthy M, O’Reilly P, Peltonen L, Pouta A, de Jong P, Snieder H, van Gilst W, Clarke R, Goel A, Hamsten A, Peden J, Seedorf U, Syvänen AC, Tognoni G, Lakatta E, Sanna S, Scheet P, Schlessinger D, Scuteri A, Dörr M, Ernst F, Felix S, Homuth G, Lorbeer R, Reffelmann T, Rettig R, Völker U, Galan P, Gut I, Hercberg S, Lathrop G, Zeleneka D, Deloukas P, Soranzo N, Williams F, Zhai G, Salomaa V, Laakso M, Elosua R, Forouhi N, Völzke H, Uiterwaal C, van der Schouw Y, Numans M, Matullo G, Navis G, Berglund G, Bingham S, Kooner J, Paterson A, Connell J, Bandinelli S, Ferrucci L, Watkins H, Spector T, Tuomilehto J, Altshuler D, Strachan D, Laan M, Meneton P, Wareham N, Uda M, Jarvelin MR, Mooser V, Melander O, Loos R, Elliott P, Abecasis G, Caulfield M, Munroe P. Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations. Am J Hum Genet 2014; 95:49-65. [PMID: 24975945 DOI: 10.1016/j.ajhg.2014.06.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/03/2014] [Indexed: 01/11/2023] Open
Abstract
Blood pressure (BP) is a heritable, quantitative trait with intraindividual variability and susceptibility to measurement error. Genetic studies of BP generally use single-visit measurements and thus cannot remove variability occurring over months or years. We leveraged the idea that averaging BP measured across time would improve phenotypic accuracy and thereby increase statistical power to detect genetic associations. We studied systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP) averaged over multiple years in 46,629 individuals of European ancestry. We identified 39 trait-variant associations across 19 independent loci (p < 5 × 10(-8)); five associations (in four loci) uniquely identified by our LTA analyses included those of SBP and MAP at 2p23 (rs1275988, near KCNK3), DBP at 2q11.2 (rs7599598, in FER1L5), and PP at 6p21 (rs10948071, near CRIP3) and 7p13 (rs2949837, near IGFBP3). Replication analyses conducted in cohorts with single-visit BP data showed positive replication of associations and a nominal association (p < 0.05). We estimated a 20% gain in statistical power with long-term average (LTA) as compared to single-visit BP association studies. Using LTA analysis, we identified genetic loci influencing BP. LTA might be one way of increasing the power of genetic associations for continuous traits in extant samples for other phenotypes that are measured serially over time.
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224
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Reidy K, Kang HM, Hostetter T, Susztak K. Molecular mechanisms of diabetic kidney disease. J Clin Invest 2014; 124:2333-40. [PMID: 24892707 DOI: 10.1172/jci72271] [Citation(s) in RCA: 594] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Diabetic kidney disease (DKD) is the leading cause of kidney failure worldwide and the single strongest predictor of mortality in patients with diabetes. DKD is a prototypical disease of gene and environmental interactions. Tight glucose control significantly decreases DKD incidence, indicating that hyperglycemia-induced metabolic alterations, including changes in energy utilization and mitochondrial dysfunction, play critical roles in disease initiation. Blood pressure control, especially with medications that inhibit the angiotensin system, is the only effective way to slow disease progression. While DKD is considered a microvascular complication of diabetes, growing evidence indicates that podocyte loss and epithelial dysfunction play important roles. Inflammation, cell hypertrophy, and dedifferentiation by the activation of classic pathways of regeneration further contribute to disease progression. Concerted clinical and basic research efforts will be needed to understand DKD pathogenesis and to identify novel drug targets.
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225
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Stunnenberg HG, Hubner NC. Genomics meets proteomics: identifying the culprits in disease. Hum Genet 2014; 133:689-700. [PMID: 24135908 PMCID: PMC4021166 DOI: 10.1007/s00439-013-1376-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/01/2013] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) revealed genomic risk loci that potentially have an impact on disease and phenotypic traits. This extensive resource holds great promise in providing novel directions for personalized medicine, including disease risk prediction, prevention and targeted medication. One of the major challenges that researchers face on the path between the initial identification of an association and precision treatment of patients is the comprehension of the biological mechanisms that underlie these associations. Currently, the focus to solve these questions lies on the integrative analysis of system-wide data on global genome variation, gene expression, transcription factor binding, epigenetic profiles and chromatin conformation. The generation of this data mainly relies on next-generation sequencing. However, due to multiple recent developments, mass spectrometry-based proteomics now offers additional, by the GWAS field so far hardly recognized possibilities for the identification of functional genome variants and, in particular, for the identification and characterization of (differentially) bound protein complexes as well as physiological target genes. In this review, we introduce these proteomics advances and suggest how they might be integrated in post-GWAS workflows. We argue that the combination of highly complementary techniques is powerful and can provide an unbiased, detailed picture of GWAS loci and their mechanistic involvement in disease.
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Affiliation(s)
- Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Nina C. Hubner
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
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226
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Heyn H. A symbiotic liaison between the genetic and epigenetic code. Front Genet 2014; 5:113. [PMID: 24822056 PMCID: PMC4013453 DOI: 10.3389/fgene.2014.00113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 04/15/2014] [Indexed: 01/30/2023] Open
Abstract
With rapid advances in sequencing technologies, we are undergoing a paradigm shift from hypothesis- to data-driven research. Genome-wide profiling efforts have given informative insights into biological processes; however, considering the wealth of variation, the major challenge still remains in their meaningful interpretation. In particular sequence variation in non-coding contexts is often challenging to interpret. Here, data integration approaches for the identification of functional genetic variability represent a possible solution. Exemplary, functional linkage analysis integrating genotype and expression data determined regulatory quantitative trait loci and proposed causal relationships. In addition to gene expression, epigenetic regulation and specifically DNA methylation was established as highly valuable surrogate mark for functional variance of the genetic code. Epigenetic modification has served as powerful mediator trait to elucidate mechanisms forming phenotypes in health and disease. Particularly, integrative studies of genetic and DNA methylation data have been able to guide interpretation strategies of risk genotypes, but also proved their value for physiological traits, such as natural human variation and aging. This Review seeks to illustrate the power of data integration in the genomic era exemplified by DNA methylation quantitative trait loci. However, the model is further extendable to virtually all traceable molecular traits.
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Affiliation(s)
- Holger Heyn
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute Barcelona, Spain
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227
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Sudarsanam P, Cohen BA. Single nucleotide variants in transcription factors associate more tightly with phenotype than with gene expression. PLoS Genet 2014; 10:e1004325. [PMID: 24784239 PMCID: PMC4006743 DOI: 10.1371/journal.pgen.1004325] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 03/10/2014] [Indexed: 01/22/2023] Open
Abstract
Mapping the polymorphisms responsible for variation in gene expression, known as Expression Quantitative Trait Loci (eQTL), is a common strategy for investigating the molecular basis of disease. Despite numerous eQTL studies, the relationship between the explanatory power of variants on gene expression versus their power to explain ultimate phenotypes remains to be clarified. We addressed this question using four naturally occurring Quantitative Trait Nucleotides (QTN) in three transcription factors that affect sporulation efficiency in wild strains of the yeast, Saccharomyces cerevisiae. We compared the ability of these QTN to explain the variation in both gene expression and sporulation efficiency. We find that the amount of gene expression variation explained by the sporulation QTN is not predictive of the amount of phenotypic variation explained. The QTN are responsible for 98% of the phenotypic variation in our strains but the median gene expression variation explained is only 49%. The alleles that are responsible for most of the variation in sporulation efficiency do not explain most of the variation in gene expression. The balance between the main effects and gene-gene interactions on gene expression variation is not the same as on sporulation efficiency. Finally, we show that nucleotide variants in the same transcription factor explain the expression variation of different sets of target genes depending on whether the variant alters the level or activity of the transcription factor. Our results suggest that a subset of gene expression changes may be more predictive of ultimate phenotypes than the number of genes affected or the total fraction of variation in gene expression variation explained by causative variants, and that the downstream phenotype is buffered against variation in the gene expression network.
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Affiliation(s)
- Priya Sudarsanam
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Barak A Cohen
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
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228
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Yang HC, Lin CW, Chen CW, Chen JJ. Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics. BMC Genomics 2014; 15:319. [PMID: 24779372 PMCID: PMC4236814 DOI: 10.1186/1471-2164-15-319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 04/15/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Gene-based analysis has become popular in genomic research because of its appealing biological and statistical properties compared with those of a single-locus analysis. However, only a few, if any, studies have discussed a mapping of expression quantitative trait loci (eQTL) in a gene-based framework. Neither study has discussed ancestry-informative eQTL nor investigated their roles in pharmacogenetics by integrating single nucleotide polymorphism (SNP)-based eQTL (s-eQTL) and gene-based eQTL (g-eQTL). RESULTS In this g-eQTL mapping study, the transcript expression levels of genes (transcript-level genes; T-genes) were correlated with the SNPs of genes (sequence-level genes; S-genes) by using a method of gene-based partial least squares (PLS). Ancestry-informative transcripts were identified using a rank-score-based multivariate association test, and ancestry-informative eQTL were identified using Fisher's exact test. Furthermore, key ancestry-predictive eQTL were selected in a flexible discriminant analysis. We analyzed SNPs and gene expression of 210 independent people of African-, Asian- and European-descent. We identified numerous cis- and trans-acting g-eQTL and s-eQTL for each population by using PLS. We observed ancestry information enriched in eQTL. Furthermore, we identified 2 ancestry-informative eQTL associated with adverse drug reactions and/or drug response. Rs1045642, located on MDR1, is an ancestry-informative eQTL (P = 2.13E-13, using Fisher's exact test) associated with adverse drug reactions to amitriptyline and nortriptyline and drug responses to morphine. Rs20455, located in KIF6, is an ancestry-informative eQTL (P = 2.76E-23, using Fisher's exact test) associated with the response to statin drugs (e.g., pravastatin and atorvastatin). The ancestry-informative eQTL of drug biotransformation genes were also observed; cross-population cis-acting expression regulators included SPG7, TAP2, SLC7A7, and CYP4F2. Finally, we also identified key ancestry-predictive eQTL and established classification models with promising training and testing accuracies in separating samples from close populations. CONCLUSIONS In summary, we developed a gene-based PLS procedure and a SAS macro for identifying g-eQTL and s-eQTL. We established data archives of eQTL for global populations. The program and data archives are accessible at http://www.stat.sinica.edu.tw/hsinchou/genetics/eQTL/HapMapII.htm. Finally, the results from our investigations regarding the interrelationship between eQTL, ancestry information, and pharmacodynamics provide rich resources for future eQTL studies and practical applications in population genetics and medical genetics.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, No 128, Academia Road, Section 2, Nankang, Taipei, Taiwan.
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229
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Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proc Natl Acad Sci U S A 2014; 111:7319-24. [PMID: 24778216 DOI: 10.1073/pnas.1324151111] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The androgen receptor (AR) is a key factor that regulates the behavior and fate of prostate cancer cells. The AR-regulated network is activated when AR binds enhancer elements and modulates specific enhancer-promoter looping. Kallikrein-related peptidase 3 (KLK3), which codes for prostate-specific antigen (PSA), is a well-known AR-regulated gene and its upstream enhancers produce bidirectional enhancer RNAs (eRNAs), termed KLK3e. Here, we demonstrate that KLK3e facilitates the spatial interaction of the KLK3 enhancer and the KLK2 promoter and enhances long-distance KLK2 transcriptional activation. KLK3e carries the core enhancer element derived from the androgen response element III (ARE III), which is required for the interaction of AR and Mediator 1 (Med1). Furthermore, we show that KLK3e processes RNA-dependent enhancer activity depending on the integrity of core enhancer elements. The transcription of KLK3e was detectable and its expression is significantly correlated with KLK3 (R(2) = 0.6213, P < 5 × 10(-11)) and KLK2 (R(2) = 0.5893, P < 5 × 10(-10)) in human prostate tissues. Interestingly, RNAi silencing of KLK3e resulted in a modest negative effect on prostate cancer cell proliferation. Accordingly, we report that an androgen-induced eRNA scaffolds the AR-associated protein complex that modulates chromosomal architecture and selectively enhances AR-dependent gene expression.
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230
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Shpak M, Hall AW, Goldberg MM, Derryberry DZ, Ni Y, Iyer VR, Cowperthwaite MC. An eQTL analysis of the human glioblastoma multiforme genome. Genomics 2014; 103:252-63. [DOI: 10.1016/j.ygeno.2014.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/11/2014] [Accepted: 02/24/2014] [Indexed: 12/20/2022]
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231
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Heyn H, Sayols S, Moutinho C, Vidal E, Sanchez-Mut J, Stefansson O, Nadal E, Moran S, Eyfjord J, Gonzalez-Suarez E, Pujana M, Esteller M. Linkage of DNA Methylation Quantitative Trait Loci to Human Cancer Risk. Cell Rep 2014; 7:331-338. [DOI: 10.1016/j.celrep.2014.03.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/10/2014] [Accepted: 03/05/2014] [Indexed: 02/03/2023] Open
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232
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Zhang X, Bailey SD, Lupien M. Laying a solid foundation for Manhattan--'setting the functional basis for the post-GWAS era'. Trends Genet 2014; 30:140-9. [PMID: 24661571 DOI: 10.1016/j.tig.2014.02.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 01/21/2023]
Abstract
Genome-wide association studies (GWAS) have identified more than 8900 genetic variants, mainly single-nucleotide polymorphisms (SNPs), associated with hundreds of human traits and diseases, which define risk-associated loci. Variants that map to coding regions can affect protein sequence, translation rate, and alternative splicing, all of which influence protein function. However, the vast majority of sequence variants map to non-coding intergenic and intronic regions, and it has been much more challenging to assess the functional nature of these variants. Recent work annotating the non-coding regions of the genome has contributed to post-GWAS studies by facilitating the identification of the functional targets of risk-associated loci. Many non-coding genetic variants within risk-associated loci alter gene expression by modulating the activity of cis-regulatory elements. We review here these recent findings, discuss their implication for the post-GWAS era, and relate their importance to the interpretation of disease-associated mutations identified through whole-genome sequencing.
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Affiliation(s)
- Xiaoyang Zhang
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA
| | - Swneke D Bailey
- The Princess Margaret Cancer Centre - University Health Network, Toronto, ON, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre - University Health Network, Toronto, ON, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada.
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233
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Tragante V, Barnes MR, Ganesh SK, Lanktree MB, Guo W, Franceschini N, Smith EN, Johnson T, Holmes MV, Padmanabhan S, Karczewski KJ, Almoguera B, Barnard J, Baumert J, Chang YPC, Elbers CC, Farrall M, Fischer ME, Gaunt TR, Gho JMIH, Gieger C, Goel A, Gong Y, Isaacs A, Kleber ME, Mateo Leach I, McDonough CW, Meijs MFL, Melander O, Nelson CP, Nolte IM, Pankratz N, Price TS, Shaffer J, Shah S, Tomaszewski M, van der Most PJ, Van Iperen EPA, Vonk JM, Witkowska K, Wong COL, Zhang L, Beitelshees AL, Berenson GS, Bhatt DL, Brown M, Burt A, Cooper-DeHoff RM, Connell JM, Cruickshanks KJ, Curtis SP, Davey-Smith G, Delles C, Gansevoort RT, Guo X, Haiqing S, Hastie CE, Hofker MH, Hovingh GK, Kim DS, Kirkland SA, Klein BE, Klein R, Li YR, Maiwald S, Newton-Cheh C, O'Brien ET, Onland-Moret NC, Palmas W, Parsa A, Penninx BW, Pettinger M, Vasan RS, Ranchalis JE, M Ridker P, Rose LM, Sever P, Shimbo D, Steele L, Stolk RP, Thorand B, Trip MD, van Duijn CM, Verschuren WM, Wijmenga C, Wyatt S, Young JH, Zwinderman AH, Bezzina CR, Boerwinkle E, Casas JP, Caulfield MJ, Chakravarti A, Chasman DI, Davidson KW, Doevendans PA, Dominiczak AF, FitzGerald GA, Gums JG, Fornage M, Hakonarson H, Halder I, Hillege HL, Illig T, Jarvik GP, Johnson JA, Kastelein JJP, Koenig W, Kumari M, März W, Murray SS, O'Connell JR, Oldehinkel AJ, Pankow JS, Rader DJ, Redline S, Reilly MP, Schadt EE, Kottke-Marchant K, Snieder H, Snyder M, Stanton AV, Tobin MD, Uitterlinden AG, van der Harst P, van der Schouw YT, Samani NJ, Watkins H, Johnson AD, Reiner AP, Zhu X, de Bakker PIW, Levy D, Asselbergs FW, Munroe PB, Keating BJ. Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci. Am J Hum Genet 2014; 94:349-60. [PMID: 24560520 DOI: 10.1016/j.ajhg.2013.12.016] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ~50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10(-7)) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification.
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Affiliation(s)
- Vinicius Tragante
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Michael R Barnes
- William Harvey Research Institute National Institute for Health Biomedical Research Unit, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Departments of Internal Medicine and Human Genetics, University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Matthew B Lanktree
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Wei Guo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Erin N Smith
- Department of Pediatrics and Rady's Children's Hospital, University of California at San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Toby Johnson
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Michael V Holmes
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Konrad J Karczewski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Berta Almoguera
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jens Baumert
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Yen-Pei Christy Chang
- Departments of Medicine and Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Clara C Elbers
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Martin Farrall
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Mary E Fischer
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Johannes M I H Gho
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Anuj Goel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Marcus E Kleber
- Medical Clinic V, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Irene Mateo Leach
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Matthijs F L Meijs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Olle Melander
- Hypertension and Cardiovascular Disease, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden; Centre of Emergency Medicine, Skåne University Hospital, Malmö 20502, Sweden
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Groby Road, Leicester LE3 9QP, UK
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Nathan Pankratz
- Institute of Human Genetics, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tom S Price
- MRC SGDP Centre, Institute of Psychiatry, London SE5 8AF, UK
| | - Jonathan Shaffer
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Sonia Shah
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Kathleen Lonsdale Building, Gower Place, London WC1E 6BT, UK
| | - Maciej Tomaszewski
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Erik P A Van Iperen
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Kate Witkowska
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Caroline O L Wong
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Li Zhang
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amber L Beitelshees
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Gerald S Berenson
- Department of Epidemiology, Tulane University, New Orleans, LA 70118, USA
| | - Deepak L Bhatt
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Morris Brown
- Clinical Pharmacology Unit, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Amber Burt
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - John M Connell
- University of Dundee, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK
| | - Karen J Cruickshanks
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA; Department of Population Health Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Sean P Curtis
- Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USA
| | - George Davey-Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Ron T Gansevoort
- Division of Nephrology, Department of Medicine, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Xiuqing Guo
- Cedars-Sinai Med Ctr-PEDS, Los Angeles, CA 90048, USA
| | - Shen Haiqing
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Claire E Hastie
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Marten H Hofker
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Department Pathology and Medical Biology, Medical Biology Division, Molecular Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - G Kees Hovingh
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Daniel S Kim
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Susan A Kirkland
- Department of Community Health and Epidemiology, Dalhousie University, Halifax, NS B3H 1V7, Canada
| | - Barbara E Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Yun R Li
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steffi Maiwald
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | | | - Eoin T O'Brien
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - N Charlotte Onland-Moret
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Walter Palmas
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Afshin Parsa
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Brenda W Penninx
- Department of Psychiatry/EMGO Institute, VU University Medical Centre, 1081 BT Amsterdam, the Netherlands
| | - Mary Pettinger
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ramachandran S Vasan
- Department of Medicine, Boston University School of Medicine, Framingham, MA 02118, USA
| | - Jane E Ranchalis
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College London, W2 1LA UK
| | - Daichi Shimbo
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Laura Steele
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronald P Stolk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Mieke D Trip
- Department of Cardiology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - W Monique Verschuren
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Sharon Wyatt
- Schools of Nursing and Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - J Hunter Young
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Connie R Bezzina
- Heart Failure Research Center, Department of Clinical and Experimental Cardiology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands; Molecular and Experimental Cardiology Group, Academic Medical Centre, 1105 AZ Amsterdam, the Netherlands
| | - Eric Boerwinkle
- Human Genetics Center and Institute of Molecular Medicine and Division of Epidemiology, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Juan P Casas
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, London WC1E 6BT, UK
| | - Mark J Caulfield
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Karina W Davidson
- Departments of Medicine & Psychiatry, Columbia University, New York, NY 10032, USA
| | - Pieter A Doevendans
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Anna F Dominiczak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Garret A FitzGerald
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John G Gums
- Departments of Pharmacotherapy and Translational Research and Community Health and Family Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Myriam Fornage
- Institute of Molecular Medicine and School of Public Health Division of Epidemiology Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Indrani Halder
- School of Medicine, University of Pittsburgh, PA 15261, USA
| | - Hans L Hillege
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Hannover Unified Biobank, Hannover Medical School, Hannover 30625, Germany
| | - Gail P Jarvik
- International Centre for Circulatory Health, Imperial College London, W2 1LA UK
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - John J P Kastelein
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Wolfgang Koenig
- Department of Internal Medicine II - Cardiology, University of Ulm Medical Centre, Ulm 89081, Germany
| | - Meena Kumari
- Department of Epidemiology and Public Health, Division of Population Health, University College London, Torrington Place, London WC1E 7HB, UK
| | - Winfried März
- Medical Clinic V, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany; Synlab Academy, Synlab Services GmbH, Mannheim 69214, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz 8036, Austria
| | - Sarah S Murray
- Department of Pathology, University of California San Diego, La Jolla, CA 92037, USA
| | - Jeffery R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - Daniel J Rader
- Cardiovascular Institute, the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Muredach P Reilly
- Cardiovascular Institute, the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | | | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alice V Stanton
- Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - André G Uitterlinden
- Departments of Epidemiology and Internal Medicine, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Yvonne T van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Groby Road, Leicester LE3 9QP, UK
| | - Hugh Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute Framingham Heart Study, Framingham, MA 01702, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul I W de Bakker
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA and Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Levy
- Center for Population Studies, National Heart, Lung, and Blood Institute, Framingham, MA 01702, USA
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London WC1E 6BT, UK
| | - Patricia B Munroe
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.
| | - Brendan J Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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An expressed retrogene of the master embryonic stem cell gene POU5F1 is associated with prostate cancer susceptibility. Am J Hum Genet 2014; 94:395-404. [PMID: 24581739 DOI: 10.1016/j.ajhg.2014.01.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/31/2014] [Indexed: 12/21/2022] Open
Abstract
Genetic association studies of prostate and other cancers have identified a major risk locus at chromosome 8q24. Several independent risk variants at this locus alter transcriptional regulatory elements, but an affected gene and mechanism for cancer predisposition have remained elusive. The retrogene POU5F1B within the locus has a preserved open reading frame encoding a homolog of the master embryonic stem cell transcription factor Oct4. We find that 8q24 risk alleles are expression quantitative trait loci correlated with reduced expression of POU5F1B in prostate tissue and that predicted deleterious POU5F1B missense variants are also associated with risk of transformation. POU5F1 is known to be self-regulated by the encoded Oct4 transcription factor. We further observe that POU5F1 expression is directly correlated with POU5F1B expression. Our results suggest that a pathway critical to self-renewal of embryonic stem cells may also have a role in the origin of cancer.
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235
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Novel insights into breast cancer genetic variance through RNA sequencing. Sci Rep 2014; 3:2256. [PMID: 23884293 PMCID: PMC3722564 DOI: 10.1038/srep02256] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/17/2013] [Indexed: 12/24/2022] Open
Abstract
Using RNA sequencing of triple-negative breast cancer (TNBC), non-TBNC and HER2-positive breast cancer sub-types, here we report novel expressed variants, allelic prevalence and abundance, and coexpression with other variation, and splicing signatures. To reveal the most prevalent variant alleles, we overlaid our findings with cancer- and population-based datasets and validated a subset of novel variants of cancer-related genes: ESRP2, GBP1, TPP1, MAD2L1BP, GLUD2 and SLC30A8. As a proof-of-principle, we demonstrated that a rare substitution in the splicing coordinator ESRP2 (R353Q) impairs its ability to bind to its substrate FGFR2 pre-mRNA. In addition, we describe novel SNPs and INDELs in cancer relevant genes with no prior reported association of point mutations with cancer, such as MTAP and MAGED1. For the first time, this study illustrates the power of RNA-sequencing in revealing the variation landscape of breast transcriptome and exemplifies analytical strategies to search regulatory interactions among cancer relevant molecules.
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236
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Wagner JR, Busche S, Ge B, Kwan T, Pastinen T, Blanchette M. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol 2014; 15:R37. [PMID: 24555846 PMCID: PMC4053980 DOI: 10.1186/gb-2014-15-2-r37] [Citation(s) in RCA: 315] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 02/20/2014] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND DNA methylation plays an essential role in the regulation of gene expression. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood. RESULTS We report the joint analysis of sequence variants, gene expression and DNA methylation in primary fibroblast samples derived from a set of 62 unrelated individuals. Approximately 2% of the most variable CpG sites are mappable in cis to sequence variation, usually within 5 kb. Via eQTL analysis with microarray data combined with mapping of allelic expression regions, we obtained a set of 2,770 regions mappable in cis to sequence variation. In 9.5% of these expressed regions, an associated SNP was also a methylation QTL. Methylation and gene expression are often correlated without direct discernible involvement of sequence variation, but not always in the expected direction of negative for promoter CpGs and positive for gene-body CpGs. Population-level correlation between methylation and expression is strongest in a subset of developmentally significant genes, including all four HOX clusters. The presence and sign of this correlation are best predicted using specific chromatin marks rather than position of the CpG site with respect to the gene. CONCLUSIONS Our results indicate a wide variety of relationships between gene expression, DNA methylation and sequence variation in untransformed adult human fibroblasts, with considerable involvement of chromatin features and some discernible involvement of sequence variation.
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Affiliation(s)
- James R Wagner
- McGill University School of Computer Science, Rm 318, 3480 University Street, Montreal, Québec H3A 0E9, Canada
| | - Stephan Busche
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
- Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
| | - Bing Ge
- Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
- Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
- Génome Québec Innovation Centre, 740 Dr. Penfield Avenue, Room 6202, Montréal, Québec H3A 0G1, Canada
| | - Mathieu Blanchette
- McGill University School of Computer Science, Rm 318, 3480 University Street, Montreal, Québec H3A 0E9, Canada
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237
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Véron A, Blein S, Cox DG. Genome-wide association studies and the clinic: a focus on breast cancer. Biomark Med 2014; 8:287-96. [DOI: 10.2217/bmm.13.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Breast cancer is the most frequently diagnosed cancer among women worldwide, and has long been considered to be a genetic disease. A wide range of genetic variants, both rare mutations and more common variants, have been shown to influence breast cancer risk. In particular, recent studies have identified a number of common genetic variants, or single nucleotide polymorphisms, that are associated with breast cancer risk. In this review, we will briefly present the genetic epidemiology of breast cancer, genome-wide association study technology and how this technology may influence breast cancer screening in the clinic.
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Affiliation(s)
- Amélie Véron
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, ISPB, Lyon, F-69622, France
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Centre Léon Bérard, F-69008 Lyon, France
| | - Sophie Blein
- Université de Lyon, F-69000 Lyon, France
- Université Lyon 1, ISPB, Lyon, F-69622, France
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Centre Léon Bérard, F-69008 Lyon, France
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238
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Meyer KB, O'Reilly M, Michailidou K, Carlebur S, Edwards SL, French JD, Prathalingham R, Dennis J, Bolla MK, Wang Q, de Santiago I, Hopper JL, Tsimiklis H, Apicella C, Southey MC, Schmidt MK, Broeks A, Van 't Veer LJ, Hogervorst FB, Muir K, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Fasching PA, Lux MP, Ekici AB, Beckmann MW, Peto J, Dos Santos Silva I, Fletcher O, Johnson N, Sawyer EJ, Tomlinson I, Kerin MJ, Miller N, Marme F, Schneeweiss A, Sohn C, Burwinkel B, Guénel P, Truong T, Laurent-Puig P, Menegaux F, Bojesen SE, Nordestgaard BG, Nielsen SF, Flyger H, Milne RL, Zamora MP, Arias JI, Benitez J, Neuhausen S, Anton-Culver H, Ziogas A, Dur CC, Brenner H, Müller H, Arndt V, Stegmaier C, Meindl A, Schmutzler RK, Engel C, Ditsch N, Brauch H, Brüning T, Ko YD, Nevanlinna H, Muranen TA, Aittomäki K, Blomqvist C, Matsuo K, Ito H, Iwata H, Yatabe Y, Dörk T, Helbig S, Bogdanova NV, Lindblom A, Margolin S, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Chenevix-Trench G, Wu AH, Tseng CC, Van Den Berg D, Stram DO, Lambrechts D, Thienpont B, Christiaens MR, Smeets A, Chang-Claude J, Rudolph A, Seibold P, Flesch-Janys D, Radice P, Peterlongo P, Bonanni B, Bernard L, Couch FJ, Olson JE, Wang X, Purrington K, Giles GG, Severi G, Baglietto L, McLean C, Haiman CA, Henderson BE, Schumacher F, Le Marchand L, Simard J, Goldberg MS, Labrèche F, Dumont M, Teo SH, Yip CH, Phuah SY, Kristensen V, Grenaker Alnæs G, Børresen-Dale AL, Zheng W, Deming-Halverson S, Shrubsole M, Long J, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Kauppila S, Andrulis IL, Knight JA, Glendon G, Tchatchou S, Devilee P, Tollenaar RAEM, Seynaeve CM, García-Closas M, Figueroa J, Chanock SJ, Lissowska J, Czene K, Darabi H, Eriksson K, Hooning MJ, Martens JWM, van den Ouweland AMW, van Deurzen CHM, Hall P, Li J, Liu J, Humphreys K, Shu XO, Lu W, Gao YT, Cai H, Cox A, Reed MWR, Blot W, Signorello LB, Cai Q, Pharoah PDP, Ghoussaini M, Harrington P, Tyrer J, Kang D, Choi JY, Park SK, Noh DY, Hartman M, Hui M, Lim WY, Buhari SA, Hamann U, Försti A, Rüdiger T, Ulmer HU, Jakubowska A, Lubinski J, Jaworska K, Durda K, Sangrajrang S, Gaborieau V, Brennan P, McKay J, Vachon C, Slager S, Fostira F, Pilarski R, Shen CY, Hsiung CN, Wu PE, Hou MF, Swerdlow A, Ashworth A, Orr N, Schoemaker MJ, Ponder BAJ, Dunning AM, Easton DF. Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1. Am J Hum Genet 2013; 93:1046-60. [PMID: 24290378 PMCID: PMC3852923 DOI: 10.1016/j.ajhg.2013.10.026] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/15/2013] [Accepted: 10/28/2013] [Indexed: 12/19/2022] Open
Abstract
The 10q26 locus in the second intron of FGFR2 is the locus most strongly associated with estrogen-receptor-positive breast cancer in genome-wide association studies. We conducted fine-scale mapping in case-control studies genotyped with a custom chip (iCOGS), comprising 41 studies (n = 89,050) of European ancestry, 9 Asian ancestry studies (n = 13,983), and 2 African ancestry studies (n = 2,028) from the Breast Cancer Association Consortium. We identified three statistically independent risk signals within the locus. Within risk signals 1 and 3, genetic analysis identified five and two variants, respectively, highly correlated with the most strongly associated SNPs. By using a combination of genetic fine mapping, data on DNase hypersensitivity, and electrophoretic mobility shift assays to study protein-DNA binding, we identified rs35054928, rs2981578, and rs45631563 as putative functional SNPs. Chromatin immunoprecipitation showed that FOXA1 preferentially bound to the risk-associated allele (C) of rs2981578 and was able to recruit ERα to this site in an allele-specific manner, whereas E2F1 preferentially bound the risk variant of rs35054928. The risk alleles were preferentially found in open chromatin and bound by Ser5 phosphorylated RNA polymerase II, suggesting that the risk alleles are associated with changes in transcription. Chromatin conformation capture demonstrated that the risk region was able to interact with the promoter of FGFR2, the likely target gene of this risk region. A role for FOXA1 in mediating breast cancer susceptibility at this locus is consistent with the finding that the FGFR2 risk locus primarily predisposes to estrogen-receptor-positive disease.
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Affiliation(s)
- Kerstin B Meyer
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
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Quigley DA, Fiorito E, Nord S, Van Loo P, Alnæs GG, Fleischer T, Tost J, Moen Vollan HK, Tramm T, Overgaard J, Bukholm IR, Hurtado A, Balmain A, Børresen-Dale AL, Kristensen V. The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors. Mol Oncol 2013; 8:273-84. [PMID: 24388359 DOI: 10.1016/j.molonc.2013.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 11/17/2022] Open
Abstract
Genome-wide association studies have identified numerous loci linked to breast cancer susceptibility, but the mechanism by which variations at these loci influence susceptibility is usually unknown. Some variants are only associated with particular clinical subtypes of breast cancer. Understanding how and why these variants influence subtype-specific cancer risk contributes to our understanding of cancer etiology. We conducted a genome-wide expression Quantitative Trait Locus (eQTL) study in a discovery set of 287 breast tumors and 97 normal mammary tissue samples and a replication set of 235 breast tumors. We found that the risk-associated allele of rs7716600 in the 5p12 estrogen receptor-positive (ER-positive) susceptibility locus was associated with elevated expression of the nearby gene MRPS30 exclusively in ER-positive tumors. We replicated this finding in 235 independent tumors. Further, we showed the rs7716600 risk genotype was associated with decreased MRPS30 promoter methylation exclusively in ER-positive breast tumors. In vitro studies in MCF-7 cells carrying the protective genotype showed that estrogen stimulation decreased MRPS30 promoter chromatin availability and mRNA levels. In contrast, in 600MPE cells carrying the risk genotype, estrogen increased MRPS30 expression and did not affect promoter availability. Our data suggest the 5p12 risk allele affects MRPS30 expression in estrogen-responsive tumor cells after tumor initiation by a mechanism affecting chromatin availability. These studies emphasize that the genetic architecture of breast cancer is context-specific, and integrated analysis of gene expression and chromatin remodeling in normal and tumor tissues will be required to explain the mechanisms of risk alleles.
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Affiliation(s)
- David A Quigley
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, USA.
| | - Elisa Fiorito
- Breast Cancer Research Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway, (NCMM), University of Oslo, Norway.
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton UK; Department of Human Genetics, VIB and KU Leuven, Leuven, Belgium.
| | - Grethe Grenaker Alnæs
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Jorg Tost
- Laboratory for Functional Genomics, Fondation Jean Dausset, Centre Etude Polymorphism Humain, (CEPH), Paris, France; Laboratory of Epigenetics, Centre National de Génotypage, Commissariat à l'énergie Atomique et, aux énergies Alternatives (CEA)-Institut de Génomique, Evry, France.
| | - Hans Kristian Moen Vollan
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Trine Tramm
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.
| | - Jens Overgaard
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.
| | - Ida R Bukholm
- Department of Breast-Endocrine Surgery, Akershus University Hospital, Oslo, Norway; Department of Oncology, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Oslo, Norway.
| | - Antoni Hurtado
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Breast Cancer Research Group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway, (NCMM), University of Oslo, Norway.
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, USA.
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital, Lørenskog, Norway.
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240
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Aran D, Hellman A. Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition: analyzing DNA methylation of transcriptional enhancers reveals missed regulatory links between cancer risk loci and genes. Bioessays 2013; 36:184-90. [PMID: 24277586 DOI: 10.1002/bies.201300119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Paradoxically, DNA sequence polymorphisms in cancer risk loci rarely correlate with the expression of cancer genes. Therefore, the molecular mechanism underlying an individual's susceptibility to cancer has remained largely unknown. However, recent evaluations of the correlations between DNA methylation and gene expression levels across healthy and cancerous genomes have revealed enrichment of disease-related DNA methylation variations within disease-associated risk loci. Moreover, it appears that transcriptional enhancers embedded in cancer risk loci often contain DNA methylation sites that closely define the expression of prominent cancer genes, despite the lack of significant correlations between gene expression levels and the surrounding disease-associated polymorphic sequences. We suggest that DNA methylation variations may obscure the effect of co-residing risk sequence alleles. Analysis of enhancer methylation data may help to reveal the regulatory circuits underlying predisposition to cancers and other common diseases.
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Affiliation(s)
- Dvir Aran
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel; School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
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241
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Edwards SL, Beesley J, French JD, Dunning AM. Beyond GWASs: illuminating the dark road from association to function. Am J Hum Genet 2013; 93:779-97. [PMID: 24210251 PMCID: PMC3824120 DOI: 10.1016/j.ajhg.2013.10.012] [Citation(s) in RCA: 544] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWASs) have enabled the discovery of common genetic variation contributing to normal and pathological traits and clinical drug responses, but recognizing the precise targets of these associations is now the major challenge. Here, we review recent approaches to the functional follow-up of GWAS loci, including fine mapping of GWAS signal(s), prioritization of putative functional SNPs by the integration of genetic epidemiological and bioinformatic methods, and in vitro and in vivo experimental verification of predicted molecular mechanisms for identifying the targeted genes. The majority of GWAS-identified variants fall in noncoding regions of the genome. Therefore, this review focuses on strategies for assessing likely mechanisms affected by noncoding variants; such mechanisms include transcriptional regulation, noncoding RNA function, and epigenetic regulation. These approaches have already accelerated progress from genetic studies to biological knowledge and might ultimately guide the development of prognostic, preventive, and therapeutic measures.
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Affiliation(s)
- Stacey L Edwards
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
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242
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Monteiro ANA, Freedman ML. Lessons from postgenome-wide association studies: functional analysis of cancer predisposition loci. J Intern Med 2013; 274:414-24. [PMID: 24127939 PMCID: PMC3801430 DOI: 10.1111/joim.12085] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the last few years, genome-wide association studies (GWASs) have identified hundreds of predisposition loci for several types of human cancers. Recent progress has been made in determining the underlying mechanisms through which different single-nucleotide polymorphisms (SNPs) affect predisposition to cancer. Although there has been much debate about the clinical utility of GWASs, less attention has been paid to how GWASs and post-GWASs functional analysis have contributed to understanding the aetiology of cancer. Most common variants associated with cancer risk are localized in nonprotein-coding regions highlighting transcriptional regulation as a common theme in the mechanism of cancer predisposition. Here, we outline strategies to functionally dissect predisposition loci and discuss their limitations as well as challenges for future studies.
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Affiliation(s)
- A N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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243
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244
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Bogdanova N, Helbig S, Dörk T. Hereditary breast cancer: ever more pieces to the polygenic puzzle. Hered Cancer Clin Pract 2013; 11:12. [PMID: 24025454 PMCID: PMC3851033 DOI: 10.1186/1897-4287-11-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 09/02/2013] [Indexed: 12/21/2022] Open
Abstract
Several susceptibility genes differentially impact on the lifetime risk for breast cancer. Technological advances over the past years have enabled the detection of genetic risk factors through high-throughput screening of large breast cancer case-control series. High- to intermediate penetrance alleles have now been identified in more than 20 genes involved in DNA damage signalling and repair, and more than 70 low-penetrance loci have been discovered through recent genome-wide association studies. In addition to classical germ-line mutation and single-nucleotide polymorphism, copy number variation and somatic mosaicism have been proposed as potential predisposing mechanisms. Many of the identified loci also appear to influence breast tumour characteristics such as estrogen receptor status. In this review, we briefly summarize present knowledge about breast cancer susceptibility genes and discuss their implications for risk prediction and clinical practice.
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Affiliation(s)
- Natalia Bogdanova
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
- Clinics of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Sonja Helbig
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
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Brown JR. Inherited susceptibility to chronic lymphocytic leukemia: evidence and prospects for the future. Ther Adv Hematol 2013; 4:298-308. [PMID: 23926461 PMCID: PMC3734903 DOI: 10.1177/2040620713495639] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in the United States and one of the most heritable cancers. A family history of the disease is perhaps the best defined risk factor, and approximately 15-20% of CLL patients have a family member with CLL or a related lymphoproliferative disorder. Much effort has been devoted to trying to elucidate the mechanisms underlying this genetic risk. Familial CLL appears to be clinically and biologically similar to sporadic CLL, and most if not all CLL appears to be preceded by monoclonal B-cell lymphocytosis (MBL), which does appear to occur at higher frequency in relatives in families with CLL. Neither linkage studies nor candidate gene association studies have proven particularly informative in CLL, but genomewide association studies have identified multiple low-risk variants that together explain about 16% of the familial risk of CLL. Studies of individual families have identified higher-risk single nucleotide polymorphisms or copy number variants associated with disease risk in those families. Current efforts to identify additional risk loci are focused on applying next-generation sequencing to the germline of informative CLL families as well as individuals with sporadic CLL.
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Affiliation(s)
- Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
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246
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Sur I, Tuupanen S, Whitington T, Aaltonen LA, Taipale J. Lessons from functional analysis of genome-wide association studies. Cancer Res 2013; 73:4180-4. [PMID: 23832660 DOI: 10.1158/0008-5472.can-13-0789] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most cancer-associated single-nucleotide polymorphisms (SNP) identified using genome-wide association studies are located outside of protein-coding regions, and their significance and mode of action have been a source of continuing debate. One proposed mechanism of action of the SNPs is that they would affect the activity of enhancer elements regulating critical target genes. In this review, we summarize recent results that substantiate this model. These studies have identified a cancer-specific enhancer element at the 8q24 gene desert that controls the expression of the MYC oncogene. We further discuss implications of the observed difference between normal growth control and cancer for drug development, and the inherent features of genome-wide association studies that may specifically lead to identification of disease-specific regulatory elements.
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Affiliation(s)
- Inderpreet Sur
- Department of Biosciences and Nutrition, SciLife Center, Karolinska Institutet, Clinical Research Center, Karolinska University Hospital, Stockholm, Sweden
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247
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The Continuum of Cancer Immunosurveillance: Prognostic, Predictive, and Mechanistic Signatures. Immunity 2013; 39:11-26. [DOI: 10.1016/j.immuni.2013.07.008] [Citation(s) in RCA: 600] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/09/2013] [Indexed: 11/21/2022]
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248
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Rhie SK, Coetzee SG, Noushmehr H, Yan C, Kim JM, Haiman CA, Coetzee GA. Comprehensive functional annotation of seventy-one breast cancer risk Loci. PLoS One 2013; 8:e63925. [PMID: 23717510 PMCID: PMC3661550 DOI: 10.1371/journal.pone.0063925] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/08/2013] [Indexed: 02/06/2023] Open
Abstract
Breast Cancer (BCa) genome-wide association studies revealed allelic frequency differences between cases and controls at index single nucleotide polymorphisms (SNPs). To date, 71 loci have thus been identified and replicated. More than 320,000 SNPs at these loci define BCa risk due to linkage disequilibrium (LD). We propose that BCa risk resides in a subgroup of SNPs that functionally affects breast biology. Such a shortlist will aid in framing hypotheses to prioritize a manageable number of likely disease-causing SNPs. We extracted all the SNPs, residing in 1 Mb windows around breast cancer risk index SNP from the 1000 genomes project to find correlated SNPs. We used FunciSNP, an R/Bioconductor package developed in-house, to identify potentially functional SNPs at 71 risk loci by coinciding them with chromatin biofeatures. We identified 1,005 SNPs in LD with the index SNPs (r(2)≥0.5) in three categories; 21 in exons of 18 genes, 76 in transcription start site (TSS) regions of 25 genes, and 921 in enhancers. Thirteen SNPs were found in more than one category. We found two correlated and predicted non-benign coding variants (rs8100241 in exon 2 and rs8108174 in exon 3) of the gene, ANKLE1. Most putative functional LD SNPs, however, were found in either epigenetically defined enhancers or in gene TSS regions. Fifty-five percent of these non-coding SNPs are likely functional, since they affect response element (RE) sequences of transcription factors. Functionality of these SNPs was assessed by expression quantitative trait loci (eQTL) analysis and allele-specific enhancer assays. Unbiased analyses of SNPs at BCa risk loci revealed new and overlooked mechanisms that may affect risk of the disease, thereby providing a valuable resource for follow-up studies.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Simon G. Coetzee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Houtan Noushmehr
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Chunli Yan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jae Mun Kim
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Gerhard A. Coetzee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
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249
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Seo JH, Li Q, Fatima A, Eklund A, Szallasi Z, Polyak K, Richardson AL, Freedman ML. Deconvoluting complex tissues for expression quantitative trait locus-based analyses. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120363. [PMID: 23650637 DOI: 10.1098/rstb.2012.0363] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Breast cancer genome-wide association studies have pinpointed dozens of variants associated with breast cancer pathogenesis. The majority of risk variants, however, are located outside of known protein-coding regions. Therefore, identifying which genes the risk variants are acting through presents an important challenge. Variants that are associated with mRNA transcript levels are referred to as expression quantitative trait loci (eQTLs). Many studies have demonstrated that eQTL-based strategies provide a direct way to connect a trait-associated locus with its candidate target gene. Performing eQTL-based analyses in human samples is complicated because of the heterogeneous nature of human tissue. We addressed this issue by devising a method to computationally infer the fraction of cell types in normal human breast tissues. We then applied this method to 13 known breast cancer risk loci, which we hypothesized were eQTLs. For each risk locus, we took all known transcripts within a 2 Mb interval and performed an eQTL analysis in 100 reduction mammoplasty cases. A total of 18 significant associations were discovered (eight in the epithelial compartment and 10 in the stromal compartment). This study highlights the ability to perform large-scale eQTL studies in heterogeneous tissues.
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Affiliation(s)
- Ji-Heui Seo
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
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250
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Abstract
Genome-wide association studies (GWASs) have unraveled a large number of cancer risk alleles. Understanding how these allelic variants predispose to disease is a major bottleneck confronting translational application. In this issue, Li and colleagues combine GWASs with The Cancer Genome Atlas (TCGA) to disambiguate the contributions of germline and somatic variants to tumorigenic gene expression programs. They find that close to half of the known risk alleles for estrogen receptor (ER)-positive breast cancer are expression quantitative trait loci (eQTLs) acting upon major determinants of gene expression in tumors.
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Affiliation(s)
- Hyun Seok Kim
- Department of Cell Biology, University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA
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