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Rouskas K, Katsareli EA, Amerikanou C, Dimopoulos AC, Glentis S, Kalantzi A, Skoulakis A, Panousis N, Ongen H, Bielser D, Planchon A, Romano L, Harokopos V, Reczko M, Moulos P, Griniatsos I, Diamantis T, Dermitzakis ET, Ragoussis J, Dedoussis G, Dimas AS. Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population. BMC Genomics 2023; 24:442. [PMID: 37543566 PMCID: PMC10403965 DOI: 10.1186/s12864-023-09532-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Expression quantitative trait loci (eQTL) studies provide insights into regulatory mechanisms underlying disease risk. Expanding studies of gene regulation to underexplored populations and to medically relevant tissues offers potential to reveal yet unknown regulatory variants and to better understand disease mechanisms. Here, we performed eQTL mapping in subcutaneous (S) and visceral (V) adipose tissue from 106 Greek individuals (Greek Metabolic study, GM) and compared our findings to those from the Genotype-Tissue Expression (GTEx) resource. RESULTS We identified 1,930 and 1,515 eGenes in S and V respectively, over 13% of which are not observed in GTEx adipose tissue, and that do not arise due to different ancestry. We report additional context-specific regulatory effects in genes of clinical interest (e.g. oncogene ST7) and in genes regulating responses to environmental stimuli (e.g. MIR21, SNX33). We suggest that a fraction of the reported differences across populations is due to environmental effects on gene expression, driving context-specific eQTLs, and suggest that environmental effects can determine the penetrance of disease variants thus shaping disease risk. We report that over half of GM eQTLs colocalize with GWAS SNPs and of these colocalizations 41% are not detected in GTEx. We also highlight the clinical relevance of S adipose tissue by revealing that inflammatory processes are upregulated in individuals with obesity, not only in V, but also in S tissue. CONCLUSIONS By focusing on an understudied population, our results provide further candidate genes for investigation regarding their role in adipose tissue biology and their contribution to disease risk and pathogenesis.
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Affiliation(s)
- Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Efthymia A Katsareli
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Charalampia Amerikanou
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Alexandros C Dimopoulos
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Hellenic Naval Academy, Hatzikyriakou Avenue, Pireaus, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Pediatric Hematology/Oncology Unit (POHemU), First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece
| | - Alexandra Kalantzi
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Anargyros Skoulakis
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | | | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Deborah Bielser
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Alexandra Planchon
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Luciana Romano
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Vaggelis Harokopos
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Martin Reczko
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Griniatsos
- First Department of Surgery, National and Kapodistrian University of Athens, Medical School, Laiko Hospital, Athens, Greece
| | - Theodoros Diamantis
- First Department of Surgery, National and Kapodistrian University of Athens, Medical School, Laiko Hospital, Athens, Greece
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- Department of Bioengineering, McGill University, Montréal, QC, Canada
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece.
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Jolly A, Du H, Borel C, Chen N, Zhao S, Grochowski CM, Duan R, Fatih JM, Dawood M, Salvi S, Jhangiani SN, Muzny DM, Koch A, Rouskas K, Glentis S, Deligeoroglou E, Bacopoulou F, Wise CA, Dietrich JE, Van den Veyver IB, Dimas AS, Brucker S, Sutton VR, Gibbs RA, Antonarakis SE, Wu N, Coban-Akdemir ZH, Zhu L, Posey JE, Lupski JR. Rare variant enrichment analysis supports GREB1L as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. HGG Adv 2023; 4:100188. [PMID: 37124138 PMCID: PMC10130500 DOI: 10.1016/j.xhgg.2023.100188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only WNT4 (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was used to further reproduce GREB1L findings in diverse genetic backgrounds. Proband and OMIM phenotypes annotated using the Human Phenotype Ontology were analyzed to quantitatively delineate the phenotypic spectrum associated with GREB1L variant alleles found in our MRKH cohort and those previously published. This study reports 18 novel GREB1L variant alleles, 16 within a multiethnic MRKH cohort and two within a congenital scoliosis cohort. Cohort-wide analyses for a burden of rare variants within a single gene identified likely damaging variants in GREB1L (MIM: 617782), a known disease gene for renal hypoplasia and uterine abnormalities (MIM: 617805), in 16 of 590 MRKH probands. GREB1L variant alleles, including a CNV null allele, were found in 8 MRKH type 1 probands and 8 MRKH type II probands. This study used quantitative phenotypic analyses in a worldwide multiethnic cohort to identify and strengthen the association of GREB1L to isolated uterine agenesis (MRKH type I) and syndromic MRKH type II.
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Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | | | - Na Chen
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - André Koch
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Efthymios Deligeoroglou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Flora Bacopoulou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jennifer E. Dietrich
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Ignatia B. Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Antigone S. Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Sara Brucker
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Stylianos E. Antonarakis
- University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, 1205 Geneva, Switzerland
- Medigenome, the Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zeynep H. Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Lan Zhu
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
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Ma C, Chen N, Jolly A, Zhao S, Coban-Akdemir Z, Tian W, Kang J, Ye Y, Wang Y, Koch A, Zhang Y, Qin C, Bonilla X, Borel C, Rall K, Chen Z, Jhangiani S, Niu Y, Li X, Qiu G, Zhang S, Luo G, Wu Z, Bacopoulou F, Deligeoroglou E, Zhang TJ, Rosenberg C, Gibbs RA, Dietrich JE, Dimas AS, Liu P, Antonarakis SE, Brucker SY, Posey JE, Lupski JR, Wu N, Zhu L. Functional characteristics of a broad spectrum of TBX6 variants in Mayer-Rokitansky-Küster-Hauser syndrome. Genet Med 2022; 24:2262-2273. [DOI: 10.1016/j.gim.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
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Galaris A, Fanidis D, Stylianaki EA, Harokopos V, Kalantzi AS, Moulos P, Dimas AS, Hatzis P, Aidinis V. Obesity Reshapes the Microbial Population Structure along the Gut-Liver-Lung Axis in Mice. Biomedicines 2022; 10:biomedicines10020494. [PMID: 35203702 PMCID: PMC8962327 DOI: 10.3390/biomedicines10020494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
The microbiome is emerging as a major player in tissue homeostasis in health and disease. Gut microbiome dysbiosis correlates with several autoimmune and metabolic diseases, while high-fat diets and ensuing obesity are known to affect the complexity and diversity of the microbiome, thus modulating pathophysiology. Moreover, the existence of a gut-liver microbial axis has been proposed, which may extend to the lung. In this context, we systematically compared the microbiomes of the gut, liver, and lung of mice fed a high-fat diet to those of littermates fed a matched control diet. We carried out deep sequencing of seven hypervariable regions of the 16S rRNA microbial gene to examine microbial diversity in the tissues of interest. Comparison of the local microbiomes indicated that lung tissue has the least diverse microbiome under healthy conditions, while microbial diversity in the healthy liver clustered closer to the gut. Obesity increased microbial complexity in all three tissues, with lung microbial diversity being the most modified. Obesity promoted the expansion of Firmicutes along the gut-liver-lung axis, highlighting staphylococcus as a possible pathologic link between obesity and systemic pathophysiology, especially in the lungs.
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Affiliation(s)
- Apostolos Galaris
- Institute of Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (A.G.); (D.F.); (E.-A.S.); (A.-S.K.); (A.S.D.)
| | - Dionysios Fanidis
- Institute of Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (A.G.); (D.F.); (E.-A.S.); (A.-S.K.); (A.S.D.)
| | - Elli-Anna Stylianaki
- Institute of Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (A.G.); (D.F.); (E.-A.S.); (A.-S.K.); (A.S.D.)
| | - Vaggelis Harokopos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (V.H.); (P.M.); (P.H.)
| | - Alexandra-Styliani Kalantzi
- Institute of Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (A.G.); (D.F.); (E.-A.S.); (A.-S.K.); (A.S.D.)
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (V.H.); (P.M.); (P.H.)
| | - Antigone S. Dimas
- Institute of Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (A.G.); (D.F.); (E.-A.S.); (A.-S.K.); (A.S.D.)
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (V.H.); (P.M.); (P.H.)
| | - Vassilis Aidinis
- Institute of Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece; (A.G.); (D.F.); (E.-A.S.); (A.-S.K.); (A.S.D.)
- Correspondence:
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5
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Chen N, Zhao S, Jolly A, Wang L, Pan H, Yuan J, Chen S, Koch A, Ma C, Tian W, Jia Z, Kang J, Zhao L, Qin C, Fan X, Rall K, Coban-Akdemir Z, Chen Z, Jhangiani S, Liang Z, Niu Y, Li X, Yan Z, Wu Y, Dong S, Song C, Qiu G, Zhang S, Liu P, Posey JE, Zhang F, Luo G, Wu Z, Su J, Zhang J, Chen EY, Rouskas K, Glentis S, Bacopoulou F, Deligeoroglou E, Chrousos G, Lyonnet S, Polak M, Rosenberg C, Dingeldein I, Bonilla X, Borel C, Gibbs RA, Dietrich JE, Dimas AS, Antonarakis SE, Brucker SY, Lupski JR, Wu N, Zhu L. Perturbations of genes essential for Müllerian duct and Wölffian duct development in Mayer-Rokitansky-Küster-Hauser syndrome. Am J Hum Genet 2021; 108:337-345. [PMID: 33434492 DOI: 10.1016/j.ajhg.2020.12.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 12/21/2020] [Indexed: 12/01/2022] Open
Abstract
Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) is associated with congenital absence of the uterus, cervix, and the upper part of the vagina; it is a sex-limited trait. Disrupted development of the Müllerian ducts (MD)/Wölffian ducts (WD) through multifactorial mechanisms has been proposed to underlie MRKHS. In this study, exome sequencing (ES) was performed on a Chinese discovery cohort (442 affected subjects and 941 female control subjects) and a replication MRKHS cohort (150 affected subjects of mixed ethnicity from North America, South America, and Europe). Phenotypic follow-up of the female reproductive system was performed on an additional cohort of PAX8-associated congenital hypothyroidism (CH) (n = 5, Chinese). By analyzing 19 candidate genes essential for MD/WD development, we identified 12 likely gene-disrupting (LGD) variants in 7 genes: PAX8 (n = 4), BMP4 (n = 2), BMP7 (n = 2), TBX6 (n = 1), HOXA10 (n = 1), EMX2 (n = 1), and WNT9B (n = 1), while LGD variants in these genes were not detected in control samples (p = 1.27E-06). Interestingly, a sex-limited penetrance with paternal inheritance was observed in multiple families. One additional PAX8 LGD variant from the replication cohort and two missense variants from both cohorts were revealed to cause loss-of-function of the protein. From the PAX8-associated CH cohort, we identified one individual presenting a syndromic condition characterized by CH and MRKHS (CH-MRKHS). Our study demonstrates the comprehensive utilization of knowledge from developmental biology toward elucidating genetic perturbations, i.e., rare pathogenic alleles involving the same loci, contributing to human birth defects.
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Affiliation(s)
- Na Chen
- Department of Obstetrics and Gynaecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; M.D./Ph.D. Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lianlei Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Department of Orthopedic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Hongxin Pan
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, Guangdong 518000, China
| | - Jian Yuan
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Shaoke Chen
- Department of Pediatrics, the Second Affiliated Hospital of Guangxi Medical University, Guangxi 530003, China
| | - André Koch
- Department of Gynecology and Obstetrics, Research Centre for Women's Health, Tübingen University Hospital, Tübingen 72076, Germany
| | - Congcong Ma
- Department of Obstetrics and Gynaecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Weijie Tian
- Department of Obstetrics and Gynaecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Ziqi Jia
- Department of Obstetrics and Gynaecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jia Kang
- Department of Obstetrics and Gynaecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Lina Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Chenglu Qin
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, Guangdong 518000, China
| | - Xin Fan
- Department of Pediatrics, the Second Affiliated Hospital of Guangxi Medical University, Guangxi 530003, China
| | - Katharina Rall
- Department of Gynecology and Obstetrics, Research Centre for Women's Health, Tübingen University Hospital, Tübingen 72076, Germany
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Shalini Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ze Liang
- Department of Obstetrics and Gynaecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Zihui Yan
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Shuangshuang Dong
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai 200011, China
| | - Chengcheng Song
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai 200011, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai 200011, China
| | - Guangnan Luo
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, Guangdong 518000, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jianzhong Su
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, China
| | - Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Eugenia Y Chen
- Baylor College of Medicine, Houston, TX 77030, USA; Departments of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA
| | - Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, Thessaloniki 57001, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece; Division of Pediatric Hematology/Oncology, First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens 11527, Greece
| | - Flora Bacopoulou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, Athens 11527, Greece
| | - Efthymios Deligeoroglou
- Division of Pediatric-Adolescent Gynecology and Reconstructive Surgery, 2(nd) Department of Obstetrics and Gynecology, School of Medicine, National and Kapodistrian University of Athens, Aretaieion Hospital, Athens 10679, Greece
| | - George Chrousos
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, Athens 11527, Greece
| | - Stanislas Lyonnet
- Institut Imagine, UMR-1163 INSERM et Universite de Paris, Hospital Universitaire Necker-Enfants Malades, Paris 75015, France
| | - Michel Polak
- Institut Imagine, UMR-1163 INSERM et Universite de Paris, Hospital Universitaire Necker-Enfants Malades, Paris 75015, France
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo 05508-090, Brazil
| | - Irene Dingeldein
- Inselspital FrauenKlinik, University of Bern, Bern 3012, Switzerland
| | - Ximena Bonilla
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1205, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1205, Switzerland
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Seuencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Dietrich
- Departments of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1205, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1205, Switzerland
| | - Sara Y Brucker
- Department of Gynecology and Obstetrics, Research Centre for Women's Health, Tübingen University Hospital, Tübingen 72076, Germany
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Departments of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Seuencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Lan Zhu
- Department of Obstetrics and Gynaecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.
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Lagou V, Mägi R, Hottenga JJ, Grallert H, Perry JRB, Bouatia-Naji N, Marullo L, Rybin D, Jansen R, Min JL, Dimas AS, Ulrich A, Zudina L, Gådin JR, Jiang L, Faggian A, Bonnefond A, Fadista J, Stathopoulou MG, Isaacs A, Willems SM, Navarro P, Tanaka T, Jackson AU, Montasser ME, O'Connell JR, Bielak LF, Webster RJ, Saxena R, Stafford JM, Pourcain BS, Timpson NJ, Salo P, Shin SY, Amin N, Smith AV, Li G, Verweij N, Goel A, Ford I, Johnson PCD, Johnson T, Kapur K, Thorleifsson G, Strawbridge RJ, Rasmussen-Torvik LJ, Esko T, Mihailov E, Fall T, Fraser RM, Mahajan A, Kanoni S, Giedraitis V, Kleber ME, Silbernagel G, Meyer J, Müller-Nurasyid M, Ganna A, Sarin AP, Yengo L, Shungin D, Luan J, Horikoshi M, An P, Sanna S, Boettcher Y, Rayner NW, Nolte IM, Zemunik T, Iperen EV, Kovacs P, Hastie ND, Wild SH, McLachlan S, Campbell S, Polasek O, Carlson O, Egan J, Kiess W, Willemsen G, Kuusisto J, Laakso M, Dimitriou M, Hicks AA, Rauramaa R, Bandinelli S, Thorand B, Liu Y, Miljkovic I, Lind L, Doney A, Perola M, Hingorani A, Kivimaki M, Kumari M, Bennett AJ, Groves CJ, Herder C, Koistinen HA, Kinnunen L, Faire UD, Bakker SJL, Uusitupa M, Palmer CNA, Jukema JW, Sattar N, Pouta A, Snieder H, Boerwinkle E, Pankow JS, Magnusson PK, Krus U, Scapoli C, de Geus EJCN, Blüher M, Wolffenbuttel BHR, Province MA, Abecasis GR, Meigs JB, Hovingh GK, Lindström J, Wilson JF, Wright AF, Dedoussis GV, Bornstein SR, Schwarz PEH, Tönjes A, Winkelmann BR, Boehm BO, März W, Metspalu A, Price JF, Deloukas P, Körner A, Lakka TA, Keinanen-Kiukaanniemi SM, Saaristo TE, Bergman RN, Tuomilehto J, Wareham NJ, Langenberg C, Männistö S, Franks PW, Hayward C, Vitart V, Kaprio J, Visvikis-Siest S, Balkau B, Altshuler D, Rudan I, Stumvoll M, Campbell H, van Duijn CM, Gieger C, Illig T, Ferrucci L, Pedersen NL, Pramstaller PP, Boehnke M, Frayling TM, Shuldiner AR, Peyser PA, Kardia SLR, Palmer LJ, Penninx BW, Meneton P, Harris TB, Navis G, Harst PVD, Smith GD, Forouhi NG, Loos RJF, Salomaa V, Soranzo N, Boomsma DI, Groop L, Tuomi T, Hofman A, Munroe PB, Gudnason V, Siscovick DS, Watkins H, Lecoeur C, Vollenweider P, Franco-Cereceda A, Eriksson P, Jarvelin MR, Stefansson K, Hamsten A, Nicholson G, Karpe F, Dermitzakis ET, Lindgren CM, McCarthy MI, Froguel P, Kaakinen MA, Lyssenko V, Watanabe RM, Ingelsson E, Florez JC, Dupuis J, Barroso I, Morris AP, Prokopenko I. Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability. Nat Commun 2021; 12:24. [PMID: 33402679 PMCID: PMC7785747 DOI: 10.1038/s41467-020-19366-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Differences between sexes contribute to variation in the levels of fasting glucose and insulin. Epidemiological studies established a higher prevalence of impaired fasting glucose in men and impaired glucose tolerance in women, however, the genetic component underlying this phenomenon is not established. We assess sex-dimorphic (73,089/50,404 women and 67,506/47,806 men) and sex-combined (151,188/105,056 individuals) fasting glucose/fasting insulin genetic effects via genome-wide association study meta-analyses in individuals of European descent without diabetes. Here we report sex dimorphism in allelic effects on fasting insulin at IRS1 and ZNF12 loci, the latter showing higher RNA expression in whole blood in women compared to men. We also observe sex-homogeneous effects on fasting glucose at seven novel loci. Fasting insulin in women shows stronger genetic correlations than in men with waist-to-hip ratio and anorexia nervosa. Furthermore, waist-to-hip ratio is causally related to insulin resistance in women, but not in men. These results position dissection of metabolic and glycemic health sex dimorphism as a steppingstone for understanding differences in genetic effects between women and men in related phenotypes.
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Affiliation(s)
- Vasiliki Lagou
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Microbiology and Immunology, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jouke- Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VU University medical center, Amsterdam, the Netherlands
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD, München-Neuherberg, Germany
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Nabila Bouatia-Naji
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
- INSERM U970, Paris Cardiovascular Research Center PARCC, 75006, Paris, France
| | - Letizia Marullo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Denis Rybin
- Boston University Data Coordinating Center, Boston, MA, USA
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - Anna Ulrich
- Department of Medicine, Imperial College London, London, UK
| | | | - Jesper R Gådin
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Longda Jiang
- Department of Medicine, Imperial College London, London, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Amélie Bonnefond
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
- Department of Medicine, Imperial College London, London, UK
| | - Joao Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- CARIM School for Cardiovascular Diseases and Maastricht Centre for Systems Biology (MaCSBio, Maastricht University, Maastricht, the Netherlands
- Department of Physiology, Maastricht University, Maastricht, the Netherlands
| | - Sara M Willems
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pau Navarro
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Toshiko Tanaka
- Translational Gerontology Branch, Longitudinal Study Section, National Institute on Aging, Baltimore, MD, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Jeff R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rebecca J Webster
- Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, University of Western Australia Centre for Medical Research, Nedlands, WA, Australia
| | - Richa Saxena
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Departmentartment of Anesthesia, Critical Care and Pain Medicine, MGH, Boston, MA, USA
| | - Jeanette M Stafford
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Beate St Pourcain
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Perttu Salo
- Public Health Genomics Unit, Department of Chronic Disease Prevention, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Najaf Amin
- Department of Epidemiology Erasmus MC, Rotterdam, the Netherlands
| | - Albert V Smith
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Guo Li
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anuj Goel
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - Paul C D Johnson
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Toby Johnson
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Karen Kapur
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | | | - Rona J Strawbridge
- Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelin Mihailov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ross M Fraser
- Usher Institute, University of Edinburgh, Edinburgh, UK
- Synpromics Ltd, Roslin Innovation Centre, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Genentech, 340 Point San Bruno Boulevard, South San Francisco, CA, 94080, USA
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Uppsala Universitet, Uppsala, Sweden
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Günther Silbernagel
- Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Julia Meyer
- Institute of Genetic Epidemiology,Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology,Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology and Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-University, Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI, University Medical Center, Johannes Gutenberg University, 55101, Mainz, Germany
| | - Andrea Ganna
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Loic Yengo
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dmitry Shungin
- Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåne University Hospital Malmö, Malmö, Sweden
- Department of Odontology, Umeå University, Umeå, Sweden
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Momoko Horikoshi
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- RIKEN, Center for Integrative Medical Sciences, Laboratory for Endocrinology, Metabolism and Kidney Disease, Yokohama, Japan
| | - Ping An
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Italy
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yvonne Boettcher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - N William Rayner
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Erik van Iperen
- Department of Clinical Epidemiology and Biostatistics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Kovacs
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Nicholas D Hastie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Sarah H Wild
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - Susan Campbell
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Olga Carlson
- Laboratory of Clinical Investigation, National Institute of Aging, Baltimore, MD, USA
| | - Josephine Egan
- Laboratory of Clinical Investigation, National Institute of Aging, Baltimore, MD, USA
| | - Wieland Kiess
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Pediatric Research Center, Department of Women's & Child Health, University of Leipzig, Leipzig, Germany
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Maria Dimitriou
- Department of Dietetics-Nutrition, Harokopio University, Athens, Greece
| | - Andrew A Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC) (Affiliated Institute of the University of LübeckLübeckGermany), Bolzano, Italy
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | | | - Barbara Thorand
- German Center for Diabetes Research (DZD, München-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Iva Miljkovic
- Department of Epidemiology, Center for Aging and Population Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Alex Doney
- Pat McPherson Centre for Pharmacogenetics and Pharmacogenomics, Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Markus Perola
- Public Health Genomics Unit, Department of Chronic Disease Prevention, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Aroon Hingorani
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Meena Kumari
- Department of Epidemiology and Public Health, University College London, London, UK
- University of Essex, Wivenhoe Park, Colchester, Essex, UK
| | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Christopher J Groves
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Christian Herder
- German Center for Diabetes Research (DZD, München-Neuherberg, Germany
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heikki A Koistinen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, P.O. Box 340, Haartmaninkatu 4, Helsinki, FI-00029, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, FI-00290, Finland
| | - Leena Kinnunen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stephan J L Bakker
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Colin N A Palmer
- Pat McPherson Centre for Pharmacogenetics and Pharmacogenomics, Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - J Wouter Jukema
- Dept of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anneli Pouta
- Department of Government Services, Finnish Institute for Health and Welfare, Helsinki, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eric Boerwinkle
- IMM Center for Human Genetics, University of Texas Health Science Center at Houston, Houston, TX, USA
- Division of Epidemiology, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MiI, USA
| | - Patrik K Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika Krus
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Eco J C N de Geus
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, VU University medical center, Amsterdam, the Netherlands
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Bruce H R Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Michael A Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- General Medicine Division, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - G Kees Hovingh
- Department of Vascular Medicine, Amsterdam UMC, Amsterdam, the Netherlands
- Novo Nordisk A/S, Copenhagen, Denmark
| | - Jaana Lindström
- Finnish Institute for Health and Welfare, Diabetes Prevention Unit, Helsinki, Finland
| | - James F Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Alan F Wright
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | - Stefan R Bornstein
- Department of Medicine, Division for Prevention and Care of Diabetes, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Peter E H Schwarz
- Department for Prevention and Care of Diabetes, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | | | - Bernhard O Boehm
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore and Imperial College London, Singapore, Singapore
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Antje Körner
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Diabetes Research Center, Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Timo A Lakka
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Sirkka M Keinanen-Kiukaanniemi
- Faculty of Medicine, Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Timo E Saaristo
- Finnish Diabetes Association, Tampere, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | - Richard N Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jaakko Tuomilehto
- Department of Chronic Disease Prevention, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Satu Männistö
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåne University Hospital Malmö, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
- Department of Public Health & Clinical Medicine, Units of Medicine and Nutritional Research, Umeå University, Umeå, Sweden
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | | | - Beverley Balkau
- Inserm, CESP Center for Research in Epidemiology and Public Health, U1018, Villejuif, France
- Univ Paris-Saclay, Univ Paris Sud, UVSQ, UMRS 1018, UMRS 1018, Villejuif, France
| | - David Altshuler
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Igor Rudan
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | | | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Centre for Medical Systems Biology, Leiden, the Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD, München-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter P Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC) (Affiliated Institute of the University of LübeckLübeckGermany), Bolzano, Italy
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Timothy M Frayling
- Genetics of Complex Traits, Peninsula Medical School, University of Exeter, Exeter, UK
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA
- The Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lyle J Palmer
- School of Public Health, University of Adelaide, Adelaide, Australia
| | - Brenda W Penninx
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Pierre Meneton
- U872 Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Tamara B Harris
- Geriatric Epidemiology Section, Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, MD, USA
| | - Gerjan Navis
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Nita G Forouhi
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Ruth J F Loos
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Leif Groop
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden
- Endocrinology, Abdominal Centre, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Albert Hofman
- Department of Epidemiology Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium for healthy ageing, the Hague, the Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine University of Iceland, Reykjavik, Iceland
| | - David S Siscovick
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Hugh Watkins
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Cecile Lecoeur
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
| | - Peter Vollenweider
- Department of Medicine, University Hospital Lausanne, Lausanne, Switzerland
| | - Anders Franco-Cereceda
- Cardiothoracic Surgery Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Per Eriksson
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics and HPA-MRC Center, School of Public Health, Imperial College London, London, UK
- Institue of Health Sciences, University of Oulu, Oulu, Finland
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
- Department of Cardiology, Karolinska University Hospital Solna, Stockholm, Sweden
| | | | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, UK
- Genentech, 340 Point San Bruno Boulevard, South San Francisco, CA, 94080, USA
| | - Philippe Froguel
- University of Lille Nord de France, Lille, France
- CNRS UMR8199, Institut Pasteur de Lille, Lille, France
- Department of Medicine, Imperial College London, London, UK
| | - Marika A Kaakinen
- Department of Medicine, Imperial College London, London, UK
- School of Biosciences and Medicine, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Richard M Watanabe
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
- Department of Physiology & Neuroscience, Keck School of Medicine of USC, Los Angeles, CA, USA
- USC Diabetes and Obesity Research Institute, Los Angeles, CA, USA
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, 94305, USA
| | - Jose C Florez
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Research Center, Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, UK
- Exeter Centre of ExcEllence in Diabetes (ExCEED), University of Exeter Medical School, Exeter, UK
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Inga Prokopenko
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
- Department of Medicine, Imperial College London, London, UK.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.
- School of Biosciences and Medicine, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK.
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation.
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7
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Glentis S, Dimopoulos AC, Rouskas K, Ntritsos G, Evangelou E, Narod SA, Mes-Masson AM, Foulkes WD, Rivera B, Tonin PN, Ragoussis J, Dimas AS. Exome Sequencing in BRCA1- and BRCA2-Negative Greek Families Identifies MDM1 and NBEAL1 as Candidate Risk Genes for Hereditary Breast Cancer. Front Genet 2019; 10:1005. [PMID: 31681433 PMCID: PMC6813924 DOI: 10.3389/fgene.2019.01005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/20/2019] [Indexed: 12/30/2022] Open
Abstract
Approximately 10% of breast cancer (BC) cases are hereditary BC (HBC), with HBC most commonly encountered in the context of hereditary breast and ovarian cancer (HBOC) syndrome. Although thousands of loss-of-function (LoF) alleles in over 20 genes have been associated with HBC susceptibility, the genetic etiology of approximately 50% of cases remains unexplained, even when polygenic risk models are considered. We focused on one of the least-studied European populations and applied whole-exome sequencing (WES) to 52 individuals from 17 Greek HBOC families, in which at least one patient was negative for known HBC risk variants. Initial screening revealed pathogenic variants in known cancer genes, including BARD1:p.Trp91* detected in a cancer-free individual, and MEN1:p.Glu260Lys detected in a BC patient. Gene- and variant-based approaches were applied to exome data to identify candidate risk variants outside of known risk genes. Findings were verified in a collection of Canadian HBOC patients of European ancestry (FBRCAX), in an independent group of Canadian BC patients (CHUM-BC) and controls (CARTaGENE), as well as in individuals from The Cancer Genome Atlas (TCGA) and the UK Biobank (UKB). Rare LoF variants were uncovered in MDM1 and NBEAL1 in Greek and Canadian HBOC patients. We also report prioritized missense variants SETBP1:c.4129G > C and C7orf34:c.248C > T. These variants comprise promising candidates whose role in cancer pathogenicity needs to be explored further.
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Affiliation(s)
- Stavros Glentis
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - Alexandros C Dimopoulos
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - Konstantinos Rouskas
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - George Ntritsos
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece.,Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Steven A Narod
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,Women's College Research Institute, Women's College Hospital, Toronto, ON, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
| | - William D Foulkes
- Department of Oncology, McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Department of Medical Genetics, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Barbara Rivera
- Department of Oncology, McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Patricia N Tonin
- Department of Medicine, McGill University, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada.,Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Oncology, McGill University, Montreal, QC, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Antigone S Dimas
- Division of Molecular Biology and Genetics, Biomedical Sciences Research Center Al. Fleming, Vari, Greece
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8
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Dimas AS, Lagou V, Barker A, Knowles JW, Mägi R, Hivert MF, Benazzo A, Rybin D, Jackson AU, Stringham HM, Song C, Fischer-Rosinsky A, Boesgaard TW, Grarup N, Abbasi FA, Assimes TL, Hao K, Yang X, Lecoeur C, Barroso I, Bonnycastle LL, Böttcher Y, Bumpstead S, Chines PS, Erdos MR, Graessler J, Kovacs P, Morken MA, Narisu N, Payne F, Stancakova A, Swift AJ, Tönjes A, Bornstein SR, Cauchi S, Froguel P, Meyre D, Schwarz PE, Häring HU, Smith U, Boehnke M, Bergman RN, Collins FS, Mohlke KL, Tuomilehto J, Quertemous T, Lind L, Hansen T, Pedersen O, Walker M, Pfeiffer AF, Spranger J, Stumvoll M, Meigs JB, Wareham NJ, Kuusisto J, Laakso M, Langenberg C, Dupuis J, Watanabe RM, Florez JC, Ingelsson E, McCarthy MI, Prokopenko I. Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity. Diabetes 2014; 63:2158-71. [PMID: 24296717 PMCID: PMC4030103 DOI: 10.2337/db13-0949] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Patients with established type 2 diabetes display both β-cell dysfunction and insulin resistance. To define fundamental processes leading to the diabetic state, we examined the relationship between type 2 diabetes risk variants at 37 established susceptibility loci, and indices of proinsulin processing, insulin secretion, and insulin sensitivity. We included data from up to 58,614 nondiabetic subjects with basal measures and 17,327 with dynamic measures. We used additive genetic models with adjustment for sex, age, and BMI, followed by fixed-effects, inverse-variance meta-analyses. Cluster analyses grouped risk loci into five major categories based on their relationship to these continuous glycemic phenotypes. The first cluster (PPARG, KLF14, IRS1, GCKR) was characterized by primary effects on insulin sensitivity. The second cluster (MTNR1B, GCK) featured risk alleles associated with reduced insulin secretion and fasting hyperglycemia. ARAP1 constituted a third cluster characterized by defects in insulin processing. A fourth cluster (TCF7L2, SLC30A8, HHEX/IDE, CDKAL1, CDKN2A/2B) was defined by loci influencing insulin processing and secretion without a detectable change in fasting glucose levels. The final group contained 20 risk loci with no clear-cut associations to continuous glycemic traits. By assembling extensive data on continuous glycemic traits, we have exposed the diverse mechanisms whereby type 2 diabetes risk variants impact disease predisposition.
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Affiliation(s)
- Antigone S. Dimas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Alexander Fleming, Biomedical Sciences Research Center, Vari, Athens, Greece
| | - Vasiliki Lagou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K
| | - Adam Barker
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Joshua W. Knowles
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Reedik Mägi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Marie-France Hivert
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
- General Medicine Division, Massachusetts General Hospital, Boston, MA
| | - Andrea Benazzo
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Denis Rybin
- Boston University Data Coordinating Center, Boston, MA
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Heather M. Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Ci Song
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Antje Fischer-Rosinsky
- Charité-Universitätsmedizin Berlin, Department of Endocrinology and Metabolism, Berlin, Germany
| | | | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fahim A. Abbasi
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Themistocles L. Assimes
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA
| | - Cécile Lecoeur
- CNRS UMR8199-Institute of Biology, Pasteur Institute, Lille 2-Droit et Santé University, Lille, France
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, U.K
- University of Cambridge Metabolic Research Laboratories and National Institute for Health Research Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Lori L. Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Yvonne Böttcher
- IFB AdiposityDiseases, Leipzig University Medical Center, Leipzig, Germany
| | | | - Peter S. Chines
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Michael R. Erdos
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Jurgen Graessler
- Department of Medicine III, Division of Prevention and Care of Diabetes, University of Dresden, Dresden, Germany
| | - Peter Kovacs
- Interdisciplinary Center for Clinical Research Leipzig, Leipzig, Germany
| | - Mario A. Morken
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | | | - Alena Stancakova
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Amy J. Swift
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Anke Tönjes
- IFB AdiposityDiseases, Leipzig University Medical Center, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Stefan R. Bornstein
- Department of Medicine III, Division of Prevention and Care of Diabetes, University of Dresden, Dresden, Germany
| | - Stéphane Cauchi
- CNRS UMR8199-Institute of Biology, Pasteur Institute, Lille 2-Droit et Santé University, Lille, France
| | - Philippe Froguel
- CNRS UMR8199-Institute of Biology, Pasteur Institute, Lille 2-Droit et Santé University, Lille, France
- Department of Genomics of Common Disease, Imperial College London, London, U.K
| | - David Meyre
- CNRS UMR8199-Institute of Biology, Pasteur Institute, Lille 2-Droit et Santé University, Lille, France
- Department of Clinical Epidemiology & Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | - Peter E.H. Schwarz
- Department of Medicine III, Division of Prevention and Care of Diabetes, University of Dresden, Dresden, Germany
| | - Hans-Ulrich Häring
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology and Clinical Chemistry, University of Tübingen, Tübingen, Germany
| | - Ulf Smith
- Lundberg Laboratory for Diabetes Research, Center of Excellence for Metabolic and Cardiovascular Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Richard N. Bergman
- Department of Physiology & Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Francis S. Collins
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Karen L. Mohlke
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- Centre for Vascular Prevention, Danube University Krems, Krems, Austria
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thomas Quertemous
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Lars Lind
- Department of Medical Sciences, Akademiska Sjukhuset, Uppsala University, Uppsala, Sweden
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Hagedorn Research Institute, Copenhagen, Denmark
- Institute of Biomedical Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Aarhus, Aarhus, Denmark
| | - Mark Walker
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - Andreas F.H. Pfeiffer
- Charité-Universitätsmedizin Berlin, Department of Endocrinology and Metabolism, Berlin, Germany
- Department of Clinical Nutrition, German Institute of Human Nutrition, Nuthetal, Germany
| | - Joachim Spranger
- Charité-Universitätsmedizin Berlin, Department of Endocrinology and Metabolism, Berlin, Germany
| | - Michael Stumvoll
- IFB AdiposityDiseases, Leipzig University Medical Center, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - James B. Meigs
- General Medicine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Nicholas J. Wareham
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Claudia Langenberg
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA
| | - Richard M. Watanabe
- Departments of Preventive Medicine and Physiology & Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jose C. Florez
- Department of Medicine, Harvard Medical School, Boston, MA
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K
- Department of Genomics of Common Disease, Imperial College London, London, U.K
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Mahajan A, Go MJ, Zhang W, Below JE, Gaulton KJ, Ferreira T, Horikoshi M, Johnson AD, Ng MCY, Prokopenko I, Saleheen D, Wang X, Zeggini E, Abecasis GR, Adair LS, Almgren P, Atalay M, Aung T, Baldassarre D, Balkau B, Bao Y, Barnett AH, Barroso I, Basit A, Been LF, Beilby J, Bell GI, Benediktsson R, Bergman RN, Boehm BO, Boerwinkle E, Bonnycastle LL, Burtt N, Cai Q, Campbell H, Carey J, Cauchi S, Caulfield M, Chan JCN, Chang LC, Chang TJ, Chang YC, Charpentier G, Chen CH, Chen H, Chen YT, Chia KS, Chidambaram M, Chines PS, Cho NH, Cho YM, Chuang LM, Collins FS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Danesh J, Das D, de Faire U, Dedoussis G, Deloukas P, Dimas AS, Dina C, Doney AS, Donnelly PJ, Dorkhan M, van Duijn C, Dupuis J, Edkins S, Elliott P, Emilsson V, Erbel R, Eriksson JG, Escobedo J, Esko T, Eury E, Florez JC, Fontanillas P, Forouhi NG, Forsen T, Fox C, Fraser RM, Frayling TM, Froguel P, Frossard P, Gao Y, Gertow K, Gieger C, Gigante B, Grallert H, Grant GB, Grrop LC, Groves CJ, Grundberg E, Guiducci C, Hamsten A, Han BG, Hara K, Hassanali N, Hattersley AT, Hayward C, Hedman AK, Herder C, Hofman A, Holmen OL, Hovingh K, Hreidarsson AB, Hu C, Hu FB, Hui J, Humphries SE, Hunt SE, Hunter DJ, Hveem K, Hydrie ZI, Ikegami H, Illig T, Ingelsson E, Islam M, Isomaa B, Jackson AU, Jafar T, James A, Jia W, Jöckel KH, Jonsson A, Jowett JBM, Kadowaki T, Kang HM, Kanoni S, Kao WHL, Kathiresan S, Kato N, Katulanda P, Keinanen-Kiukaanniemi KM, Kelly AM, Khan H, Khaw KT, Khor CC, Kim HL, Kim S, Kim YJ, Kinnunen L, Klopp N, Kong A, Korpi-Hyövälti E, Kowlessur S, Kraft P, Kravic J, Kristensen MM, Krithika S, Kumar A, Kumate J, Kuusisto J, Kwak SH, Laakso M, Lagou V, Lakka TA, Langenberg C, Langford C, Lawrence R, Leander K, Lee JM, Lee NR, Li M, Li X, Li Y, Liang J, Liju S, Lim WY, Lind L, Lindgren CM, Lindholm E, Liu CT, Liu JJ, Lobbens S, Long J, Loos RJF, Lu W, Luan J, Lyssenko V, Ma RCW, Maeda S, Mägi R, Männisto S, Matthews DR, Meigs JB, Melander O, Metspalu A, Meyer J, Mirza G, Mihailov E, Moebus S, Mohan V, Mohlke KL, Morris AD, Mühleisen TW, Müller-Nurasyid M, Musk B, Nakamura J, Nakashima E, Navarro P, Ng PK, Nica AC, Nilsson PM, Njølstad I, Nöthen MM, Ohnaka K, Ong TH, Owen KR, Palmer CNA, Pankow JS, Park KS, Parkin M, Pechlivanis S, Pedersen NL, Peltonen L, Perry JRB, Peters A, Pinidiyapathirage JM, Platou CG, Potter S, Price JF, Qi L, Radha V, Rallidis L, Rasheed A, Rathman W, Rauramaa R, Raychaudhuri S, Rayner NW, Rees SD, Rehnberg E, Ripatti S, Robertson N, Roden M, Rossin EJ, Rudan I, Rybin D, Saaristo TE, Salomaa V, Saltevo J, Samuel M, Sanghera DK, Saramies J, Scott J, Scott LJ, Scott RA, Segrè AV, Sehmi J, Sennblad B, Shah N, Shah S, Shera AS, Shu XO, Shuldiner AR, Sigurđsson G, Sijbrands E, Silveira A, Sim X, Sivapalaratnam S, Small KS, So WY, Stančáková A, Stefansson K, Steinbach G, Steinthorsdottir V, Stirrups K, Strawbridge RJ, Stringham HM, Sun Q, Suo C, Syvänen AC, Takayanagi R, Takeuchi F, Tay WT, Teslovich TM, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tikkanen E, Trakalo J, Tremoli E, Trip MD, Tsai FJ, Tuomi T, Tuomilehto J, Uitterlinden AG, Valladares-Salgado A, Vedantam S, Veglia F, Voight BF, Wang C, Wareham NJ, Wennauer R, Wickremasinghe AR, Wilsgaard T, Wilson JF, Wiltshire S, Winckler W, Wong TY, Wood AR, Wu JY, Wu Y, Yamamoto K, Yamauchi T, Yang M, Yengo L, Yokota M, Young R, Zabaneh D, Zhang F, Zhang R, Zheng W, Zimmet PZ, Altshuler D, Bowden DW, Cho YS, Cox NJ, Cruz M, Hanis CL, Kooner J, Lee JY, Seielstad M, Teo YY, Boehnke M, Parra EJ, Chambers JC, Tai ES, McCarthy MI, Morris AP. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet 2014; 46:234-44. [PMID: 24509480 PMCID: PMC3969612 DOI: 10.1038/ng.2897] [Citation(s) in RCA: 777] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/17/2014] [Indexed: 11/18/2022]
Abstract
To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS) including 26,488 cases and 83,964 controls of European, East Asian, South Asian, and Mexican and Mexican American ancestry. We observed significant excess in directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven novel T2D susceptibility loci. Furthermore, we observed considerable improvements in fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterisation of complex trait loci, and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.
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Grundberg E, Meduri E, Sandling JK, Hedman ÅK, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, Wilk A, Barrett A, Small KS, Ge B, Caron M, Shin SY, Lathrop M, Dermitzakis ET, McCarthy MI, Spector TD, Bell JT, Deloukas P, Ahmadi KR, Ainali C, Barrett A, Bataille V, Bell JT, Buil A, Deloukas P, Dermitzakis ET, Dimas AS, Durbin R, Glass D, Grundberg E, Hassanali N, Hedman ÅK, Ingle C, Knowles D, Krestyaninova M, Lindgren CM, Lowe CE, McCarthy MI, Meduri E, di Meglio P, Min JL, Montgomery SB, Nestle FO, Nica AC, Nisbet J, O’Rahilly S, Parts L, Potter S, Sandling J, Sekowska M, Shin SY, Small KS, Soranzo N, Spector TD, Surdulescu G, Travers ME, Tsaprouni L, Tsoka S, Wilk A, Yang TP, Zondervan KT. Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements. Am J Hum Genet 2013. [DOI: 10.1016/j.ajhg.2013.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Randall JC, Winkler TW, Kutalik Z, Berndt SI, Jackson AU, Monda KL, Kilpeläinen TO, Esko T, Mägi R, Li S, Workalemahu T, Feitosa MF, Croteau-Chonka DC, Day FR, Fall T, Ferreira T, Gustafsson S, Locke AE, Mathieson I, Scherag A, Vedantam S, Wood AR, Liang L, Steinthorsdottir V, Thorleifsson G, Dermitzakis ET, Dimas AS, Karpe F, Min JL, Nicholson G, Clegg DJ, Person T, Krohn JP, Bauer S, Buechler C, Eisinger K, Bonnefond A, Froguel P, Hottenga JJ, Prokopenko I, Waite LL, Harris TB, Smith AV, Shuldiner AR, McArdle WL, Caulfield MJ, Munroe PB, Grönberg H, Chen YDI, Li G, Beckmann JS, Johnson T, Thorsteinsdottir U, Teder-Laving M, Khaw KT, Wareham NJ, Zhao JH, Amin N, Oostra BA, Kraja AT, Province MA, Cupples LA, Heard-Costa NL, Kaprio J, Ripatti S, Surakka I, Collins FS, Saramies J, Tuomilehto J, Jula A, Salomaa V, Erdmann J, Hengstenberg C, Loley C, Schunkert H, Lamina C, Wichmann HE, Albrecht E, Gieger C, Hicks AA, Johansson Å, Pramstaller PP, Kathiresan S, Speliotes EK, Penninx B, Hartikainen AL, Jarvelin MR, Gyllensten U, Boomsma DI, Campbell H, Wilson JF, Chanock SJ, Farrall M, Goel A, Medina-Gomez C, Rivadeneira F, Estrada K, Uitterlinden AG, Hofman A, Zillikens MC, den Heijer M, Kiemeney LA, Maschio A, Hall P, Tyrer J, Teumer A, Völzke H, Kovacs P, Tönjes A, Mangino M, Spector TD, Hayward C, Rudan I, Hall AS, Samani NJ, Attwood AP, Sambrook JG, Hung J, Palmer LJ, Lokki ML, Sinisalo J, Boucher G, Huikuri H, Lorentzon M, Ohlsson C, Eklund N, Eriksson JG, Barlassina C, Rivolta C, Nolte IM, Snieder H, Van der Klauw MM, Van Vliet-Ostaptchouk JV, Gejman PV, Shi J, Jacobs KB, Wang Z, Bakker SJL, Mateo Leach I, Navis G, van der Harst P, Martin NG, Medland SE, Montgomery GW, Yang J, Chasman DI, Ridker PM, Rose LM, Lehtimäki T, Raitakari O, Absher D, Iribarren C, Basart H, Hovingh KG, Hyppönen E, Power C, Anderson D, Beilby JP, Hui J, Jolley J, Sager H, Bornstein SR, Schwarz PEH, Kristiansson K, Perola M, Lindström J, Swift AJ, Uusitupa M, Atalay M, Lakka TA, Rauramaa R, Bolton JL, Fowkes G, Fraser RM, Price JF, Fischer K, KrjutÅ¡kov K, Metspalu A, Mihailov E, Langenberg C, Luan J, Ong KK, Chines PS, Keinanen-Kiukaanniemi SM, Saaristo TE, Edkins S, Franks PW, Hallmans G, Shungin D, Morris AD, Palmer CNA, Erbel R, Moebus S, Nöthen MM, Pechlivanis S, Hveem K, Narisu N, Hamsten A, Humphries SE, Strawbridge RJ, Tremoli E, Grallert H, Thorand B, Illig T, Koenig W, Müller-Nurasyid M, Peters A, Boehm BO, Kleber ME, März W, Winkelmann BR, Kuusisto J, Laakso M, Arveiler D, Cesana G, Kuulasmaa K, Virtamo J, Yarnell JWG, Kuh D, Wong A, Lind L, de Faire U, Gigante B, Magnusson PKE, Pedersen NL, Dedoussis G, Dimitriou M, Kolovou G, Kanoni S, Stirrups K, Bonnycastle LL, Njølstad I, Wilsgaard T, Ganna A, Rehnberg E, Hingorani A, Kivimaki M, Kumari M, Assimes TL, Barroso I, Boehnke M, Borecki IB, Deloukas P, Fox CS, Frayling T, Groop LC, Haritunians T, Hunter D, Ingelsson E, Kaplan R, Mohlke KL, O'Connell JR, Schlessinger D, Strachan DP, Stefansson K, van Duijn CM, Abecasis GR, McCarthy MI, Hirschhorn JN, Qi L, Loos RJF, Lindgren CM, North KE, Heid IM. Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. PLoS Genet 2013; 9:e1003500. [PMID: 23754948 PMCID: PMC3674993 DOI: 10.1371/journal.pgen.1003500] [Citation(s) in RCA: 303] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 03/15/2013] [Indexed: 12/28/2022] Open
Abstract
Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5×10(-8)), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits.
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Affiliation(s)
- Joshua C. Randall
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas W. Winkler
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Anne U. Jackson
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Keri L. Monda
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tuomas O. Kilpeläinen
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Shengxu Li
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Tsegaselassie Workalemahu
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Mary F. Feitosa
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Damien C. Croteau-Chonka
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Felix R. Day
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Tove Fall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Stefan Gustafsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Adam E. Locke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Iain Mathieson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andre Scherag
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Sailaja Vedantam
- Divisions of Genetics and Endocrinology and Program in Genomics, Children's Hospital, Boston, Massachusetts, United States of America
- Metabolism Initiative and Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew R. Wood
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, United Kingdom
| | - Liming Liang
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | | | | | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Antigone S. Dimas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Biomedical Sciences Research Center Al. Fleming, Vari, Greece
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Josine L. Min
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - George Nicholson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- MRC Harwell, Harwell, United Kingdom
| | - Deborah J. Clegg
- University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Thomas Person
- University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jon P. Krohn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sabrina Bauer
- Regensburg University Medical Center, Innere Medizin I, Regensburg, Germany
| | - Christa Buechler
- Regensburg University Medical Center, Innere Medizin I, Regensburg, Germany
| | - Kristina Eisinger
- Regensburg University Medical Center, Innere Medizin I, Regensburg, Germany
| | | | | | - Philippe Froguel
- CNRS UMR8199-IBL-Institut Pasteur de Lille, Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, United Kingdom
| | | | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Lindsay L. Waite
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Alan R. Shuldiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, United States of America
| | - Wendy L. McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - 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, United Kingdom
| | - 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, United Kingdom
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yii-Der Ida Chen
- Department of OB/GYN and Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
| | - Guo Li
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
| | - Jacques S. Beckmann
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois (CHUV) University Hospital, Lausanne, Switzerland
| | - Toby Johnson
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- 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, United Kingdom
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | | | - Kay-Tee Khaw
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Centre for Medical Systems Biology & Netherlands Consortium on Healthy Aging, Leiden, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Aldi T. Kraja
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael A. Province
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Nancy L. Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Jaakko Kaprio
- National Institute for Health and Welfare, Unit for Child and Adolescent Psychiatry, Helsinki, Finland
- Finnish Twin Cohort Study, Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Samuli Ripatti
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, Helsinki, Finland
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, Helsinki, Finland
| | - Francis S. Collins
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | | | - Jaakko Tuomilehto
- Red RECAVA Grupo RD06/0014/0015, Hospital Universitario, La Paz, Madrid, Spain
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
- National Institute for Health and Welfare, Diabetes Prevention Unit, Helsinki, Finland
- South Ostrobothnia Central Hospital, Seinajoki, Finland
| | - Antti Jula
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Population Studies Unit, Turku, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Chronic Disease Epidemiology and Prevention Unit, Helsinki, Finland
| | - Jeanette Erdmann
- Nordic Center of Cardiovascular Research (NCCR), Lübeck, Germany
- Universität zu Lübeck, Medizinische Klinik II, Lübeck, Germany
| | - Christian Hengstenberg
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Christina Loley
- Universität zu Lübeck, Medizinische Klinik II, Lübeck, Germany
- Deutsches Herzzentrum München and DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München and DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - H. Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, and Klinikum Grosshadern, Munich, Germany
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Andrew A. Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano/Bozen, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University Hospital, Uppsala, Sweden
| | - Peter P. Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano/Bozen, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Sekar Kathiresan
- Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Elizabeth K. Speliotes
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Brenda Penninx
- Department of Psychiatry, University Medical Centre Groningen, Groningen, The Netherlands
| | - Anna-Liisa Hartikainen
- Department of Clinical Sciences/Obstetrics and Gynecology, University of Oulu, Oulu, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- National Institute for Health and Welfare, Oulu, Finland
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Martin Farrall
- Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Anuj Goel
- Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Carolina Medina-Gomez
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Karol Estrada
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - M. Carola Zillikens
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Martin den Heijer
- Department of Internal Medicine, VU University Medical Centre, Amsterdam, The Netherlands
| | - Lambertus A. Kiemeney
- Department of Epidemiology, Biostatistics and HTA, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Comprehensive Cancer Center East, Nijmegen, The Netherlands
| | - Andrea Maschio
- Istituto di Neurogenetica e Neurofarmacologia del CNR, Monserrato, Cagliari, Italy
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Peter Kovacs
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Leipzig, Germany
| | - Anke Tönjes
- University of Leipzig, IFB Adiposity Diseases, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alistair S. Hall
- Division of Cardiovascular and Neuronal Remodelling, Multidisciplinary Cardiovascular Research Centre, Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds, United Kingdom
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom
| | - Antony Paul Attwood
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer G. Sambrook
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Centre, Cambridge, United Kingdom
| | - Joseph Hung
- School of Medicine and Pharmacology, The University of Western Australia, Nedlands, Western Austrailia, Australia
- Busselton Population Medical Research Foundation Inc., Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Lyle J. Palmer
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Canada
| | - Marja-Liisa Lokki
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Juha Sinisalo
- Division of Cardiology, Cardiovascular Laboratory, Helsinki University Central Hospital, Helsinki, Finland
| | | | - Heikki Huikuri
- Institute of Clinical Medicine, Department of Internal Medicine, University of Oulu, Oulu, Finland
| | - Mattias Lorentzon
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Claes Ohlsson
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niina Eklund
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, Helsinki, Finland
| | - Johan G. Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
- Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland
| | - Cristina Barlassina
- University of Milan, Department of Medicine, Surgery and Dentistry, Milano, Italy
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Ilja M. Nolte
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Melanie M. Van der Klauw
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jana V. Van Vliet-Ostaptchouk
- LifeLines Cohort Study, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Pablo V. Gejman
- University of Chicago, Chicago, Illinois, United States of America
- Northshore University Healthsystem, Evanston, Ilinois, United States of America
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Kevin B. Jacobs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States of America
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States of America
| | - Stephan J. L. Bakker
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Irene Mateo Leach
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerjan Navis
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Nicholas G. Martin
- Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Queensland, Australia
| | - Sarah E. Medland
- Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Queensland, Australia
| | - Grant W. Montgomery
- Molecular Epidemiology Laboratory, Queensland Institute of Medical Research, Queensland, Australia
| | - Jian Yang
- Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, Queensland, Australia
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lynda M. Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- The Department of Clinical Physiology, Turku University Hospital, Turku, Finland
| | - Devin Absher
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, California, United States of America
| | - Hanneke Basart
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Kees G. Hovingh
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Elina Hyppönen
- Centre For Paediatric Epidemiolgy and Biostatistics/MRC Centre of Epidemiology for Child Health, University College of London Institute of Child Health, London, United Kingdom
| | - Chris Power
- Centre For Paediatric Epidemiolgy and Biostatistics/MRC Centre of Epidemiology for Child Health, University College of London Institute of Child Health, London, United Kingdom
| | - Denise Anderson
- Telethon Institute for Child Health Research, West Perth, Western Australia, Australia
- Centre for Child Health Research, The University of Western Australia, Perth, Australia
| | - John P. Beilby
- Busselton Population Medical Research Foundation Inc., Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- PathWest Laboratory of Western Australia, Department of Molecular Genetics, QEII Medical Centre, Nedlands, Western Australia, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
| | - Jennie Hui
- Busselton Population Medical Research Foundation Inc., Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- PathWest Laboratory of Western Australia, Department of Molecular Genetics, QEII Medical Centre, Nedlands, Western Australia, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
- School of Population Health, The University of Western Australia, Nedlands, Western Austrailia, Australia
| | - Jennifer Jolley
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Hendrik Sager
- Medizinische Klinik II, Universität zu Lübeck, Lübeck, Germany
| | - Stefan R. Bornstein
- Department of Medicine III, University of Dresden, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Peter E. H. Schwarz
- Department of Medicine III, University of Dresden, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Kati Kristiansson
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, Helsinki, Finland
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Unit of Public Health Genomics, Helsinki, Finland
| | - Jaana Lindström
- National Institute for Health and Welfare, Diabetes Prevention Unit, Helsinki, Finland
| | - Amy J. Swift
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Matti Uusitupa
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Research Unit, Kuopio University Hospital, Kuopio, Finland
| | - Mustafa Atalay
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Timo A. Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Jennifer L. Bolton
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Gerry Fowkes
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ross M. Fraser
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jackie F. Price
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | | | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Ken K. Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
- MRC Unit for Lifelong Health & Ageing, London, United Kingdom
| | - Peter S. Chines
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Sirkka M. Keinanen-Kiukaanniemi
- Faculty of Medicine, Institute of Health Sciences, University of Oulu, Oulu, Finland
- Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Timo E. Saaristo
- Finnish Diabetes Association, Tampere, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | - Sarah Edkins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Paul W. Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Public Health & Clinical Medicine, Umeå University,Umeå, Sweden
| | - Göran Hallmans
- Department of Public Health & Clinical Medicine, Umeå University,Umeå, Sweden
| | - Dmitry Shungin
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
- Department of Public Health & Clinical Medicine, Umeå University,Umeå, Sweden
- Department of Odontology, Umeå University, Umea, Sweden
| | - Andrew David Morris
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Colin N. A. Palmer
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Raimund Erbel
- Clinic of Cardiology, West German Heart Centre, University Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sonali Pechlivanis
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Anders Hamsten
- Atherosclerosis Research Unit, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Steve E. Humphries
- Cardiovascular Genetics, British Heart Foundation Laboratories, Rayne Building, University College London, London, United Kingdom
| | - Rona J. Strawbridge
- Atherosclerosis Research Unit, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elena Tremoli
- Department of Pharmacological Sciences, University of Milan, Monzino Cardiology Center, IRCCS, Milan, Italy
| | - Harald Grallert
- Unit for Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Illig
- Unit for Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Wolfgang Koenig
- Department of Internal Medicine II – Cardiology, University of Ulm Medical Center, Ulm, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Bernhard O. Boehm
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, Ulm, Germany
| | - Marcus E. Kleber
- LURIC Study nonprofit LLC, Freiburg, Germany
- Mannheim Institute of Public Health, Social and Preventive Medicine, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Winfried März
- Mannheim Institute of Public Health, Social and Preventive Medicine, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
- Synlab Academy, Mannheim, Germany
| | | | - Johanna Kuusisto
- Department of Medicine, University of Kuopio and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Kuopio and Kuopio University Hospital, Kuopio, Finland
| | - Dominique Arveiler
- Department of Epidemiology and Public Health, Faculty of Medicine, Strasbourg, France
| | - Giancarlo Cesana
- Department of Clinical Medicine, University of Milano-Bicocca, Monza, Italy
| | - Kari Kuulasmaa
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Chronic Disease Epidemiology and Prevention Unit, Helsinki, Finland
| | - Jarmo Virtamo
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Chronic Disease Epidemiology and Prevention Unit, Helsinki, Finland
| | | | - Diana Kuh
- MRC Unit for Lifelong Health & Ageing, London, United Kingdom
| | - Andrew Wong
- MRC Unit for Lifelong Health & Ageing, London, United Kingdom
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Akademiska Sjukhuset, Uppsala, Sweden
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bruna Gigante
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - George Dedoussis
- Department of Dietetics-Nutrition, Harokopio University, Athens, Greece
| | - Maria Dimitriou
- Department of Dietetics-Nutrition, Harokopio University, Athens, Greece
| | - Genovefa Kolovou
- 1st Cardiology Department, Onassis Cardiac Surgery Center, Athens, Greece
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Lori L. Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Inger Njølstad
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Tom Wilsgaard
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Andrea Ganna
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Emil Rehnberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Aroon Hingorani
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Meena Kumari
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Themistocles L. Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ingrid B. Borecki
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Caroline S. Fox
- Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Timothy Frayling
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, United Kingdom
| | - Leif C. Groop
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Talin Haritunians
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - David Hunter
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erik Ingelsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeffrey R. O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, Baltimore, Maryland, United States of America
| | - David P. Strachan
- Division of Community Health Sciences, St George's, University of London, London, United Kingdom
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
- Center of Medical Systems Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Gonçalo R. Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
| | - Joel N. Hirschhorn
- Divisions of Genetics and Endocrinology and Program in Genomics, Children's Hospital, Boston, Massachusetts, United States of America
- Metabolism Initiative and Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lu Qi
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruth J. F. Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
- Genetics of Obesity and Related Metabolic Traits Program,The Charles Bronfman Institute of Personalized Medicine, Child Health and Development Institute, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kari E. North
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Iris M. Heid
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
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12
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Grundberg E, Small KS, Hedman ÅK, Nica AC, Buil A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A, Nisbett J, Sekowska M, Wilk A, Shin SY, Glass D, Travers M, Min JL, Ring S, Ho K, Thorleifsson G, Kong A, Thorsteindottir U, Ainali C, Dimas AS, Hassanali N, Ingle C, Knowles D, Krestyaninova M, Lowe CE, Di Meglio P, Montgomery SB, Parts L, Potter S, Surdulescu G, Tsaprouni L, Tsoka S, Bataille V, Durbin R, Nestle FO, O'Rahilly S, Soranzo N, Lindgren CM, Zondervan KT, Ahmadi KR, Schadt EE, Stefansson K, Smith GD, McCarthy MI, Deloukas P, Dermitzakis ET, Spector TD. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet 2012; 44:1084-9. [PMID: 22941192 PMCID: PMC3784328 DOI: 10.1038/ng.2394] [Citation(s) in RCA: 575] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 08/08/2012] [Indexed: 12/16/2022]
Abstract
Sequence-based variation in gene expression is a key driver of disease risk. Common variants regulating expression in cis have been mapped in many expression quantitative trait locus (eQTL) studies, typically in single tissues from unrelated individuals. Here, we present a comprehensive analysis of gene expression across multiple tissues conducted in a large set of mono- and dizygotic twins that allows systematic dissection of genetic (cis and trans) and non-genetic effects on gene expression. Using identity-by-descent estimates, we show that at least 40% of the total heritable cis effect on expression cannot be accounted for by common cis variants, a finding that reveals the contribution of low-frequency and rare regulatory variants with respect to both transcriptional regulation and complex trait susceptibility. We show that a substantial proportion of gene expression heritability is trans to the structural gene, and we identify several replicating trans variants that act predominantly in a tissue-restricted manner and may regulate the transcription of many genes.
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13
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Dimas AS, Nica AC, Montgomery SB, Stranger BE, Raj T, Buil A, Giger T, Lappalainen T, Gutierrez-Arcelus M, McCarthy MI, Dermitzakis ET. Sex-biased genetic effects on gene regulation in humans. Genome Res 2012; 22:2368-75. [PMID: 22960374 PMCID: PMC3514666 DOI: 10.1101/gr.134981.111] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Human regulatory variation, reported as expression quantitative trait loci (eQTLs), contributes to differences between populations and tissues. The contribution of eQTLs to differences between sexes, however, has not been investigated to date. Here we explore regulatory variation in females and males and demonstrate that 12%–15% of autosomal eQTLs function in a sex-biased manner. We show that genes possessing sex-biased eQTLs are expressed at similar levels across the sexes and highlight cases of genes controlling sexually dimorphic and shared traits that are under the control of distinct regulatory elements in females and males. This study illustrates that sex provides important context that can modify the effects of functional genetic variants.
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Affiliation(s)
- Antigone S Dimas
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
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Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, Prokopenko I, Kang HM, Dina C, Esko T, Fraser RM, Kanoni S, Kumar A, Lagou V, Langenberg C, Luan J, Lindgren CM, Müller-Nurasyid M, Pechlivanis S, Rayner NW, Scott LJ, Wiltshire S, Yengo L, Kinnunen L, Rossin EJ, Raychaudhuri S, Johnson AD, Dimas AS, Loos RJF, Vedantam S, Chen H, Florez JC, Fox C, Liu CT, Rybin D, Couper DJ, Kao WHL, Li M, Cornelis MC, Kraft P, Sun Q, van Dam RM, Stringham HM, Chines PS, Fischer K, Fontanillas P, Holmen OL, Hunt SE, Jackson AU, Kong A, Lawrence R, Meyer J, Perry JRB, Platou CGP, Potter S, Rehnberg E, Robertson N, Sivapalaratnam S, Stančáková A, Stirrups K, Thorleifsson G, Tikkanen E, Wood AR, Almgren P, Atalay M, Benediktsson R, Bonnycastle LL, Burtt N, Carey J, Charpentier G, Crenshaw AT, Doney ASF, Dorkhan M, Edkins S, Emilsson V, Eury E, Forsen T, Gertow K, Gigante B, Grant GB, Groves CJ, Guiducci C, Herder C, Hreidarsson AB, Hui J, James A, Jonsson A, Rathmann W, Klopp N, Kravic J, Krjutškov K, Langford C, Leander K, Lindholm E, Lobbens S, Männistö S, Mirza G, Mühleisen TW, Musk B, Parkin M, Rallidis L, Saramies J, Sennblad B, Shah S, Sigurðsson G, Silveira A, Steinbach G, Thorand B, Trakalo J, Veglia F, Wennauer R, Winckler W, Zabaneh D, Campbell H, van Duijn C, Uitterlinden AG, Hofman A, Sijbrands E, Abecasis GR, Owen KR, Zeggini E, Trip MD, Forouhi NG, Syvänen AC, Eriksson JG, Peltonen L, Nöthen MM, Balkau B, Palmer CNA, Lyssenko V, Tuomi T, Isomaa B, Hunter DJ, Qi L, Shuldiner AR, Roden M, Barroso I, Wilsgaard T, Beilby J, Hovingh K, Price JF, Wilson JF, Rauramaa R, Lakka TA, Lind L, Dedoussis G, Njølstad I, Pedersen NL, Khaw KT, Wareham NJ, Keinanen-Kiukaanniemi SM, Saaristo TE, Korpi-Hyövälti E, Saltevo J, Laakso M, Kuusisto J, Metspalu A, Collins FS, Mohlke KL, Bergman RN, Tuomilehto J, Boehm BO, Gieger C, Hveem K, Cauchi S, Froguel P, Baldassarre D, Tremoli E, Humphries SE, Saleheen D, Danesh J, Ingelsson E, Ripatti S, Salomaa V, Erbel R, Jöckel KH, Moebus S, Peters A, Illig T, de Faire U, Hamsten A, Morris AD, Donnelly PJ, Frayling TM, Hattersley AT, Boerwinkle E, Melander O, Kathiresan S, Nilsson PM, Deloukas P, Thorsteinsdottir U, Groop LC, Stefansson K, Hu F, Pankow JS, Dupuis J, Meigs JB, Altshuler D, Boehnke M, McCarthy MI. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 2012; 44:981-90. [PMID: 22885922 PMCID: PMC3442244 DOI: 10.1038/ng.2383] [Citation(s) in RCA: 1413] [Impact Index Per Article: 117.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/11/2012] [Indexed: 11/09/2022]
Abstract
To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis.
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Affiliation(s)
- Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK.
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15
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Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET. Patterns of cis regulatory variation in diverse human populations. PLoS Genet 2012; 8:e1002639. [PMID: 22532805 PMCID: PMC3330104 DOI: 10.1371/journal.pgen.1002639] [Citation(s) in RCA: 385] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 02/18/2012] [Indexed: 01/18/2023] Open
Abstract
The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations.
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Affiliation(s)
- Barbara E. Stranger
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen B. Montgomery
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Antigone S. Dimas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
- Max Planck Institute Intelligent Systems and Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Leopold Parts
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Oliver Stegle
- Max Planck Institute Intelligent Systems and Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Catherine E. Ingle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Magda Sekowska
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - George Davey Smith
- MRC CAiTE centre, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - David Evans
- MRC CAiTE centre, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Maria Gutierrez-Arcelus
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Alkes Price
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Epidemiology and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Towfique Raj
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - James Nisbett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Alexandra C. Nica
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Claude Beazley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Emmanouil T. Dermitzakis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- * E-mail:
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16
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Strawbridge RJ, Dupuis J, Prokopenko I, Barker A, Ahlqvist E, Rybin D, Petrie JR, Travers ME, Bouatia-Naji N, Dimas AS, Nica A, Wheeler E, Chen H, Voight BF, Taneera J, Kanoni S, Peden JF, Turrini F, Gustafsson S, Zabena C, Almgren P, Barker DJ, Barnes D, Dennison EM, Eriksson JG, Eriksson P, Eury E, Folkersen L, Fox CS, Frayling TM, Goel A, Gu HF, Horikoshi M, Isomaa B, Jackson AU, Jameson KA, Kajantie E, Kerr-Conte J, Kuulasmaa T, Kuusisto J, Loos RJ, Luan J, Makrilakis K, Manning AK, Martínez-Larrad MT, Narisu N, Nastase Mannila M, Öhrvik J, Osmond C, Pascoe L, Payne F, Sayer AA, Sennblad B, Silveira A, Stančáková A, Stirrups K, Swift AJ, Syvänen AC, Tuomi T, van 't Hooft FM, Walker M, Weedon MN, Xie W, Zethelius B, Ongen H, Mälarstig A, Hopewell JC, Saleheen D, Chambers J, Parish S, Danesh J, Kooner J, Östenson CG, Lind L, Cooper CC, Serrano-Ríos M, Ferrannini E, Forsen TJ, Clarke R, Franzosi MG, Seedorf U, Watkins H, Froguel P, Johnson P, Deloukas P, Collins FS, Laakso M, Dermitzakis ET, Boehnke M, McCarthy MI, Wareham NJ, Groop L, Pattou F, Gloyn AL, Dedoussis GV, Lyssenko V, Meigs JB, Barroso I, Watanabe RM, Ingelsson E, Langenberg C, Hamsten A, Florez JC. Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. Diabetes 2011; 60:2624-34. [PMID: 21873549 PMCID: PMC3178302 DOI: 10.2337/db11-0415] [Citation(s) in RCA: 257] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/29/2011] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS We have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates. RESULTS Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets. CONCLUSIONS We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis.
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Affiliation(s)
- Rona J. Strawbridge
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
| | - Inga Prokopenko
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Adam Barker
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, U.K
| | - Emma Ahlqvist
- Department of Clinical Sciences, Diabetes and Endocrinology, University Hospital and Malmö, Lund University, Malmö, Sweden
| | - Denis Rybin
- Boston University Data Coordinating Center, Boston, Massachusetts
| | - John R. Petrie
- BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, U.K
| | - Mary E. Travers
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, U.K
| | - Nabila Bouatia-Naji
- Université Lille-Nord de France, Lille, France
- CNRS UMR 8199, Institut Pasteur de Lille, Lille, France
| | - Antigone S. Dimas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Alexandra Nica
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Eleanor Wheeler
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
| | - Han Chen
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Benjamin F. Voight
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts
| | - Jalal Taneera
- Department of Clinical Sciences, Diabetes and Endocrinology, University Hospital and Malmö, Lund University, Malmö, Sweden
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
- Department of Dietetics-Nutrition, Harokopio University, Athens, Greece
| | - John F. Peden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Cardiovascular Medicine, University of Oxford, Oxford, U.K
| | - Fabiola Turrini
- Department of Clinical Sciences, Diabetes and Endocrinology, University Hospital and Malmö, Lund University, Malmö, Sweden
- Department of Medicine, University of Verona, Verona, Italy
| | - Stefan Gustafsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Carina Zabena
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
- Fundación Investigación Biomédica del Hospital Clínico San Carlos, Madrid, Spain
| | - Peter Almgren
- Department of Clinical Sciences, Diabetes and Endocrinology, University Hospital and Malmö, Lund University, Malmö, Sweden
| | - David J.P. Barker
- Heart Research Center, Oregon Health and Science University, Portland, Oregon
| | - Daniel Barnes
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, U.K
| | - Elaine M. Dennison
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, U.K
| | - Johan G. Eriksson
- National Institute for Health and Welfare, Helsinki, Finland
- Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland
- Folkhälsan Research Centre, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
| | - Per Eriksson
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Elodie Eury
- Université Lille-Nord de France, Lille, France
- CNRS UMR 8199, Institut Pasteur de Lille, Lille, France
| | - Lasse Folkersen
- Experimental Cardiovascular Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Caroline S. Fox
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Timothy M. Frayling
- Institute of Biomedical and Clinical Sciences, Peninsula Medical School, University of Exeter, Exeter, U.K
| | - Anuj Goel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Cardiovascular Medicine, University of Oxford, Oxford, U.K
| | - Harvest F. Gu
- Endocrinology and Diabetes Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Momoko Horikoshi
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Bo Isomaa
- Folkhälsan Research Centre, Helsinki, Finland
- Malmska Municipal Health Care Center and Hospital, Jakobstad, Finland
| | - Anne U. Jackson
- Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Karen A. Jameson
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, U.K
| | - Eero Kajantie
- National Institute for Health and Welfare, Helsinki, Finland
- Hospital for Children and Adolescents, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Julie Kerr-Conte
- Université Lille-Nord de France, Lille, France
- INSERM UMR 859, Lille, France
| | - Teemu Kuulasmaa
- Department of Medicine, University of Kuopio and Kuopio University Hospital, Kuopio, Finland
| | - Johanna Kuusisto
- Department of Medicine, University of Kuopio and Kuopio University Hospital, Kuopio, Finland
| | - Ruth J.F. Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, U.K
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, U.K
| | - Konstantinos Makrilakis
- First Department of Propaedeutic Medicine, Laiko General Hospital, Athens University Medical School, Athens, Greece
| | - Alisa K. Manning
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - María Teresa Martínez-Larrad
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
- Fundación Investigación Biomédica del Hospital Clínico San Carlos, Madrid, Spain
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria Nastase Mannila
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - John Öhrvik
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Clive Osmond
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, U.K
| | - Laura Pascoe
- Institute of Cell and Molecular Biosciences, Newcastle University, Newcastle, U.K
| | - Felicity Payne
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
| | - Avan A. Sayer
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, U.K
| | - Bengt Sennblad
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Angela Silveira
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Alena Stančáková
- Department of Medicine, University of Kuopio and Kuopio University Hospital, Kuopio, Finland
| | - Kathy Stirrups
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Amy J. Swift
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tiinamaija Tuomi
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Medicine, Helsinki University Central Hospital, and Research Program of Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Ferdinand M. van 't Hooft
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Mark Walker
- Institute of Cellular Medicine, Newcastle University, Newcastle, U.K
| | - Michael N. Weedon
- Institute of Biomedical and Clinical Sciences, Peninsula Medical School, University of Exeter, Exeter, U.K
| | - Weijia Xie
- Institute of Biomedical and Clinical Sciences, Peninsula Medical School, University of Exeter, Exeter, U.K
| | - Björn Zethelius
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | | | | | | | | | | | - Halit Ongen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Cardiovascular Medicine, University of Oxford, Oxford, U.K
- Department of Cardiovascular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, U.K
| | - Anders Mälarstig
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | | | - Danish Saleheen
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
- Center for Non-Communicable Diseases Pakistan, Karachi, Pakistan
| | - John Chambers
- Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, U.K
- Cardiology, Ealing Hospital NHS Trust, Middlesex, U.K
| | - Sarah Parish
- Clinical Trial Service Unit, University of Oxford, Oxford, U.K
| | - John Danesh
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
| | - Jaspal Kooner
- Cardiology, Ealing Hospital NHS Trust, Middlesex, U.K
- National Heart and Lung Institute, Imperial College London, London, U.K
| | - Claes-Göran Östenson
- Endocrinology and Diabetes Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Lars Lind
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cyrus C. Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, U.K
| | - Manuel Serrano-Ríos
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
- Fundación Investigación Biomédica del Hospital Clínico San Carlos, Madrid, Spain
| | - Ele Ferrannini
- Department of Internal Medicine and CNR Institute of Clinical Physiology, University of Pisa School of Medicine, Pisa, Italy
| | - Tom J. Forsen
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
- Vaasa Health Care Center, Vaasa, Finland
| | - Robert Clarke
- Clinical Trial Service Unit, University of Oxford, Oxford, U.K
| | - Maria Grazia Franzosi
- Department of Cardiovascular Research, Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - Udo Seedorf
- Leibniz Institute for Arteriosclerosis Research, University of Münster, Münster, Germany
| | - Hugh Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Cardiovascular Medicine, University of Oxford, Oxford, U.K
| | - Philippe Froguel
- Université Lille-Nord de France, Lille, France
- CNRS UMR 8199, Institut Pasteur de Lille, Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, U.K
| | - Paul Johnson
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- DRWF Human Islet Isolation Facility and Oxford Islet Transplant Programme, University of Oxford, Oxford, U.K
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | | | - Markku Laakso
- Department of Medicine, University of Kuopio and Kuopio University Hospital, Kuopio, Finland
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Michael Boehnke
- Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Mark I. McCarthy
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, U.K
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, U.K
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, University Hospital and Malmö, Lund University, Malmö, Sweden
| | - François Pattou
- Université Lille-Nord de France, Lille, France
- INSERM UMR 859, Lille, France
| | - Anna L. Gloyn
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, U.K
| | | | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, University Hospital and Malmö, Lund University, Malmö, Sweden
| | - James B. Meigs
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Inês Barroso
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, U.K
| | - Richard M. Watanabe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Erik Ingelsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, U.K
| | - Anders Hamsten
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jose C. Florez
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
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17
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Nica AC, Parts L, Glass D, Nisbet J, Barrett A, Sekowska M, Travers M, Potter S, Grundberg E, Small K, Hedman ÅK, Bataille V, Tzenova Bell J, Surdulescu G, Dimas AS, Ingle C, Nestle FO, di Meglio P, Min JL, Wilk A, Hammond CJ, Hassanali N, Yang TP, Montgomery SB, O'Rahilly S, Lindgren CM, Zondervan KT, Soranzo N, Barroso I, Durbin R, Ahmadi K, Deloukas P, McCarthy MI, Dermitzakis ET, Spector TD. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet 2011; 7:e1002003. [PMID: 21304890 PMCID: PMC3033383 DOI: 10.1371/journal.pgen.1002003] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 12/15/2010] [Indexed: 12/16/2022] Open
Abstract
While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity in multiple primary tissues is not yet well understood. We explore in depth the role of cis-regulatory variation in three human tissues: lymphoblastoid cell lines (LCL), skin, and fat. The samples (156 LCL, 160 skin, 166 fat) were derived simultaneously from a subset of well-phenotyped healthy female twins of the MuTHER resource. We discover an abundance of cis-eQTLs in each tissue similar to previous estimates (858 or 4.7% of genes). In addition, we apply factor analysis (FA) to remove effects of latent variables, thus more than doubling the number of our discoveries (1,822 eQTL genes). The unique study design (Matched Co-Twin Analysis—MCTA) permits immediate replication of eQTLs using co-twins (93%–98%) and validation of the considerable gain in eQTL discovery after FA correction. We highlight the challenges of comparing eQTLs between tissues. After verifying previous significance threshold-based estimates of tissue-specificity, we show their limitations given their dependency on statistical power. We propose that continuous estimates of the proportion of tissue-shared signals and direct comparison of the magnitude of effect on the fold change in expression are essential properties that jointly provide a biologically realistic view of tissue-specificity. Under this framework we demonstrate that 30% of eQTLs are shared among the three tissues studied, while another 29% appear exclusively tissue-specific. However, even among the shared eQTLs, a substantial proportion (10%–20%) have significant differences in the magnitude of fold change between genotypic classes across tissues. Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits. Regulation of gene expression is a fundamental cellular process determining a large proportion of the phenotypic variance. Previous studies have identified genetic loci influencing gene expression levels (eQTLs), but the complexity of their tissue-specific properties has not yet been well-characterized. In this study, we perform cis-eQTL analysis in a unique matched co-twin design for three human tissues derived simultaneously from the same set of individuals. The study design allows validation of the substantial discoveries we make in each tissue. We explore in depth the tissue-dependent features of regulatory variants and estimate the proportions of shared and specific effects. We use continuous measures of eQTL sharing to circumvent the statistical power limitations of comparing direct overlap of eQTLs in multiple tissues. In this framework, we demonstrate that 30% of eQTLs are shared among tissues, while 29% are exclusively tissue-specific. Furthermore, we show that the fold change in expression between eQTL genotypic classes differs between tissues. Even among shared eQTLs, we report a substantial proportion (10%–20%) of significant tissue differences in magnitude of these effects. The complexities we highlight here are essential for understanding the impact of regulatory variants on complex traits.
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Affiliation(s)
- Alexandra C. Nica
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Leopold Parts
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel Glass
- Department of Twin Research, King's College London, London, United Kingdom
| | - James Nisbet
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Amy Barrett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Magdalena Sekowska
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Mary Travers
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Simon Potter
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Elin Grundberg
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Twin Research, King's College London, London, United Kingdom
| | - Kerrin Small
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Twin Research, King's College London, London, United Kingdom
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Veronique Bataille
- Department of Twin Research, King's College London, London, United Kingdom
| | - Jordana Tzenova Bell
- Department of Twin Research, King's College London, London, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Antigone S. Dimas
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Catherine Ingle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Frank O. Nestle
- St. John's Institute of Dermatology, King's College London, London, United Kingdom
| | - Paola di Meglio
- St. John's Institute of Dermatology, King's College London, London, United Kingdom
| | - Josine L. Min
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alicja Wilk
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | | | - Neelam Hassanali
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tsun-Po Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Stephen B. Montgomery
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Steve O'Rahilly
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Krina T. Zondervan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Twin Research, King's College London, London, United Kingdom
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Kourosh Ahmadi
- Department of Twin Research, King's College London, London, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- * E-mail: (ETD); (TDS); (MIM); (PD)
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
- * E-mail: (ETD); (TDS); (MIM); (PD)
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- * E-mail: (ETD); (TDS); (MIM); (PD)
| | - Timothy D. Spector
- Department of Twin Research, King's College London, London, United Kingdom
- * E-mail: (ETD); (TDS); (MIM); (PD)
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18
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Borel C, Deutsch S, Letourneau A, Migliavacca E, Montgomery SB, Dimas AS, Vejnar CE, Attar H, Gagnebin M, Gehrig C, Falconnet E, Dupré Y, Dermitzakis ET, Antonarakis SE. Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts. Genome Res 2010; 21:68-73. [PMID: 21147911 DOI: 10.1101/gr.109371.110] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
MicroRNAs (miRNAs) are regulatory noncoding RNAs that affect the production of a significant fraction of human mRNAs via post-transcriptional regulation. Interindividual variation of the miRNA expression levels is likely to influence the expression of miRNA target genes and may therefore contribute to phenotypic differences in humans, including susceptibility to common disorders. The extent to which miRNA levels are genetically controlled is largely unknown. In this report, we assayed the expression levels of miRNAs in primary fibroblasts from 180 European newborns of the GenCord project and performed association analysis to identify eQTLs (expression quantitative traits loci). We detected robust expression for 121 miRNAs out of 365 interrogated. We have identified significant cis- (10%) and trans- (11%) eQTLs. Furthermore, we detected one genomic locus (rs1522653) that influences the expression levels of five miRNAs, thus unraveling a novel mechanism for coregulation of miRNA expression.
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Affiliation(s)
- Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
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19
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Anttila V, Stefansson H, Kallela M, Todt U, Terwindt GM, Calafato MS, Nyholt DR, Dimas AS, Freilinger T, Müller-Myhsok B, Artto V, Inouye M, Alakurtti K, Kaunisto MA, Hämäläinen E, de Vries B, Stam AH, Weller CM, Heinze A, Heinze-Kuhn K, Goebel I, Borck G, Göbel H, Steinberg S, Wolf C, Björnsson A, Gudmundsson G, Kirchmann M, Hauge A, Werge T, Schoenen J, Eriksson JG, Hagen K, Stovner L, Wichmann HE, Meitinger T, Alexander M, Moebus S, Schreiber S, Aulchenko YS, Breteler MMB, Uitterlinden AG, Hofman A, van Duijn CM, Tikka-Kleemola P, Vepsäläinen S, Lucae S, Tozzi F, Muglia P, Barrett J, Kaprio J, Färkkilä M, Peltonen L, Stefansson K, Zwart JA, Ferrari MD, Olesen J, Daly M, Wessman M, van den Maagdenberg AMJM, Dichgans M, Kubisch C, Dermitzakis ET, Frants RR, Palotie A. Genome-wide association study of migraine implicates a common susceptibility variant on 8q22.1. Nat Genet 2010; 42:869-73. [PMID: 20802479 PMCID: PMC2948563 DOI: 10.1038/ng.652] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 07/02/2010] [Indexed: 11/17/2022]
Abstract
Migraine is a common episodic neurological disorder, typically presenting with recurrent attacks of severe headache and autonomic dysfunction. Apart from rare monogenic subtypes, no genetic or molecular markers for migraine have been convincingly established. We identified the minor allele of rs1835740 on chromosome 8q22.1 to be associated with migraine (p=5.12 × 10−9, OR 1.23 [1.150-1.324]) in a genome-wide association study of 2,748 migraineurs from three European headache clinics and 10,747 population-matched controls. The association was replicated in 3,202 cases and 40,062 controls for an overall meta-analysis p-value of 1.60 × 10−11 (OR 1.18 [1.127 – 1.244]). rs1835740 is located between the astrocyte elevated gene 1 (MTDH/AEG-1) and plasma glutamate carboxypeptidase (PGCP). In an expression quantitative trait study in lymphoblastoid cell lines transcript levels of the MTDH/AEG-1 were found to have a significant correlation to rs1835740. Our data establish rs1835740 as the first genetic risk factor for migraine.
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Affiliation(s)
- Verneri Anttila
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
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20
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Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P, Dermitzakis ET. Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics 2010; 26:2474-6. [PMID: 20702402 PMCID: PMC2944204 DOI: 10.1093/bioinformatics/btq452] [Citation(s) in RCA: 263] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Summary: Genevar (GENe Expression VARiation) is a database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression. Genevar allows researchers to investigate expression quantitative trait loci (eQTL) associations within a gene locus of interest in real time. The database and application can be installed on a standard computer in database mode and, in addition, on a server to share discoveries among affiliations or the broader community over the Internet via web services protocols. Availability:http://www.sanger.ac.uk/resources/software/genevar Contact:emmanouil.dermitzakis@unige.ch
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Affiliation(s)
- Tsun-Po Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
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21
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Ritchie ME, Forrest MS, Dimas AS, Daelemans C, Dermitzakis ET, Deloukas P, Tavaré S. Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. BMC Bioinformatics 2010; 11:280. [PMID: 20504309 PMCID: PMC2887809 DOI: 10.1186/1471-2105-11-280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 05/26/2010] [Indexed: 12/03/2022] Open
Abstract
Background High-throughput measurement of allele-specific expression (ASE) is a relatively new and exciting application area for array-based technologies. In this paper, we explore several data sets which make use of Illumina's GoldenGate BeadArray technology to measure ASE. This platform exploits coding SNPs to obtain relative expression measurements for alleles at approximately 1500 positions in the genome. Results We analyze data from a mixture experiment where genomic DNA samples from pairs of individuals of known genotypes are pooled to create allelic imbalances at varying levels for the majority of SNPs on the array. We observe that GoldenGate has less sensitivity at detecting subtle allelic imbalances (around 1.3 fold) compared to extreme imbalances, and note the benefit of applying local background correction to the data. Analysis of data from a dye-swap control experiment allowed us to quantify dye-bias, which can be reduced considerably by careful normalization. The need to filter the data before carrying out further downstream analysis to remove non-responding probes, which show either weak, or non-specific signal for each allele, was also demonstrated. Throughout this paper, we find that a linear model analysis of the data from each SNP is a flexible modelling strategy that allows for testing of allelic imbalances in each sample when replicate hybridizations are available. Conclusions Our analysis shows that local background correction carried out by Illumina's software, together with quantile normalization of the red and green channels within each array, provides optimal performance in terms of false positive rates. In addition, we strongly encourage intensity-based filtering to remove SNPs which only measure non-specific signal. We anticipate that a similar analysis strategy will prove useful when quantifying ASE on Illumina's higher density Infinium BeadChips.
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Affiliation(s)
- Matthew E Ritchie
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, 3052, Australia.
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22
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Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I, Dermitzakis ET. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 2010; 6:e1000895. [PMID: 20369022 PMCID: PMC2848550 DOI: 10.1371/journal.pgen.1000895] [Citation(s) in RCA: 324] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 03/04/2010] [Indexed: 12/16/2022] Open
Abstract
The recent success of genome-wide association studies (GWAS) is now followed by the challenge to determine how the reported susceptibility variants mediate complex traits and diseases. Expression quantitative trait loci (eQTLs) have been implicated in disease associations through overlaps between eQTLs and GWAS signals. However, the abundance of eQTLs and the strong correlation structure (LD) in the genome make it likely that some of these overlaps are coincidental and not driven by the same functional variants. In the present study, we propose an empirical methodology, which we call Regulatory Trait Concordance (RTC) that accounts for local LD structure and integrates eQTLs and GWAS results in order to reveal the subset of association signals that are due to cis eQTLs. We simulate genomic regions of various LD patterns with both a single or two causal variants and show that our score outperforms SNP correlation metrics, be they statistical (r2) or historical (D'). Following the observation of a significant abundance of regulatory signals among currently published GWAS loci, we apply our method with the goal to prioritize relevant genes for each of the respective complex traits. We detect several potential disease-causing regulatory effects, with a strong enrichment for immunity-related conditions, consistent with the nature of the cell line tested (LCLs). Furthermore, we present an extension of the method in trans, where interrogating the whole genome for downstream effects of the disease variant can be informative regarding its unknown primary biological effect. We conclude that integrating cellular phenotype associations with organismal complex traits will facilitate the biological interpretation of the genetic effects on these traits. Genome-wide association studies have led to the identification of susceptibility loci for a variety of human complex traits. What is still largely missing, however, is the understanding of the biological context in which these candidate variants act and of how they determine each trait. Given the localization of many GWAS loci outside coding regions and the important role of regulatory variation in shaping phenotypic variance, gene expression has been proposed as a plausible informative intermediate phenotype. Here we show that for a subset of the currently published GWAS this is indeed the case, by observing a significant excess of regulatory variants among disease loci. We propose an empirical methodology (regulatory trait concordance—RTC) able to integrate expression and disease data in order to detect causal regulatory effects. We show that the RTC outperforms simple correlation metrics under various simulated linkage disequilibrium (LD) scenarios. Our method is able to recover previously suspected causal regulatory effects from the literature and, as expected given the nature of the tested tissue, an overrepresentation of immunity-related candidates is observed. As the number of available tissues will increase, this prioritization approach will become even more useful in understanding the implication of regulatory variants in disease etiology.
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Affiliation(s)
- Alexandra C. Nica
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Stephen B. Montgomery
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Antigone S. Dimas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Barbara E. Stranger
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Claude Beazley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Emmanouil T. Dermitzakis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- * E-mail:
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23
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Abstract
The regulation of gene expression is one of the most important cellular functions that determines developmental and somatic cell fates. Studies that attempt to describe the molecular interactions that govern gene regulation highlight the complexity and multidimensionality of this process. The recent explosion of information on genetic variation has added yet another dimension to this complexity. Genetic variation in elements that control gene expression directly or indirectly through interactions with other elements or molecules, contributes to observed expression level differences between individuals of the same species. In this short review we will address some of the key principles of the past and recent studies describing the degree and nature of regulatory variation with a focus on human populations.
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Affiliation(s)
- Antigone S Dimas
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva CH-1211, Switzerland.
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24
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Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M, Gagnebin M, Nisbett J, Deloukas P, Dermitzakis ET, Antonarakis SE. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 2009; 325:1246-50. [PMID: 19644074 PMCID: PMC2867218 DOI: 10.1126/science.1174148] [Citation(s) in RCA: 590] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Studies correlating genetic variation to gene expression facilitate the interpretation of common human phenotypes and disease. As functional variants may be operating in a tissue-dependent manner, we performed gene expression profiling and association with genetic variants (single-nucleotide polymorphisms) on three cell types of 75 individuals. We detected cell type-specific genetic effects, with 69 to 80% of regulatory variants operating in a cell type-specific manner, and identified multiple expressive quantitative trait loci (eQTLs) per gene, unique or shared among cell types and positively correlated with the number of transcripts per gene. Cell type-specific eQTLs were found at larger distances from genes and at lower effect size, similar to known enhancers. These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity.
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Affiliation(s)
- Antigone S Dimas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1HH, Cambridge, UK
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25
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Dimas AS, Stranger BE, Beazley C, Finn RD, Ingle CE, Forrest MS, Ritchie ME, Deloukas P, Tavaré S, Dermitzakis ET. Modifier effects between regulatory and protein-coding variation. PLoS Genet 2008; 4:e1000244. [PMID: 18974877 PMCID: PMC2570624 DOI: 10.1371/journal.pgen.1000244] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 09/29/2008] [Indexed: 01/28/2023] Open
Abstract
Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants, yet a large fraction of the genetic effects is still unaccounted for. Analyzing genetic interactions between variants (epistasis) is one of the potential ways forward. We investigated the abundance and functional impact of a specific type of epistasis, namely the interaction between regulatory and protein-coding variants. Using genotype and gene expression data from the 210 unrelated individuals of the original four HapMap populations, we have explored the combined effects of regulatory and protein-coding single nucleotide polymorphisms (SNPs). We predict that about 18% (1,502 out of 8,233 nsSNPs) of protein-coding variants are differentially expressed among individuals and demonstrate that regulatory variants can modify the functional effect of a coding variant in cis. Furthermore, we show that such interactions in cis can affect the expression of downstream targets of the gene containing the protein-coding SNP. In this way, a cis interaction between regulatory and protein-coding variants has a trans impact on gene expression. Given the abundance of both types of variants in human populations, we propose that joint consideration of regulatory and protein-coding variants may reveal additional genetic effects underlying complex traits and disease and may shed light on causes of differential penetrance of known disease variants. The ultimate goal of genome-wide association studies (GWAS) is to explain the proportion of variation in a phenotypic trait that can be attributed to genetic factors. The past two years have seen a plethora of successes in this field, yet, for most traits, a large fraction of variation remains unexplained. Epistasis, or interaction between genetic variants, is a largely under-explored factor, which may shed some light in this area. We use the HapMap populations to investigate interactions between regulatory and protein-coding variants and their impact on gene expression. We show that if a specific protein-coding variant has a functional impact, this can be modified by a co-segregating regulatory variant (cis interaction). Furthermore, the authors demonstrate that such modification effects between variants at one locus may affect the expression of other genes in the cell in a trans manner. The aim of this article is to present a framework though which variation can be considered in the context of GWAS. Viewing variation from this underappreciated angle may, in some cases, provide an explanation for differential penetrance of complex disease traits, but also for non-replication of GWAS results that may arise as a consequence of such interactions.
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Affiliation(s)
- Antigone S. Dimas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Barbara E. Stranger
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Claude Beazley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Robert D. Finn
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Catherine E. Ingle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Matthew S. Forrest
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Matthew E. Ritchie
- Department of Oncology, University of Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Simon Tavaré
- Department of Oncology, University of Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
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