101
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Svishcheva GR, Belonogova NM, Zorkoltseva IV, Kirichenko AV, Axenovich TI. Gene-based association tests using GWAS summary statistics. Bioinformatics 2020; 35:3701-3708. [PMID: 30860568 DOI: 10.1093/bioinformatics/btz172] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/12/2019] [Accepted: 03/11/2019] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION A huge number of genome-wide association studies (GWAS) summary statistics freely available in databases provide a new material for gene-based association analysis aimed at identifying rare genetic variants. Only a few of the many popular gene-based methods developed for individual genotype and phenotype data are adapted for the practical use of the GWAS summary statistics as input. RESULTS We analytically prove and numerically illustrate that all popular powerful methods developed for gene-based association analysis of individual phenotype and genotype data can be modified to utilize GWAS summary statistics. We have modified and implemented all of the popular methods, including burden and kernel machine-based tests, multiple and functional linear regression, principal components analysis and others, in the R package sumFREGAT. Using real summary statistics for coronary artery disease, we show that the new package is able to detect genes not found by the existing packages. AVAILABILITY AND IMPLEMENTATION The R package sumFREGAT is freely and publicly available at: https://CRAN.R-project.org/package=sumFREGAT. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gulnara R Svishcheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Vavilov Institute of General Genetics, the Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda M Belonogova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina V Zorkoltseva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly V Kirichenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatiana I Axenovich
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.,Department of Biotechnology, L.K. Ernst Federal Center for Animal Husbandry, Dubrovitsy, Russia
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102
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Wallace C. Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses. PLoS Genet 2020; 16:e1008720. [PMID: 32310995 PMCID: PMC7192519 DOI: 10.1371/journal.pgen.1008720] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/30/2020] [Accepted: 03/17/2020] [Indexed: 01/03/2023] Open
Abstract
Horizontal integration of summary statistics from different GWAS traits can be used to evaluate evidence for their shared genetic causality. One popular method to do this is a Bayesian method, coloc, which is attractive in requiring only GWAS summary statistics and no linkage disequilibrium estimates and is now being used routinely to perform thousands of comparisons between traits. Here we show that while most users do not adjust default software values, misspecification of prior parameters can substantially alter posterior inference. We suggest data driven methods to derive sensible prior values, and demonstrate how sensitivity analysis can be used to assess robustness of posterior inference. The flexibility of coloc comes at the expense of an unrealistic assumption of a single causal variant per trait. This assumption can be relaxed by stepwise conditioning, but this requires external software and an LD matrix aligned to study alleles. We have now implemented conditioning within coloc, and propose a new alternative method, masking, that does not require LD and approximates conditioning when causal variants are independent. Importantly, masking can be used in combination with conditioning where allelically aligned LD estimates are available for only a single trait. We have implemented these developments in a new version of coloc which we hope will enable more informed choice of priors and overcome the restriction of the single causal variant assumptions in coloc analysis.
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Affiliation(s)
- Chris Wallace
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, and MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
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103
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Cole JB, Florez JC, Hirschhorn JN. Comprehensive genomic analysis of dietary habits in UK Biobank identifies hundreds of genetic associations. Nat Commun 2020; 11:1467. [PMID: 32193382 PMCID: PMC7081342 DOI: 10.1038/s41467-020-15193-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023] Open
Abstract
Unhealthful dietary habits are leading risk factors for life-altering diseases and mortality. Large-scale biobanks now enable genetic analysis of traits with modest heritability, such as diet. We perform a genomewide association on 85 single food intake and 85 principal component-derived dietary patterns from food frequency questionnaires in UK Biobank. We identify 814 associated loci, including olfactory receptor associations with fruit and tea intake; 136 associations are only identified using dietary patterns. Mendelian randomization suggests our top healthful dietary pattern driven by wholemeal vs. white bread consumption is causally influenced by factors correlated with education but is not strongly causal for coronary artery disease or type 2 diabetes. Overall, we demonstrate the value in complementary phenotyping approaches to complex dietary datasets, and the utility of genomic analysis to understand the relationships between diet and human health.
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Affiliation(s)
- Joanne B Cole
- Programs in Metabolism and Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Jose C Florez
- Programs in Metabolism and Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joel N Hirschhorn
- Programs in Metabolism and Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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104
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Shared genetic etiology underlying Alzheimer's disease and major depressive disorder. Transl Psychiatry 2020; 10:88. [PMID: 32152295 PMCID: PMC7062839 DOI: 10.1038/s41398-020-0769-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 01/22/2023] Open
Abstract
Patients with late-onset Alzheimer's disease (LOAD) frequently manifest comorbid neuropsychiatric symptoms with depression and anxiety being most frequent, and individuals with major depressive disorder (MDD) have an increased prevalence of LOAD. This suggests shared etiologies and intersecting pathways between LOAD and MDD. We performed pleiotropy analyses using LOAD and MDD GWAS data sets from the International Genomics of Alzheimer's Project (IGAP) and the Psychiatric Genomics Consortium (PGC), respectively. We found a moderate enrichment for SNPs associated with LOAD across increasingly stringent levels of significance with the MDD GWAS association (LOAD|MDD), of maximum four and eightfolds, including and excluding the APOE-region, respectively. Association analysis excluding the APOE-region identified numerous SNPs corresponding to 40 genes, 9 of which are known LOAD-risk loci primarily in chromosome 11 regions that contain the SPI1 gene and MS4A genes cluster, and others were novel pleiotropic risk-loci for LOAD conditional with MDD. The most significant associated SNPs on chromosome 11 overlapped with eQTLs found in whole-blood and monocytes, suggesting functional roles in gene regulation. The reverse conditional association analysis (MDD|LOAD) showed a moderate level, ~sevenfold, of polygenic overlap, however, no SNP showed significant association. Pathway analyses replicated previously reported LOAD biological pathways related to immune response and regulation of endocytosis. In conclusion, we provide insights into the overlapping genetic signatures underpinning the common phenotypic manifestations and inter-relationship between LOAD and MDD. This knowledge is crucial to the development of actionable targets for novel therapies to treat depression preceding dementia, in an effort to delay or ultimately prevent the onset of LOAD.
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105
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Ray JP, de Boer CG, Fulco CP, Lareau CA, Kanai M, Ulirsch JC, Tewhey R, Ludwig LS, Reilly SK, Bergman DT, Engreitz JM, Issner R, Finucane HK, Lander ES, Regev A, Hacohen N. Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features. Nat Commun 2020; 11:1237. [PMID: 32144282 PMCID: PMC7060350 DOI: 10.1038/s41467-020-15022-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/17/2020] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we use seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in five disease-relevant immune cell lines, based on a set of features related to regulatory potential. Trait/disease-associated variants are enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 have at least one variant meeting one or both of these criteria, 5 of which are further supported by genetic fine-mapping. Our work provides a comprehensive strategy to characterize genetic variation at important disease-associated loci, and aids in the effort to identify trait causal genetic variants.
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Affiliation(s)
- John P Ray
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Carl G de Boer
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Caleb A Lareau
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jacob C Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Ryan Tewhey
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Steven K Reilly
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Drew T Bergman
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Society of Fellows, Harvard University, Cambridge, MA, 02138, USA
| | - Robbyn Issner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA.
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, 02114, USA.
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106
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Heller R. Comments on: Hierarchical inference for genome-wide association studies: a view on methodology with software. Comput Stat 2020. [DOI: 10.1007/s00180-019-00942-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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107
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Wang AT, Shetty A, O'Connor E, Bell C, Pomerantz MM, Freedman ML, Gusev A. Allele-Specific QTL Fine Mapping with PLASMA. Am J Hum Genet 2020; 106:170-187. [PMID: 32004450 PMCID: PMC7011109 DOI: 10.1016/j.ajhg.2019.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/29/2019] [Indexed: 12/22/2022] Open
Abstract
Although quantitative trait locus (QTL) associations have been identified for many molecular traits such as gene expression, it remains challenging to distinguish the causal nucleotide from nearby variants. In addition to traditional QTLs by association, allele-specific (AS) QTLs are a powerful measure of cis-regulation that are concordant with traditional QTLs but typically less susceptible to technical/environmental noise. However, existing methods for estimating causal variant probabilities (i.e., fine mapping) cannot produce valid estimates from asQTL signals due to complexities in linkage disequilibrium (LD). We introduce PLASMA (Population Allele-Specific Mapping), a fine-mapping method that integrates QTL and asQTL information to improve accuracy. In simulations, PLASMA accurately prioritizes causal variants over a wide range of genetic architectures. Applied to RNA-seq data from 524 kidney tumor samples, PLASMA achieves a greater power at 50 samples than conventional QTL-based fine mapping at 500 samples, with more than 17% of loci fine mapped to within five causal variants, compared to 2% by QTL-based fine mapping, and a 6.9-fold overall reduction in median credible set size compared to QTL-based fine mapping when applied to H3K27AC ChIP-seq from just 28 prostate tumor/normal samples. Variants in the PLASMA credible sets for RNA-seq and ChIP-seq were enriched for open chromatin and chromatin looping, respectively, at a comparable or greater degree than credible variants from existing methods while containing far fewer markers. Our results demonstrate how integrating AS activity can substantially improve the detection of causal variants from existing molecular data.
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Affiliation(s)
- Austin T Wang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Anamay Shetty
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cambridge University, Cambridge CB2 1TN, UK
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Brigham & Women's Hospital, Division of Genetics, Boston, MA 02215, USA.
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108
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Wu C, Pan W. A powerful fine-mapping method for transcriptome-wide association studies. Hum Genet 2020; 139:199-213. [PMID: 31844974 PMCID: PMC6983348 DOI: 10.1007/s00439-019-02098-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/07/2019] [Indexed: 01/14/2023]
Abstract
Transcriptome-wide association studies (TWAS) have been recently applied to successfully identify many novel genes associated with complex traits. While appealing, TWAS tend to identify multiple significant genes per locus, and many of them may not be causal due to confounding through linkage disequilibrium (LD) among SNPs. Here we introduce a powerful fine-mapping method that prioritizes putative causal genes by accounting for local LD. We apply a weighted adaptive test with eQTL-derived weights to maintain high power across various scenarios. Through simulations, we show that our new approach yielded a well-controlled Type I error rate while achieving higher power and AUC than competing methods. We applied our approach to a schizophrenia GWAS summary dataset and successfully prioritized some well-known schizophrenia-related genes, such as C4A. Importantly, our approach identified some putative causal genes (e.g., B3GAT1 and RGS6) that were missed by competing methods and TWAS. Our results suggest that our approach is a useful tool to prioritize putative causal genes, gaining insights into the mechanisms of complex traits.
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Affiliation(s)
- Chong Wu
- Department of Statistics, Florida State University, Tallahassee, FL, USA.
| | - Wei Pan
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA.
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109
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Yang TL, Shen H, Liu A, Dong SS, Zhang L, Deng FY, Zhao Q, Deng HW. A road map for understanding molecular and genetic determinants of osteoporosis. Nat Rev Endocrinol 2020; 16:91-103. [PMID: 31792439 PMCID: PMC6980376 DOI: 10.1038/s41574-019-0282-7] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/18/2019] [Indexed: 12/16/2022]
Abstract
Osteoporosis is a highly prevalent disorder characterized by low bone mineral density and an increased risk of fracture, termed osteoporotic fracture. Notably, bone mineral density, osteoporosis and osteoporotic fracture are highly heritable; however, determining the genetic architecture, and especially the underlying genomic and molecular mechanisms, of osteoporosis in vivo in humans is still challenging. In addition to susceptibility loci identified in genome-wide association studies, advances in various omics technologies, including genomics, transcriptomics, epigenomics, proteomics and metabolomics, have all been applied to dissect the pathogenesis of osteoporosis. However, each technology individually cannot capture the entire view of the disease pathology and thus fails to comprehensively identify the underlying pathological molecular mechanisms, especially the regulatory and signalling mechanisms. A change to the status quo calls for integrative multi-omics and inter-omics analyses with approaches in 'systems genetics and genomics'. In this Review, we highlight findings from genome-wide association studies and studies using various omics technologies individually to identify mechanisms of osteoporosis. Furthermore, we summarize current studies of data integration to understand, diagnose and inform the treatment of osteoporosis. The integration of multiple technologies will provide a road map to illuminate the complex pathogenesis of osteoporosis, especially from molecular functional aspects, in vivo in humans.
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Affiliation(s)
- Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Hui Shen
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Anqi Liu
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Qi Zhao
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA.
- School of Basic Medical Science, Central South University, Changsha, China.
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110
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Liu L, Zhao M, Xie ZG, Liu J, Peng HP, Pei YF, Sun HP, Zhang L. Twelve New Genomic Loci Associated With Bone Mineral Density. Front Endocrinol (Lausanne) 2020; 11:243. [PMID: 32390946 PMCID: PMC7188784 DOI: 10.3389/fendo.2020.00243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022] Open
Abstract
Aiming to identify more genomic loci associated with bone mineral density (BMD), we conducted a joint association analysis of 2 genome-wide association study (GWAS) by the integrative association method multi-trait analysis of GWAS (MTAG). The first one is the single GWAS of estimated heel BMD (eBMD) in the UK biobank (UKB) cohort (N = 426,824), and the second one is the GWAS meta-analysis of total body BMD (TB-BMD) in 66,628 participants from 30 studies. Approximate conditional association analysis was performed in the identified novel loci to identify secondary association signal. Statistical fine-mapping was conducted to prioritize plausible credible risk variants (CRVs). Candidate genes were prioritized based on the analyses of cis- expression quantitative trait locus (cis-eQTL) and cis-protein QTL (cis-pQTL) information as well as the functional category of the SNP. By integrating the information carried in over 490,000 participants, this largest joint analysis of BMD GWAS identified 12 novel genomic loci at the genome-wide significance level (GWS, p = 5.0 × 10-8), nine of which were for eBMD and four were for TB-BMD, explaining an additional 0.11 and 0.23% heritability for the two traits, respectively. These loci include 1p33 (lead SNP rs10493130, peBMD = 3.19 × 10-8), 5q13.2 (rs4703589, peBMD = 4.78 × 10-8), 5q31.3 (rs9324887, pTB-BMD = 1.36 × 10-9), 6p21.32 (rs6905837, peBMD = 3.32 × 10-8), 6q14.1 (rs10806234, peBMD = 2.63 × 10-8), 7q21.11 (rs10806234, pTB-BMD = 3.37 × 10-8), 8q24.12 (rs11995866, peBMD = 6.72 × 10-9), 12p13.31 (rs1639122, peBMD = 4.43 × 10-8), 12p12.1 (rs58489179, peBMD = 4.74 × 10-8), 12q24.23 (rs75499226, peBMD = 1.44 × 10-8), 19q13.31 (rs7255083, pTB-BMD = 2.18 × 10-8) and 22q11.23 (rs13056137, pTB-BMD = 2.54 × 10-8). All lead SNPs in these 12 loci are nominally significant in both original studies as well as consistent in effect direction between them, providing solid evidence of replication. Approximate conditional analysis identified one secondary signal in 5q13.2 (rs11738874, pconditional = 5.06 × 10-9). Statistical fine-mapping analysis prioritized 269 CRVs. A total of 65 candidate genes were prioritized, including those with known biological function to bone development (such as FGF1, COL11A2 and DEPTOR). Our findings provide novel insights into a better understanding of the genetic mechanism underlying bone development as well as candidate genes for future functional investigation.
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Affiliation(s)
- Lu Liu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Jiangsu, China
- Kunshan Hospital of Traditional Chinese Medicine, Jiangsu, China
| | - Min Zhao
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Jiangsu, China
| | - Zong-Gang Xie
- The Second Affiliated Hospital of Soochow University, Jiangsu, China
| | - Ju Liu
- Kunshan Hospital of Traditional Chinese Medicine, Jiangsu, China
| | - Hui-Ping Peng
- Kunshan Hospital of Traditional Chinese Medicine, Jiangsu, China
| | - Yu-Fang Pei
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Jiangsu, China
- *Correspondence: Yu-Fang Pei
| | - Hong-Peng Sun
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Jiangsu, China
- Department of Children Health and Social Medicine, School of Public Health, Medical College of Soochow University, Jiangsu, China
- Hong-Peng Sun
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Jiangsu, China
- Lei Zhang
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111
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Barešić A, Nash AJ, Dahoun T, Howes O, Lenhard B. Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks. Mol Psychiatry 2020; 25:6-18. [PMID: 31616042 PMCID: PMC6906185 DOI: 10.1038/s41380-019-0518-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 06/18/2019] [Accepted: 07/09/2019] [Indexed: 01/30/2023]
Abstract
Recent genome-wide association studies have identified numerous loci associated with neuropsychiatric disorders. The majority of these are in non-coding regions, and are commonly assigned to the nearest gene along the genome. However, this approach neglects the three-dimensional organisation of the genome, and the fact that the genome contains arrays of extremely conserved non-coding elements termed genomic regulatory blocks (GRBs), which can be utilized to detect genes under long-range developmental regulation. Here we review a GRB-based approach to assign loci in non-coding regions to potential target genes, and apply it to reanalyse the results of one of the largest schizophrenia GWAS (SWG PGC, 2014). We further apply this approach to GWAS data from two related neuropsychiatric disorders-autism spectrum disorder and bipolar disorder-to show that it is applicable to developmental disorders in general. We find that disease-associated SNPs are overrepresented in GRBs and that the GRB model is a powerful tool for linking these SNPs to their correct target genes under long-range regulation. Our analysis identifies novel genes not previously implicated in schizophrenia and corroborates a number of predicted targets from the original study. The results are available as an online resource in which the genomic context and the strength of enhancer-promoter associations can be browsed for each schizophrenia-associated SNP.
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Affiliation(s)
- Anja Barešić
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Alexander Jolyon Nash
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Tarik Dahoun
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX37 JX, UK
| | - Oliver Howes
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008, Bergen, Norway.
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112
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Improved polygenic prediction by Bayesian multiple regression on summary statistics. Nat Commun 2019; 10:5086. [PMID: 31704910 PMCID: PMC6841727 DOI: 10.1038/s41467-019-12653-0] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/30/2019] [Indexed: 01/21/2023] Open
Abstract
Accurate prediction of an individual’s phenotype from their DNA sequence is one of the great promises of genomics and precision medicine. We extend a powerful individual-level data Bayesian multiple regression model (BayesR) to one that utilises summary statistics from genome-wide association studies (GWAS), SBayesR. In simulation and cross-validation using 12 real traits and 1.1 million variants on 350,000 individuals from the UK Biobank, SBayesR improves prediction accuracy relative to commonly used state-of-the-art summary statistics methods at a fraction of the computational resources. Furthermore, using summary statistics for variants from the largest GWAS meta-analysis (n ≈ 700, 000) on height and BMI, we show that on average across traits and two independent data sets that SBayesR improves prediction R2 by 5.2% relative to LDpred and by 26.5% relative to clumping and p value thresholding. Various approaches are being used for polygenic prediction including Bayesian multiple regression methods that require access to individual-level genotype data. Here, the authors extend BayesR to utilise GWAS summary statistics (SBayesR) and show that it outperforms other summary statistic-based methods.
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113
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Quick C, Fuchsberger C, Taliun D, Abecasis G, Boehnke M, Kang HM. emeraLD: rapid linkage disequilibrium estimation with massive datasets. Bioinformatics 2019; 35:164-166. [PMID: 30204848 DOI: 10.1093/bioinformatics/bty547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/28/2018] [Indexed: 01/08/2023] Open
Abstract
Summary Estimating linkage disequilibrium (LD) is essential for a wide range of summary statistics-based association methods for genome-wide association studies. Large genetic datasets, e.g. the TOPMed WGS project and UK Biobank, enable more accurate and comprehensive LD estimates, but increase the computational burden of LD estimation. Here, we describe emeraLD (Efficient Methods for Estimation and Random Access of LD), a computational tool that leverages sparsity and haplotype structure to estimate LD up to 2 orders of magnitude faster than current tools. Availability and implementation emeraLD is implemented in C++, and is open source under GPLv3. Source code and documentation are freely available at http://github.com/statgen/emeraLD. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Corbin Quick
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.,Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.,Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gonçalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
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114
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Tin A, Marten J, Halperin Kuhns VL, Li Y, Wuttke M, Kirsten H, Sieber KB, Qiu C, Gorski M, Yu Z, Giri A, Sveinbjornsson G, Li M, Chu AY, Hoppmann A, O'Connor LJ, Prins B, Nutile T, Noce D, Akiyama M, Cocca M, Ghasemi S, van der Most PJ, Horn K, Xu Y, Fuchsberger C, Sedaghat S, Afaq S, Amin N, Ärnlöv J, Bakker SJL, Bansal N, Baptista D, Bergmann S, Biggs ML, Biino G, Boerwinkle E, Bottinger EP, Boutin TS, Brumat M, Burkhardt R, Campana E, Campbell A, Campbell H, Carroll RJ, Catamo E, Chambers JC, Ciullo M, Concas MP, Coresh J, Corre T, Cusi D, Felicita SC, de Borst MH, De Grandi A, de Mutsert R, de Vries APJ, Delgado G, Demirkan A, Devuyst O, Dittrich K, Eckardt KU, Ehret G, Endlich K, Evans MK, Gansevoort RT, Gasparini P, Giedraitis V, Gieger C, Girotto G, Gögele M, Gordon SD, Gudbjartsson DF, Gudnason V, Haller T, Hamet P, Harris TB, Hayward C, Hicks AA, Hofer E, Holm H, Huang W, Hutri-Kähönen N, Hwang SJ, Ikram MA, Lewis RM, Ingelsson E, Jakobsdottir J, Jonsdottir I, Jonsson H, Joshi PK, Josyula NS, Jung B, Kähönen M, Kamatani Y, Kanai M, Kerr SM, Kiess W, Kleber ME, Koenig W, Kooner JS, Körner A, Kovacs P, Krämer BK, Kronenberg F, Kubo M, Kühnel B, La Bianca M, Lange LA, Lehne B, Lehtimäki T, Liu J, Loeffler M, Loos RJF, Lyytikäinen LP, Magi R, Mahajan A, Martin NG, März W, Mascalzoni D, Matsuda K, Meisinger C, Meitinger T, Metspalu A, Milaneschi Y, O'Donnell CJ, Wilson OD, Gaziano JM, Mishra PP, Mohlke KL, Mononen N, Montgomery GW, Mook-Kanamori DO, Müller-Nurasyid M, Nadkarni GN, Nalls MA, Nauck M, Nikus K, Ning B, Nolte IM, Noordam R, O'Connell JR, Olafsson I, Padmanabhan S, Penninx BWJH, Perls T, Peters A, Pirastu M, Pirastu N, Pistis G, Polasek O, Ponte B, Porteous DJ, Poulain T, Preuss MH, Rabelink TJ, Raffield LM, Raitakari OT, Rettig R, Rheinberger M, Rice KM, Rizzi F, Robino A, Rudan I, Krajcoviechova A, Cifkova R, Rueedi R, Ruggiero D, Ryan KA, Saba Y, Salvi E, Schmidt H, Schmidt R, Shaffer CM, Smith AV, Smith BH, Spracklen CN, Strauch K, Stumvoll M, Sulem P, Tajuddin SM, Teren A, Thiery J, Thio CHL, Thorsteinsdottir U, Toniolo D, Tönjes A, Tremblay J, Uitterlinden AG, Vaccargiu S, van der Harst P, van Duijn CM, Verweij N, Völker U, Vollenweider P, Waeber G, Waldenberger M, Whitfield JB, Wild SH, Wilson JF, Yang Q, Zhang W, Zonderman AB, Bochud M, Wilson JG, Pendergrass SA, Ho K, Parsa A, Pramstaller PP, Psaty BM, Böger CA, Snieder H, Butterworth AS, Okada Y, Edwards TL, Stefansson K, Susztak K, Scholz M, Heid IM, Hung AM, Teumer A, Pattaro C, Woodward OM, Vitart V, Köttgen A. Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels. Nat Genet 2019; 51:1459-1474. [PMID: 31578528 PMCID: PMC6858555 DOI: 10.1038/s41588-019-0504-x] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022]
Abstract
Elevated serum urate levels cause gout and correlate with cardiometabolic diseases via poorly understood mechanisms. We performed a trans-ancestry genome-wide association study of serum urate in 457,690 individuals, identifying 183 loci (147 previously unknown) that improve the prediction of gout in an independent cohort of 334,880 individuals. Serum urate showed significant genetic correlations with many cardiometabolic traits, with genetic causality analyses supporting a substantial role for pleiotropy. Enrichment analysis, fine-mapping of urate-associated loci and colocalization with gene expression in 47 tissues implicated the kidney and liver as the main target organs and prioritized potentially causal genes and variants, including the transcriptional master regulators in the liver and kidney, HNF1A and HNF4A. Experimental validation showed that HNF4A transactivated the promoter of ABCG2, encoding a major urate transporter, in kidney cells, and that HNF4A p.Thr139Ile is a functional variant. Transcriptional coregulation within and across organs may be a general mechanism underlying the observed pleiotropy between urate and cardiometabolic traits.
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Affiliation(s)
- Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Welch Centre for Prevention, Epidemiology and Clinical Research, Baltimore, MD, USA.
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Yong Li
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Karsten B Sieber
- Target Sciences-Genetics, GlaxoSmithKline, Collegeville, PA, USA
| | - Chengxiang Qiu
- Department of Medicine and Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Mathias Gorski
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Zhi Yu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ayush Giri
- Division of Quantitative Sciences, Department of Obstetrics & Gynecology, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | | | - Man Li
- Department of Medicine, Division of Nephrology and Hypertension, University of Utah, Salt Lake City, UT, USA
| | | | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Luke J O'Connor
- Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bram Prins
- Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Teresa Nutile
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso-CNR, Naples, Italy
| | - Damia Noce
- Eurac Research, Institute for Biomedicine, Bolzano, Italy
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Centre for Integrative Medical Sciences, Yokohama (Kanagawa), Japan
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Massimiliano Cocca
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Yizhe Xu
- Department of Medicine, Division of Nephrology and Hypertension, University of Utah, Salt Lake City, UT, USA
| | | | - Sanaz Sedaghat
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Saima Afaq
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
- Institute of Public Health & Social Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society, Division of Family Medicine and Primary Care, Karolinska Institutet, Stockholm, Sweden
- School of Health and Social Studies, Dalarna University, Falun, Sweden
| | - Stephan J L Bakker
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | | | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Eric Boerwinkle
- Human Genetics Centre, University of Texas Health Science Centre, Houston, TX, USA
| | - Erwin P Bottinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thibaud S Boutin
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Marco Brumat
- University of Trieste, Department of Medicine, Surgery and Health Sciences, Trieste, Italy
| | - Ralph Burkhardt
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Eric Campana
- University of Trieste, Department of Medicine, Surgery and Health Sciences, Trieste, Italy
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eulalia Catamo
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Cardiology, Ealing Hospital, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Marina Ciullo
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso-CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tanguy Corre
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Daniele Cusi
- Institute of Biomedical Technologies, Italy National Research Council, Milano, Italy
- Bio4Dreams, Milano, Italy
| | | | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Aiko P J de Vries
- Section of Nephrology, Department of Internal Medicine, Leiden University Medical Centre, Leiden, the Netherlands
| | - Graciela Delgado
- Fifth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ayşe Demirkan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Katalin Dittrich
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Georg Ehret
- Cardiology, Geneva University Hospitals, Geneva, Switzerland
| | - Karlhans Endlich
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Ron T Gansevoort
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Paolo Gasparini
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
- University of Trieste, Department of Medicine, Surgery and Health Sciences, Trieste, Italy
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Uppsala University, Uppsala, Sweden
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Giorgia Girotto
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
- University of Trieste, Department of Medicine, Surgery and Health Sciences, Trieste, Italy
| | - Martin Gögele
- Eurac Research, Institute for Biomedicine, Bolzano, Italy
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, Kópavogur, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Toomas Haller
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pavel Hamet
- Montreal University Hospital Research Centre, Centre Hospitalier de lUniversité de Montréal, Montreal, Quebec, Canada
- Medpharmgene, Montreal, Quebec, Canada
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew A Hicks
- Eurac Research, Institute for Biomedicine, Bolzano, Italy
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Hilma Holm
- deCODE Genetics, Amgen Inc., Reykjavik, Iceland
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Centre, Shanghai, China
- Shanghai Industrial Technology Institute, Shanghai, China
| | - Nina Hutri-Kähönen
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Pediatrics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Shih-Jen Hwang
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA
- The Centre for Population Studies, National Heart, Lung, and Blood Institute, Framingham, MA, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Raychel M Lewis
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Johanna Jakobsdottir
- Icelandic Heart Association, Kópavogur, Iceland
- The Centre of Public Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Helgi Jonsson
- Landspitalinn University Hospital, Reykjavík, Iceland
- University of Iceland, Reykjavík, Iceland
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Navya Shilpa Josyula
- Geisinger Research, Biomedical and Translational Informatics Institute, Rockville, MD, USA
| | - Bettina Jung
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Centre for Integrative Medical Sciences, Yokohama (Kanagawa), Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiro Kanai
- Laboratory for Statistical Analysis, RIKEN Centre for Integrative Medical Sciences, Yokohama (Kanagawa), Japan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Wieland Kiess
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Marcus E Kleber
- Fifth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology and Biostatistics, University of Ulm, Ulm, Germany
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, 323 School of Public Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Antje Körner
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Integrated Research and Treatment Centre Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Bernhard K Krämer
- Fifth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Michiaki Kubo
- RIKEN Centre for Integrative Medical Sciences, Yokohama (Kanagawa), Japan
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
| | - Martina La Bianca
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, USA
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jun Liu
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Reedik Magi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Winfried März
- Fifth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | | | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Christa Meisinger
- Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- Ludwig-Maximilians-Universität München at UNIKA-T Augsburg, Augsburg, Germany
| | - Thomas Meitinger
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Christopher J O'Donnell
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Otis D Wilson
- Vanderbilt University Medical Centre, Division of Nephrology & Hypertension, Nashville, TN, USA
| | - J Michael Gaziano
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts Veterans Epidemiology Research and Information Center, VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Centre, Leiden, the Netherlands
| | - Martina Müller-Nurasyid
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Boting Ning
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Thomas Perls
- Department of Medicine, Geriatrics Section, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Mario Pirastu
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Sassari, Sassari, Italy
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Giorgio Pistis
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
- Gen-info Ltd, Zagreb, Croatia
| | - Belen Ponte
- Nephrology Service, Department of Specialties in Internal Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Tanja Poulain
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ton J Rabelink
- Section of Nephrology, Department of Internal Medicine, Leiden University Medical Centre, Leiden, the Netherlands
- Einthoven Laboratory of Experimental Vascular Research, Leiden University Medical Centre, Leiden, the Netherlands
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Rainer Rettig
- Institute of Physiology, University Medicine Greifswald, Karlsburg, Germany
| | - Myriam Rheinberger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Federica Rizzi
- Department of Health Sciences, University of Milan, Milano, Italy
- ePhood Scientific Unit, ePhood SRL, Milano, Italy
| | - Antonietta Robino
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Alena Krajcoviechova
- Center for Cardiovascular Prevention, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
- Thomayer Hospital, Prague, Czech Republic
| | - Renata Cifkova
- Center for Cardiovascular Prevention, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
- Department of Medicine II, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso-CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Kathleen A Ryan
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yasaman Saba
- Molecular Biology and Biochemistry, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | - Erika Salvi
- Department of Health Sciences, University of Milan, Milano, Italy
- Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Centre for Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Christian M Shaffer
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Albert V Smith
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | | | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Michael Stumvoll
- Division of Endocrinology, Nephrology and Rheumatology, University of Leipzig, Leipzig, Germany
| | | | - Salman M Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Andrej Teren
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Heart Centre Leipzig, Leipzig, Germany
| | - Joachim Thiery
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | - Anke Tönjes
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Johanne Tremblay
- Montreal University Hospital Research Centre, Centre Hospitalier de lUniversité de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Simona Vaccargiu
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Sassari, Sassari, Italy
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Durrer Centre for Cardiovascular Research, the Netherlands Heart Institute, Utrecht, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Genomics plc, Oxford, UK
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter Vollenweider
- Internal Medicine, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Gerard Waeber
- Internal Medicine, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sarah H Wild
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London, UK
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Centre, Jackson, MS, USA
| | - Sarah A Pendergrass
- Geisinger Research, Biomedical and Translational Informatics Institute, Danville, PA, USA
| | - Kevin Ho
- Kidney Health Research Institute, Geisinger, Danville, PA, USA
- Department of Nephrology, Geisinger, Danville, PA, USA
| | - Afshin Parsa
- Division of Kidney, Urologic and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Service, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Nephrology and Rheumatology, Kliniken Südostbayern AG, Traunstein, Germany
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adam S Butterworth
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Centre for Integrative Medical Sciences, Osaka, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Centre, Nashville, TN, USA
- Department of Veterans Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | | | - Katalin Susztak
- Department of Medicine and Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Adriana M Hung
- Vanderbilt University Medical Centre, Division of Nephrology & Hypertension, Nashville, TN, USA
- Department of Veterans Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | | | - Owen M Woodward
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany.
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Teumer A, Li Y, Ghasemi S, Prins BP, Wuttke M, Hermle T, Giri A, Sieber KB, Qiu C, Kirsten H, Tin A, Chu AY, Bansal N, Feitosa MF, Wang L, Chai JF, Cocca M, Fuchsberger C, Gorski M, Hoppmann A, Horn K, Li M, Marten J, Noce D, Nutile T, Sedaghat S, Sveinbjornsson G, Tayo BO, van der Most PJ, Xu Y, Yu Z, Gerstner L, Ärnlöv J, Bakker SJL, Baptista D, Biggs ML, Boerwinkle E, Brenner H, Burkhardt R, Carroll RJ, Chee ML, Chee ML, Chen M, Cheng CY, Cook JP, Coresh J, Corre T, Danesh J, de Borst MH, De Grandi A, de Mutsert R, de Vries APJ, Degenhardt F, Dittrich K, Divers J, Eckardt KU, Ehret G, Endlich K, Felix JF, Franco OH, Franke A, Freedman BI, Freitag-Wolf S, Gansevoort RT, Giedraitis V, Gögele M, Grundner-Culemann F, Gudbjartsson DF, Gudnason V, Hamet P, Harris TB, Hicks AA, Holm H, Foo VHX, Hwang SJ, Ikram MA, Ingelsson E, Jaddoe VWV, Jakobsdottir J, Josyula NS, Jung B, Kähönen M, Khor CC, Kiess W, Koenig W, Körner A, Kovacs P, Kramer H, Krämer BK, Kronenberg F, Lange LA, Langefeld CD, Lee JJM, Lehtimäki T, Lieb W, Lim SC, Lind L, Lindgren CM, Liu J, Loeffler M, Lyytikäinen LP, Mahajan A, Maranville JC, Mascalzoni D, McMullen B, Meisinger C, Meitinger T, Miliku K, Mook-Kanamori DO, Müller-Nurasyid M, Mychaleckyj JC, Nauck M, Nikus K, Ning B, Noordam R, Connell JO, Olafsson I, Palmer ND, Peters A, Podgornaia AI, Ponte B, Poulain T, Pramstaller PP, Rabelink TJ, Raffield LM, Reilly DF, Rettig R, Rheinberger M, Rice KM, Rivadeneira F, Runz H, Ryan KA, Sabanayagam C, Saum KU, Schöttker B, Shaffer CM, Shi Y, Smith AV, Strauch K, Stumvoll M, Sun BB, Szymczak S, Tai ES, Tan NYQ, Taylor KD, Teren A, Tham YC, Thiery J, Thio CHL, Thomsen H, Thorsteinsdottir U, Tönjes A, Tremblay J, Uitterlinden AG, van der Harst P, Verweij N, Vogelezang S, Völker U, Waldenberger M, Wang C, Wilson OD, Wong C, Wong TY, Yang Q, Yasuda M, Akilesh S, Bochud M, Böger CA, Devuyst O, Edwards TL, Ho K, Morris AP, Parsa A, Pendergrass SA, Psaty BM, Rotter JI, Stefansson K, Wilson JG, Susztak K, Snieder H, Heid IM, Scholz M, Butterworth AS, Hung AM, Pattaro C, Köttgen A. Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria. Nat Commun 2019; 10:4130. [PMID: 31511532 PMCID: PMC6739370 DOI: 10.1038/s41467-019-11576-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/23/2019] [Indexed: 02/08/2023] Open
Abstract
Increased levels of the urinary albumin-to-creatinine ratio (UACR) are associated with higher risk of kidney disease progression and cardiovascular events, but underlying mechanisms are incompletely understood. Here, we conduct trans-ethnic (n = 564,257) and European-ancestry specific meta-analyses of genome-wide association studies of UACR, including ancestry- and diabetes-specific analyses, and identify 68 UACR-associated loci. Genetic correlation analyses and risk score associations in an independent electronic medical records database (n = 192,868) reveal connections with proteinuria, hyperlipidemia, gout, and hypertension. Fine-mapping and trans-Omics analyses with gene expression in 47 tissues and plasma protein levels implicate genes potentially operating through differential expression in kidney (including TGFB1, MUC1, PRKCI, and OAF), and allow coupling of UACR associations to altered plasma OAF concentrations. Knockdown of OAF and PRKCI orthologs in Drosophila nephrocytes reduces albumin endocytosis. Silencing fly PRKCI further impairs slit diaphragm formation. These results generate a priority list of genes and pathways for translational research to reduce albuminuria.
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Affiliation(s)
- Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany.
| | - Yong Li
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Bram P Prins
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Tobias Hermle
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Ayush Giri
- Division of Quantitative Sciences, Department of Obstetrics & Gynecology, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Karsten B Sieber
- Target Sciences - Genetics, GlaxoSmithKline, Collegeville, PA, USA
| | - Chengxiang Qiu
- Renal Electrolyte and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, USA
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Epidemiology and Clinical Research, Welch Centre for Prevention, Baltimore, MD, USA
| | - Audrey Y Chu
- Genetics, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Massimiliano Cocca
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Christian Fuchsberger
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Mathias Gorski
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Man Li
- Department of Medicine, Division of Nephrology and Hypertension, University of Utah, Salt Lake City, UT, USA
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Damia Noce
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Teresa Nutile
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso" - CNR, Naples, Italy
| | - Sanaz Sedaghat
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yizhe Xu
- Department of Medicine, Division of Nephrology and Hypertension, University of Utah, Salt Lake City, UT, USA
| | - Zhi Yu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lea Gerstner
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society, Division of Family Medicine and Primary Care, Karolinska Institutet, Stockholm, Sweden
- School of Health and Social Studies, Dalarna University, Falun, Sweden
| | - Stephan J L Bakker
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Eric Boerwinkle
- Human Genetics Centre, University of Texas Health Science Centre, Houston, TX, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Ralph Burkhardt
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Miao-Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Mengmeng Chen
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tanguy Corre
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John Danesh
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alessandro De Grandi
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Aiko P J de Vries
- Section of Nephrology, Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Katalin Dittrich
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Jasmin Divers
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kai-Uwe Eckardt
- Intensive Care Medicine, Charité, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Georg Ehret
- Cardiology, Geneva University Hospitals, Geneva, Switzerland
| | - Karlhans Endlich
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Barry I Freedman
- Internal Medicine - Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, USA
| | - Ron T Gansevoort
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Uppsala University, Uppsala, Sweden
| | - Martin Gögele
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Pavel Hamet
- Montreal University Hospital Research Centre, CHUM, Montreal, QC, Canada
- Medpharmgene, Montreal, QC, Canada
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Andrew A Hicks
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Hilma Holm
- deCODE Genetics, Amgen Inc., Reykjavik, Iceland
| | - Valencia Hui Xian Foo
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Shih-Jen Hwang
- NHLBI's Framingham Heart Study, Framingham, MA, USA
- The Centre for Population Studies, NHLBI, Framingham, MA, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johanna Jakobsdottir
- Icelandic Heart Association, Holtasmari 1, Kopavogur, IS-201, Iceland
- The Centre of Public Health Sciences, University of Iceland, Sturlugata 8, Reykjavík, IS-101, Iceland
| | - Navya Shilpa Josyula
- Geisinger Research, Biomedical and Translational Informatics Institute, Rockville, MD, USA
| | - Bettina Jung
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Chiea-Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Wieland Kiess
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology and Biostatistics, University of Ulm, Ulm, Germany
| | - Antje Körner
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Integrated Research and Treatment Centre Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
- Division of Nephrology and Hypertension, Loyola University Chicago, Chicago, IL, USA
| | - Bernhard K Krämer
- 5th Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jeannette Jen-Mai Lee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Kiel University, Kiel, Germany
| | - Su-Chi Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Diabetes Centre, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Lars Lind
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Cecilia M Lindgren
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | | | - Deborah Mascalzoni
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | | | - Christa Meisinger
- Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Epidemiology Ludwig- Maximilians-Universität München at UNIKA-T Augsburg, Augsburg, Germany
| | - Thomas Meitinger
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Kozeta Miliku
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Centre, Leiden, The Netherlands
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, Munich, Germany
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Josyf C Mychaleckyj
- Centre for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Boting Ning
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Annette Peters
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | | | - Belen Ponte
- Service de Néphrologie, Geneva University Hospitals, Geneva, Switzerland
| | - Tanja Poulain
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Peter P Pramstaller
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Ton J Rabelink
- Section of Nephrology, Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
- Einthoven Laboratory of Experimental Vascular Research, Leiden University Medical Centre, Leiden, The Netherlands
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | | | - Rainer Rettig
- Institute of Physiology, University Medicine Greifswald, Karlsburg, Germany
| | - Myriam Rheinberger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Heiko Runz
- MRL, Merck & Co., Inc., Kenilworth, NJ, USA
- Biogen Inc., Cambridge, MA, USA
| | - Kathleen A Ryan
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Kai-Uwe Saum
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Christian M Shaffer
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Albert V Smith
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, Munich, Germany
| | - Michael Stumvoll
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, USA
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas Y Q Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Andrej Teren
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Heart Centre Leipzig, Leipzig, Germany
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Joachim Thiery
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | | | - Anke Tönjes
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Johanne Tremblay
- Montreal University Hospital Research Centre, CHUM, Montreal, QC, Canada
- CRCHUM, Montreal, QC, Canada
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Durrer Centre for Cardiovascular Research, The Netherlands Heart Institute, Utrecht, The Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Suzanne Vogelezang
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Chaolong Wang
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Otis D Wilson
- Vanderbilt University Medical Centre, Division of Nephrology & Hypertension, Nashville, TN, USA
| | - Charlene Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Masayuki Yasuda
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shreeram Akilesh
- Kidney Research Institute, University of Washington, Seattle, WA, USA
- Anatomic Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Nephrology, Diabetology and Rheumatology, Kliniken Südostbayern, Traunstein, Germany
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Centre, Nashville, TN, USA
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Kevin Ho
- Kidney Health Research Institute (KHRI), Geisinger, Danville, PA, USA
- Department of Nephrology, Geisinger, Danville, PA, USA
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Afshin Parsa
- Division of Kidney, Urologic and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sarah A Pendergrass
- Geisinger Research, Biomedical and Translational Informatics Institute, Danville, PA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Service, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Centre, Torrance, CA, USA
- Department of Medicine, Harbor-UCLA Medical Centre, Torrance, CA, USA
| | | | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Centre, Jackson, MS, USA
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Adriana M Hung
- Vanderbilt University Medical Centre, Division of Nephrology & Hypertension, Nashville, TN, USA
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy.
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Luo Y, Suliman S, Asgari S, Amariuta T, Baglaenko Y, Martínez-Bonet M, Ishigaki K, Gutierrez-Arcelus M, Calderon R, Lecca L, León SR, Jimenez J, Yataco R, Contreras C, Galea JT, Becerra M, Nejentsev S, Nigrovic PA, Moody DB, Murray MB, Raychaudhuri S. Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians. Nat Commun 2019; 10:3765. [PMID: 31434886 PMCID: PMC6704092 DOI: 10.1038/s41467-019-11664-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 07/24/2019] [Indexed: 12/13/2022] Open
Abstract
Of the 1.8 billion people worldwide infected with Mycobacterium tuberculosis, 5-15% will develop active tuberculosis (TB). Approximately half will progress to active TB within the first 18 months after infection, presumably because they fail to mount an effective initial immune response. Here, in a genome-wide genetic study of early TB progression, we genotype 4002 active TB cases and their household contacts in Peru. We quantify genetic heritability ([Formula: see text]) of early TB progression to be 21.2% (standard error 0.08). This suggests TB progression has a strong genetic basis, and is comparable to traits with well-established genetic bases. We identify a novel association between early TB progression and variants located in a putative enhancer region on chromosome 3q23 (rs73226617, OR = 1.18; P = 3.93 × 10-8). With in silico and in vitro analyses we identify rs73226617 or rs148722713 as the likely functional variant and ATP1B3 as a potential causal target gene with monocyte specific function.
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Affiliation(s)
- Yang Luo
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samira Asgari
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffany Amariuta
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Yuriy Baglaenko
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marta Martínez-Bonet
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | - Jerome T Galea
- School of Social Work, University of South Florida, Tampa, FL, USA
| | - Mercedes Becerra
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sergey Nejentsev
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Peter A Nigrovic
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - D Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Megan B Murray
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Arthritis Research UK Centre for Genetics and Genomics, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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117
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A global overview of pleiotropy and genetic architecture in complex traits. Nat Genet 2019; 51:1339-1348. [PMID: 31427789 DOI: 10.1038/s41588-019-0481-0] [Citation(s) in RCA: 604] [Impact Index Per Article: 120.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022]
Abstract
After a decade of genome-wide association studies (GWASs), fundamental questions in human genetics, such as the extent of pleiotropy across the genome and variation in genetic architecture across traits, are still unanswered. The current availability of hundreds of GWASs provides a unique opportunity to address these questions. We systematically analyzed 4,155 publicly available GWASs. For a subset of well-powered GWASs on 558 traits, we provide an extensive overview of pleiotropy and genetic architecture. We show that trait-associated loci cover more than half of the genome, and 90% of these overlap with loci from multiple traits. We find that potential causal variants are enriched in coding and flanking regions, as well as in regulatory elements, and show variation in polygenicity and discoverability of traits. Our results provide insights into how genetic variation contributes to trait variation. All GWAS results can be queried and visualized at the GWAS ATLAS resource ( https://atlas.ctglab.nl ).
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Wuttke M, Li Y, Li M, Sieber KB, Feitosa MF, Gorski M, Tin A, Wang L, Chu AY, Hoppmann A, Kirsten H, Giri A, Chai JF, Sveinbjornsson G, Tayo BO, Nutile T, Fuchsberger C, Marten J, Cocca M, Ghasemi S, Xu Y, Horn K, Noce D, van der Most PJ, Sedaghat S, Yu Z, Akiyama M, Afaq S, Ahluwalia TS, Almgren P, Amin N, Ärnlöv J, Bakker SJL, Bansal N, Baptista D, Bergmann S, Biggs ML, Biino G, Boehnke M, Boerwinkle E, Boissel M, Bottinger EP, Boutin TS, Brenner H, Brumat M, Burkhardt R, Butterworth AS, Campana E, Campbell A, Campbell H, Canouil M, Carroll RJ, Catamo E, Chambers JC, Chee ML, Chee ML, Chen X, Cheng CY, Cheng Y, Christensen K, Cifkova R, Ciullo M, Concas MP, Cook JP, Coresh J, Corre T, Sala CF, Cusi D, Danesh J, Daw EW, de Borst MH, De Grandi A, de Mutsert R, de Vries APJ, Degenhardt F, Delgado G, Demirkan A, Di Angelantonio E, Dittrich K, Divers J, Dorajoo R, Eckardt KU, Ehret G, Elliott P, Endlich K, Evans MK, Felix JF, Foo VHX, Franco OH, Franke A, Freedman BI, Freitag-Wolf S, Friedlander Y, Froguel P, Gansevoort RT, Gao H, Gasparini P, Gaziano JM, Giedraitis V, Gieger C, Girotto G, Giulianini F, Gögele M, Gordon SD, Gudbjartsson DF, Gudnason V, Haller T, Hamet P, Harris TB, Hartman CA, Hayward C, Hellwege JN, Heng CK, Hicks AA, Hofer E, Huang W, Hutri-Kähönen N, Hwang SJ, Ikram MA, Indridason OS, Ingelsson E, Ising M, Jaddoe VWV, Jakobsdottir J, Jonas JB, Joshi PK, Josyula NS, Jung B, Kähönen M, Kamatani Y, Kammerer CM, Kanai M, Kastarinen M, Kerr SM, Khor CC, Kiess W, Kleber ME, Koenig W, Kooner JS, Körner A, Kovacs P, Kraja AT, Krajcoviechova A, Kramer H, Krämer BK, Kronenberg F, Kubo M, Kühnel B, Kuokkanen M, Kuusisto J, La Bianca M, Laakso M, Lange LA, Langefeld CD, Lee JJM, Lehne B, Lehtimäki T, Lieb W, Lim SC, Lind L, Lindgren CM, Liu J, Liu J, Loeffler M, Loos RJF, Lucae S, Lukas MA, Lyytikäinen LP, Mägi R, Magnusson PKE, Mahajan A, Martin NG, Martins J, März W, Mascalzoni D, Matsuda K, Meisinger C, Meitinger T, Melander O, Metspalu A, Mikaelsdottir EK, Milaneschi Y, Miliku K, Mishra PP, Mohlke KL, Mononen N, Montgomery GW, Mook-Kanamori DO, Mychaleckyj JC, Nadkarni GN, Nalls MA, Nauck M, Nikus K, Ning B, Nolte IM, Noordam R, O'Connell J, O'Donoghue ML, Olafsson I, Oldehinkel AJ, Orho-Melander M, Ouwehand WH, Padmanabhan S, Palmer ND, Palsson R, Penninx BWJH, Perls T, Perola M, Pirastu M, Pirastu N, Pistis G, Podgornaia AI, Polasek O, Ponte B, Porteous DJ, Poulain T, Pramstaller PP, Preuss MH, Prins BP, Province MA, Rabelink TJ, Raffield LM, Raitakari OT, Reilly DF, Rettig R, Rheinberger M, Rice KM, Ridker PM, Rivadeneira F, Rizzi F, Roberts DJ, Robino A, Rossing P, Rudan I, Rueedi R, Ruggiero D, Ryan KA, Saba Y, Sabanayagam C, Salomaa V, Salvi E, Saum KU, Schmidt H, Schmidt R, Schöttker B, Schulz CA, Schupf N, Shaffer CM, Shi Y, Smith AV, Smith BH, Soranzo N, Spracklen CN, Strauch K, Stringham HM, Stumvoll M, Svensson PO, Szymczak S, Tai ES, Tajuddin SM, Tan NYQ, Taylor KD, Teren A, Tham YC, Thiery J, Thio CHL, Thomsen H, Thorleifsson G, Toniolo D, Tönjes A, Tremblay J, Tzoulaki I, Uitterlinden AG, Vaccargiu S, van Dam RM, van der Harst P, van Duijn CM, Velez Edward DR, Verweij N, Vogelezang S, Völker U, Vollenweider P, Waeber G, Waldenberger M, Wallentin L, Wang YX, Wang C, Waterworth DM, Bin Wei W, White H, Whitfield JB, Wild SH, Wilson JF, Wojczynski MK, Wong C, Wong TY, Xu L, Yang Q, Yasuda M, Yerges-Armstrong LM, Zhang W, Zonderman AB, Rotter JI, Bochud M, Psaty BM, Vitart V, Wilson JG, Dehghan A, Parsa A, Chasman DI, Ho K, Morris AP, Devuyst O, Akilesh S, Pendergrass SA, Sim X, Böger CA, Okada Y, Edwards TL, Snieder H, Stefansson K, Hung AM, Heid IM, Scholz M, Teumer A, Köttgen A, Pattaro C. A catalog of genetic loci associated with kidney function from analyses of a million individuals. Nat Genet 2019; 51:957-972. [PMID: 31152163 PMCID: PMC6698888 DOI: 10.1038/s41588-019-0407-x] [Citation(s) in RCA: 461] [Impact Index Per Article: 92.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/29/2019] [Indexed: 12/18/2022]
Abstract
Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through trans-ancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these, 147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
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Affiliation(s)
- Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Renal Division, Department of Medicine IV, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Man Li
- Division of Nephrology and Hypertension, Department of Medicine, University of Utah, Salt Lake City, USA
| | - Karsten B Sieber
- Target Sciences-Genetics, GlaxoSmithKline, Collegeville, PA, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Mathias Gorski
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, MD, USA
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Ayush Giri
- Division of Quantitative Sciences, Department of Obstetrics & Gynecology, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | | | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
| | - Teresa Nutile
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso'-CNR, Naples, Italy
| | - Christian Fuchsberger
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Massimiliano Cocca
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Yizhe Xu
- Division of Nephrology and Hypertension, Department of Medicine, University of Utah, Salt Lake City, USA
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Damia Noce
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sanaz Sedaghat
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Zhi Yu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Saima Afaq
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
- Institute of Public Health & Social Sciences, Khyber Medical University, Peshawar, Pakistan
| | | | - Peter Almgren
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clincial Sciences in Malmö, Lund University, Malmö, Sweden
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Johan Ärnlöv
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- School of Health and Social Studies, Dalarna University, Stockholm, Sweden
| | - Stephan J L Bakker
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | | | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Mathilde Boissel
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Erwin P Bottinger
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Digital Health Center, Hasso Plattner Institute and University of Potsdam, Potsdam, Germany
| | - Thibaud S Boutin
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Marco Brumat
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Ralph Burkhardt
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Eric Campana
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Archie Campbell
- Center for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Center for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Mickaël Canouil
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eulalia Catamo
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Miao-Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, Southern Denmark University, Odense, Denmark
| | - Renata Cifkova
- Center for Cardiovascular Prevention, Charles University in Prague, First Faculty of Medicine and Thomayer Hospital, Prague, Czech Republic
- Department of Medicine II, Charles University in Prague, First Faculty of Medicine, Prague, Czech Republic
| | - Marina Ciullo
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso'-CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tanguy Corre
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Daniele Cusi
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy
- Bio4Dreams-Business Nursery for Life Sciences, Milan, Italy
| | - John Danesh
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - E Warwick Daw
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Martin H de Borst
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alessandro De Grandi
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Aiko P J de Vries
- Section of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Graciela Delgado
- Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Emanuele Di Angelantonio
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Katalin Dittrich
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Center for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Jasmin Divers
- Public Health Sciences-Biostatistics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Kai-Uwe Eckardt
- Intensive Care Medicine, Charité, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Georg Ehret
- Cardiology, Geneva University Hospitals, Geneva, Switzerland
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College NIHR Biomedical Research Center, Imperial College London, London, UK
- Dementia Research Institute, Imperial College London, London, UK
- Health Data Research UK-London, London, UK
| | - Karlhans Endlich
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, US National Institutes of Health, Baltimore, MD, USA
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Valencia Hui Xian Foo
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Barry I Freedman
- Section on Nephrology, Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Yechiel Friedlander
- School of Public Health and Community Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Philippe Froguel
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - Ron T Gansevoort
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - He Gao
- Department of Epidemiology and Biostatistics, MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center, VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
| | - Vilmantas Giedraitis
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Giorgia Girotto
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Martin Gögele
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Toomas Haller
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pavel Hamet
- Montreal University Hospital Research Center, CHUM, Montreal, Quebec, Canada
- Medpharmgene, Montreal, Quebec, Canada
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, US National Institutes of Health, Bethesda, MD, USA
| | - Catharina A Hartman
- Interdisciplinary Center of Psychopathology and Emotion Regulation (ICPE), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jacklyn N Hellwege
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Andrew A Hicks
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai, China
- Shanghai Industrial Technology Institute, Shanghai, China
| | - Nina Hutri-Kähönen
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
- Department of Pediatrics, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Shih-Jen Hwang
- NHLBI's Framingham Heart Study, Framingham, MA, USA
- The Center for Population Studies, NHLBI, Framingham, MA, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Olafur S Indridason
- Division of Nephrology, Internal Medicine Services, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | - Erik Ingelsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Marcus Ising
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Peter K Joshi
- Center for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Navya Shilpa Josyula
- Geisinger Research, Biomedical and Translational Informatics Institute, Rockville, MD, USA
| | - Bettina Jung
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Candace M Kammerer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Masahiro Kanai
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Mika Kastarinen
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Chiea-Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Wieland Kiess
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Center for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Marcus E Kleber
- Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology and Biostatistics, University of Ulm, Ulm, Germany
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Antje Körner
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Center for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Integrated Research and Treatment Center Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Aldi T Kraja
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Alena Krajcoviechova
- Center for Cardiovascular Prevention, Charles University in Prague, First Faculty of Medicine and Thomayer Hospital, Prague, Czech Republic
- Department of Medicine II, Charles University in Prague, First Faculty of Medicine, Prague, Czech Republic
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
- Division of Nephrology and Hypertension, Loyola University Chicago, Chicago, IL, USA
| | - Bernhard K Krämer
- Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama (Kanagawa), Japan
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Mikko Kuokkanen
- The Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
| | - Johanna Kuusisto
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Martina La Bianca
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Markku Laakso
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, USA
| | - Carl D Langefeld
- Public Health Sciences-Biostatistics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jeannette Jen-Mai Lee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Kiel University, Kiel, Germany
| | - Su-Chi Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Diabetes Center, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Lars Lind
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Cecilia M Lindgren
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jun Liu
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Mary Ann Lukas
- Target Sciences-Genetics, GlaxoSmithKline, Albuquerque, NM, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anubha Mahajan
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, UK
- Oxford Center for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jade Martins
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Winfried März
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
- Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Deborah Mascalzoni
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Christa Meisinger
- Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Epidemiology, Ludwig- Maximilians-Universität München at UNIKA-T Augsburg, Augsburg, Germany
| | - Thomas Meitinger
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Olle Melander
- Hypertension and Cardiovascular Disease, Department of Clincial Sciences Malmö, Lund University, Malmö, Sweden
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Yuri Milaneschi
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Kozeta Miliku
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Charlottesville, VA, USA
| | - Girish N Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
| | - Boting Ning
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Michelle L O'Donoghue
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
- TIMI Study Group, Boston, MA, USA
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | - Albertine J Oldehinkel
- Interdisciplinary Center of Psychopathology and Emotion Regulation (ICPE), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marju Orho-Melander
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clincial Sciences in Malmö, Lund University, Malmö, Sweden
| | - Willem H Ouwehand
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | | | - Runolfur Palsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Division of Nephrology, Internal Medicine Services, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | - Brenda W J H Penninx
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Thomas Perls
- Department of Medicine, Geriatrics Section, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland
| | - Mario Pirastu
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Sassari, Li Punti, Sassari, Italy
| | - Nicola Pirastu
- Center for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Giorgio Pistis
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | | | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
- Gen-info Ltd, Zagreb, Croatia
| | - Belen Ponte
- Service de Néphrologie, Geneva University Hospitals, Geneva, Switzerland
| | - David J Porteous
- Center for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Center for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Tanja Poulain
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Peter P Pramstaller
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| | - Michael H Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bram P Prins
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ton J Rabelink
- Section of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory of Experimental Vascular Research, Leiden University Medical Center, Leiden, the Netherlands
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Center of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | | | - Rainer Rettig
- Institute of Physiology, University Medicine Greifswald, Karlsburg, Germany
| | - Myriam Rheinberger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Federica Rizzi
- Department of Health Sciences, University of Milan, Milano, Italy
- ePhood Scientific Unit, ePhood SRL, Milano, Italy
| | - David J Roberts
- NHS Blood and Transplant, BRC Oxford Haematology Theme; Nuffield Division of Clinical Laboratory Sciences; University of Oxford, Oxford, UK
| | - Antonietta Robino
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | | | - Igor Rudan
- Center for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso'-CNR, Naples, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Kathleen A Ryan
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yasaman Saba
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | | | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Erika Salvi
- Department of Health Sciences, University of Milan, Milano, Italy
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Kai-Uwe Saum
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Center for Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Christina-Alexandra Schulz
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clincial Sciences in Malmö, Lund University, Malmö, Sweden
| | - Nicole Schupf
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, USA
| | - Christian M Shaffer
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Albert V Smith
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | | | | | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Michael Stumvoll
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Per O Svensson
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
- Department of Cardiology, Södersjukhuset, Stockholm, Sweden
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Salman M Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, US National Institutes of Health, Baltimore, MD, USA
| | - Nicholas Y Q Tan
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Andrej Teren
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Heart Center Leipzig, Leipzig, Germany
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Joachim Thiery
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | - Anke Tönjes
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Johanne Tremblay
- Montreal University Hospital Research Center, CHUM, Montreal, Quebec, Canada
- CRCHUM, Montreal, Canada
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Simona Vaccargiu
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Sassari, Li Punti, Sassari, Italy
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Durrer Center for Cardiovascular Research, The Netherlands Heart Institute, Utrecht, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Digna R Velez Edward
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Department of Obstetrics and Gynecology, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Suzanne Vogelezang
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter Vollenweider
- Internal Medicine, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Gerard Waeber
- Internal Medicine, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Lars Wallentin
- Cardiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Chaolong Wang
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Wen Bin Wei
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Harvey White
- Green Lane Cardiovascular Service, Auckland City Hospital and University of Auckland, Auckland, New Zealand
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sarah H Wild
- Center for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Center for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Charlene Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Liang Xu
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Masayuki Yasuda
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | | | - Weihua Zhang
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- Department of Epidemiology and Biostatistics, MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, US National Institutes of Health, Baltimore, MD, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Murielle Bochud
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Service, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, MRC-PHE Center for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Afshin Parsa
- Division of Kidney, Urologic and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kevin Ho
- Kidney Health Research Institute (KHRI), Geisinger, Danville, PA, USA
- Department of Nephrology, Geisinger, Danville, PA, USA
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, UK
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Shreeram Akilesh
- Kidney Research Institute, University of Washington, Seattle, WA, USA
- Anatomic Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Sarah A Pendergrass
- Geisinger Research, Biomedical and Translational Informatics Institute, Danville, PA, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Nephrology and Rheumatology, Kliniken Südostbayern, Regensburg, Germany
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Osaka, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Todd L Edwards
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Adriana M Hung
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Medical Center, Division of Nephrology & Hypertension, Nashville, TN, USA
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy.
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Ge T, Chen CY, Ni Y, Feng YCA, Smoller JW. Polygenic prediction via Bayesian regression and continuous shrinkage priors. Nat Commun 2019; 10:1776. [PMID: 30992449 PMCID: PMC6467998 DOI: 10.1038/s41467-019-09718-5] [Citation(s) in RCA: 714] [Impact Index Per Article: 142.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/25/2019] [Indexed: 01/23/2023] Open
Abstract
Polygenic risk scores (PRS) have shown promise in predicting human complex traits and diseases. Here, we present PRS-CS, a polygenic prediction method that infers posterior effect sizes of single nucleotide polymorphisms (SNPs) using genome-wide association summary statistics and an external linkage disequilibrium (LD) reference panel. PRS-CS utilizes a high-dimensional Bayesian regression framework, and is distinct from previous work by placing a continuous shrinkage (CS) prior on SNP effect sizes, which is robust to varying genetic architectures, provides substantial computational advantages, and enables multivariate modeling of local LD patterns. Simulation studies using data from the UK Biobank show that PRS-CS outperforms existing methods across a wide range of genetic architectures, especially when the training sample size is large. We apply PRS-CS to predict six common complex diseases and six quantitative traits in the Partners HealthCare Biobank, and further demonstrate the improvement of PRS-CS in prediction accuracy over alternative methods.
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Affiliation(s)
- Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Chia-Yen Chen
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Yang Ni
- Department of Statistics, Texas A&M University, College Station, TX, 77843, USA
| | - Yen-Chen Anne Feng
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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Tardaguila M, Soranzo N. Resolving variant-to-function relationships in hematopoiesis. Nat Genet 2019; 51:581-583. [DOI: 10.1038/s41588-019-0386-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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121
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Ulirsch JC, Lareau CA, Bao EL, Ludwig LS, Guo MH, Benner C, Satpathy AT, Kartha VK, Salem RM, Hirschhorn JN, Finucane HK, Aryee MJ, Buenrostro JD, Sankaran VG. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet 2019; 51:683-693. [PMID: 30858613 PMCID: PMC6441389 DOI: 10.1038/s41588-019-0362-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 01/28/2019] [Indexed: 11/16/2022]
Abstract
Widespread linkage disequilibrium and incomplete annotation of cell-to-cell state variation represent substantial challenges to elucidating mechanisms of trait-associated genetic variation. Here, we perform genetic fine-mapping for blood cell traits in the UK Biobank to identify putative causal variants. These variants are enriched in genes encoding for proteins in trait-relevant biological pathways and in accessible chromatin of hematopoietic progenitors. For regulatory variants, we explore patterns of developmental enhancer activity, predict molecular mechanisms, and identify likely target genes. In several instances, we localize multiple independent variants to the same regulatory element or gene. We further observe that variants with pleiotropic effects preferentially act in common progenitor populations to direct the production of distinct lineages. Finally, we leverage fine-mapped variants in conjunction with continuous epigenomic annotations to identify trait-cell type enrichments within closely related populations and in single cells. Our study provides a comprehensive framework for single-variant and single-cell analyses of genetic associations. Fine mapping of blood cell traits in UK Biobank identifies putative causal variants and enrichment of fine-mapped variants in accessible chromatin of hematopoietic progenitor cells. The study provides an analytical framework for single-variant and single-cell analyses of genetic associations.
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Affiliation(s)
- Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Caleb A Lareau
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Leif S Ludwig
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael H Guo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Christian Benner
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vinay K Kartha
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Rany M Salem
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Schmidt Fellows Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
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Chaudhuri JP, Karamanov S, Scott L, Liehr T, Walther JU. Leukocyte Nucleus Reveals a Linear Order of Chromosomes Separated in Two Parental Genomes That Favors the Process of Gene Activation. J Histochem Cytochem 2019; 67:151-158. [PMID: 30452875 PMCID: PMC6393843 DOI: 10.1369/0022155418812879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/22/2018] [Indexed: 11/22/2022] Open
Abstract
Analysis of trisomy 8 cells and the chromosome-specific fluorescence in situ hybridization (FISH) signals on the ring-shaped nucleus of a neutrophil reveal that homologue chromosomes orient in diametrical opposition to each other. This positioning results in a separation of the two haploid sets of parental chromosomes organized as two exclusive groups. These two groups impart the nucleus a symmetry that fortifies immune protection by accelerating chemotaxis. The ring form of the nucleus is a legacy of the orientation of chromosomes as a rosette during metaphase and telophase stages. A dual control maintains this spatial order: (1) chromosomes are tethered to the centriole all through the cell cycle, and (2) during their circular orientation in telophase the chromosomes bind to each other with lamins, which reorganize the nuclear membrane of the daughter nuclei, generating an additional anchorage. Here, chromosomes serve as temporary packets to assure proper distribution of the nuclear DNA during mitosis. The remainder time of the cell cycle the chromosomes are chained together across the telomeres, allowing a continuous sequence of genes of the two genomes, maternal and paternal, thus facilitating easy reading of the gene sequence. Exceptions to these orders are either physiological and temporary, or pathological and disease causing.
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Affiliation(s)
- Jyoti P. Chaudhuri
- LMU Kinderpoliklinik, Tumorcytogenetic Unit, Munich, Germany
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
| | | | | | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
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Taylor K, Davey Smith G, Relton CL, Gaunt TR, Richardson TG. Prioritizing putative influential genes in cardiovascular disease susceptibility by applying tissue-specific Mendelian randomization. Genome Med 2019; 11:6. [PMID: 30704512 PMCID: PMC6354354 DOI: 10.1186/s13073-019-0613-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/08/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The extent to which changes in gene expression can influence cardiovascular disease risk across different tissue types has not yet been systematically explored. We have developed an analysis pipeline that integrates tissue-specific gene expression, Mendelian randomization and multiple-trait colocalization to develop functional mechanistic insight into the causal pathway from a genetic variant to a complex trait. METHODS We undertook an expression quantitative trait loci-wide association study to uncover genetic variants associated with both nearby gene expression and cardiovascular traits. Fine-mapping was performed to prioritize possible causal variants for detected associations. Two-sample Mendelian randomization (MR) was then applied using findings from genome-wide association studies (GWAS) to investigate whether changes in gene expression within certain tissue types may influence cardiovascular trait variation. We subsequently used Bayesian multiple-trait colocalization to further interrogate the findings and also gain insight into whether DNA methylation, as well as gene expression, may play a role in disease susceptibility. Finally, we applied our analysis pipeline genome-wide using summary statistics from large-scale GWAS. RESULTS Eight genetic loci were associated with changes in gene expression and measures of cardiovascular function. Our MR analysis provided evidence of tissue-specific effects at multiple loci, of which the effects at the ADCY3 and FADS1 loci for body mass index and cholesterol, respectively, were particularly insightful. Multiple-trait colocalization uncovered evidence which suggested that changes in DNA methylation at the promoter region upstream of FADS1/TMEM258 may also affect cardiovascular trait variation along with gene expression. Furthermore, colocalization analyses uncovered evidence of tissue specificity between gene expression in liver tissue and cholesterol levels. Applying our pipeline genome-wide using summary statistics from GWAS uncovered 233 association signals at loci which represent promising candidates for further evaluation. CONCLUSIONS Disease susceptibility can be influenced by differential changes in tissue-specific gene expression and DNA methylation. The approach undertaken in our study can be used to elucidate mechanisms in disease, as well as helping prioritize putative causal genes at associated loci where multiple nearby genes may be co-regulated. Future studies which continue to uncover quantitative trait loci for molecular traits across various tissue and cell types will further improve our capability to understand and prevent disease.
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Affiliation(s)
- Kurt Taylor
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- National Institute for Health Research Biomedical Research Centre, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- National Institute for Health Research Biomedical Research Centre, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- National Institute for Health Research Biomedical Research Centre, Bristol, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
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124
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Banerjee S, Zeng L, Schunkert H, Söding J. Bayesian multiple logistic regression for case-control GWAS. PLoS Genet 2018; 14:e1007856. [PMID: 30596640 PMCID: PMC6329526 DOI: 10.1371/journal.pgen.1007856] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 01/11/2019] [Accepted: 11/28/2018] [Indexed: 12/21/2022] Open
Abstract
Genetic variants in genome-wide association studies (GWAS) are tested for disease association mostly using simple regression, one variant at a time. Standard approaches to improve power in detecting disease-associated SNPs use multiple regression with Bayesian variable selection in which a sparsity-enforcing prior on effect sizes is used to avoid overtraining and all effect sizes are integrated out for posterior inference. For binary traits, the logistic model has not yielded clear improvements over the linear model. For multi-SNP analysis, the logistic model required costly and technically challenging MCMC sampling to perform the integration. Here, we introduce the quasi-Laplace approximation to solve the integral and avoid MCMC sampling. We expect the logistic model to perform much better than multiple linear regression except when predicted disease risks are spread closely around 0.5, because only close to its inflection point can the logistic function be well approximated by a linear function. Indeed, in extensive benchmarks with simulated phenotypes and real genotypes, our Bayesian multiple LOgistic REgression method (B-LORE) showed considerable improvements (1) when regressing on many variants in multiple loci at heritabilities ≥ 0.4 and (2) for unbalanced case-control ratios. B-LORE also enables meta-analysis by approximating the likelihood functions of individual studies by multivariate normal distributions, using their means and covariance matrices as summary statistics. Our work should make sparse multiple logistic regression attractive also for other applications with binary target variables. B-LORE is freely available from: https://github.com/soedinglab/b-lore.
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Affiliation(s)
- Saikat Banerjee
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | | | - Johannes Söding
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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Fonseca PADS, dos Santos FC, Lam S, Suárez-Vega A, Miglior F, Schenkel FS, Diniz LDAF, Id-Lahoucine S, Carvalho MRS, Cánovas A. Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results. J Anim Sci 2018; 96:4978-4999. [PMID: 30304443 PMCID: PMC6276581 DOI: 10.1093/jas/sky382] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022] Open
Abstract
Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency. Several genome-wide association studies (GWAS) have identified genomic regions associated with these fertility traits. The aims of this study were as follows: 1) to perform a systematic review of GWAS results for spermatic and testicular traits in cattle and 2) to identify key functional candidate genes for these traits. The identification of functional candidate genes was performed using a systems biology approach, where genes shared between traits and studies were evaluated by a guilt by association gene prioritization (GUILDify and ToppGene software) in order to identify the best functional candidates. These candidate genes were integrated and analyzed in order to identify overlapping patterns among traits and breeds. Results showed that GWAS for testicular-related traits have been developed for beef breeds only, whereas the majority of GWAS for spermatic-related traits were conducted using dairy breeds. When comparing traits measured within the same study, the highest number of genes shared between different traits was observed, indicating a high impact of the population genetic structure and environmental effects. Several chromosomal regions were enriched for functional candidate genes associated with fertility traits. Moreover, multiple functional candidate genes were enriched for markers in a species-specific basis, taurine (Bos taurus) or indicine (Bos indicus). For the different candidate regions identified in the GWAS in the literature, functional candidate genes were detected as follows: B. Taurus chromosome X (BTX) (TEX11, IRAK, CDK16, ATP7A, ATRX, HDAC6, FMR1, L1CAM, MECP2, etc.), BTA17 (TRPV4 and DYNLL1), and BTA14 (MOS, FABP5, ZFPM2). These genes are responsible for regulating important metabolic pathways or biological processes associated with fertility, such as progression of spermatogenesis, control of ciliary activity, development of Sertoli cells, DNA integrity in spermatozoa, and homeostasis of testicular cells. This study represents the first systematic review on male fertility traits in cattle using a system biology approach to identify key candidate genes for these traits.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Stephanie Lam
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Aroa Suárez-Vega
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Filippo Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Samir Id-Lahoucine
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
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Giambartolomei C, Zhenli Liu J, Zhang W, Hauberg M, Shi H, Boocock J, Pickrell J, Jaffe AE, Pasaniuc B, Roussos P. A Bayesian framework for multiple trait colocalization from summary association statistics. Bioinformatics 2018; 34:2538-2545. [PMID: 29579179 PMCID: PMC6061859 DOI: 10.1093/bioinformatics/bty147] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 02/13/2018] [Accepted: 03/08/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation Most genetic variants implicated in complex diseases by genome-wide association studies (GWAS) are non-coding, making it challenging to understand the causative genes involved in disease. Integrating external information such as quantitative trait locus (QTL) mapping of molecular traits (e.g. expression, methylation) is a powerful approach to identify the subset of GWAS signals explained by regulatory effects. In particular, expression QTLs (eQTLs) help pinpoint the responsible gene among the GWAS regions that harbor many genes, while methylation QTLs (mQTLs) help identify the epigenetic mechanisms that impact gene expression which in turn affect disease risk. In this work, we propose multiple-trait-coloc (moloc), a Bayesian statistical framework that integrates GWAS summary data with multiple molecular QTL data to identify regulatory effects at GWAS risk loci. Results We applied moloc to schizophrenia (SCZ) and eQTL/mQTL data derived from human brain tissue and identified 52 candidate genes that influence SCZ through methylation. Our method can be applied to any GWAS and relevant functional data to help prioritize disease associated genes. Availability and implementation: moloc is available for download as an R package (https://github.com/clagiamba/moloc). We also developed a web site to visualize the biological findings (icahn.mssm.edu/moloc). The browser allows searches by gene, methylation probe and scenario of interest. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jimmy Zhenli Liu
- New York Genome Center, New York, NY, USA
- Department of Computational Biology and Genomics, Biogen, Cambridge, MA, USA
| | - Wen Zhang
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mads Hauberg
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Biomedicine, The Lundbeck Foundation Initiative of Integrative Psychiatric Research (iPSYCH), Aarhus University, Aarhus, Denmark
| | - Huwenbo Shi
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - James Boocock
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Andrew E Jaffe
- Departments of Mental Health and Biostatistics, Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Panos Roussos
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
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Schaid DJ, Chen W, Larson NB. From genome-wide associations to candidate causal variants by statistical fine-mapping. Nat Rev Genet 2018; 19:491-504. [PMID: 29844615 PMCID: PMC6050137 DOI: 10.1038/s41576-018-0016-z] [Citation(s) in RCA: 475] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advancing from statistical associations of complex traits with genetic markers to understanding the functional genetic variants that influence traits is often a complex process. Fine-mapping can select and prioritize genetic variants for further study, yet the multitude of analytical strategies and study designs makes it challenging to choose an optimal approach. We review the strengths and weaknesses of different fine-mapping approaches, emphasizing the main factors that affect performance. Topics include interpreting results from genome-wide association studies (GWAS), the role of linkage disequilibrium, statistical fine-mapping approaches, trans-ethnic studies, genomic annotation and data integration, and other analysis and design issues.
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Affiliation(s)
- Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.
| | - Wenan Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicholas B Larson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
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128
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Abstract
It is useful to detect allelic heterogeneity (AH), i.e., the presence of multiple causal SNPs in a locus, which, for example, may guide the development of new methods for fine mapping and determine how to interpret an appearing epistasis. In contrast to Mendelian traits, the existence and extent of AH for complex traits had been largely unknown until Hormozdiari et al. proposed a Bayesian method, called causal variants identification in associated regions (CAVIAR), and uncovered widespread AH in complex traits. However, there are several limitations with CAVIAR. First, it assumes a maximum number of causal SNPs in a locus, typically up to six, to save computing time; this assumption, as will be shown, may influence the outcome. Second, its computational time can be too demanding to be feasible since it examines all possible combinations of causal SNPs (under the assumed upper bound). Finally, it outputs a posterior probability of AH, which may be difficult to calibrate with a commonly used nominal significance level. Here, we introduce an intersection-union test (IUT) based on a joint/conditional regression model with all the SNPs in a locus to infer AH. We also propose two sequential IUT-based testing procedures to estimate the number of causal SNPs. Our proposed methods are applicable to not only individual-level genotypic and phenotypic data, but also genome-wide association study (GWAS) summary statistics. We provide numerical examples based on both simulated and real data, including large-scale schizophrenia (SCZ) and high-density lipoprotein (HDL) GWAS summary data sets, to demonstrate the effectiveness of the new methods. In particular, for both the SCZ and HDL data, our proposed IUT not only was faster, but also detected more AH loci than CAVIAR. Our proposed methods are expected to be useful in further uncovering the extent of AH in complex traits.
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129
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Inshaw JRJ, Cutler AJ, Burren OS, Stefana MI, Todd JA. Approaches and advances in the genetic causes of autoimmune disease and their implications. Nat Immunol 2018; 19:674-684. [PMID: 29925982 DOI: 10.1038/s41590-018-0129-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/04/2018] [Indexed: 12/18/2022]
Abstract
Genome-wide association studies are transformative in revealing the polygenetic basis of common diseases, with autoimmune diseases leading the charge. Although the field is just over 10 years old, advances in understanding the underlying mechanistic pathways of these conditions, which result from a dense multifactorial blend of genetic, developmental and environmental factors, have already been informative, including insights into therapeutic possibilities. Nevertheless, the challenge of identifying the actual causal genes and pathways and their biological effects on altering disease risk remains for many identified susceptibility regions. It is this fundamental knowledge that will underpin the revolution in patient stratification, the discovery of therapeutic targets and clinical trial design in the next 20 years. Here we outline recent advances in analytical and phenotyping approaches and the emergence of large cohorts with standardized gene-expression data and other phenotypic data that are fueling a bounty of discovery and improved understanding of human physiology.
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Affiliation(s)
- Jamie R J Inshaw
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Antony J Cutler
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Oliver S Burren
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - M Irina Stefana
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
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130
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Deng Y, Pan W. Improved Use of Small Reference Panels for Conditional and Joint Analysis with GWAS Summary Statistics. Genetics 2018; 209:401-408. [PMID: 29674520 PMCID: PMC5972416 DOI: 10.1534/genetics.118.300813] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/04/2018] [Indexed: 02/08/2023] Open
Abstract
Due to issues of practicality and confidentiality of genomic data sharing on a large scale, typically only meta- or mega-analyzed genome-wide association study (GWAS) summary data, not individual-level data, are publicly available. Reanalyses of such GWAS summary data for a wide range of applications have become more and more common and useful, which often require the use of an external reference panel with individual-level genotypic data to infer linkage disequilibrium (LD) among genetic variants. However, with a small sample size in only hundreds, as for the most popular 1000 Genomes Project European sample, estimation errors for LD are not negligible, leading to often dramatically increased numbers of false positives in subsequent analyses of GWAS summary data. To alleviate the problem in the context of association testing for a group of SNPs, we propose an alternative estimator of the covariance matrix with an idea similar to multiple imputation. We use numerical examples based on both simulated and real data to demonstrate the severe problem with the use of the 1000 Genomes Project reference panels, and the improved performance of our new approach.
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Affiliation(s)
- Yangqing Deng
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Wei Pan
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota 55455
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Sazonovs A, Barrett JC. Rare-Variant Studies to Complement Genome-Wide Association Studies. Annu Rev Genomics Hum Genet 2018; 19:97-112. [PMID: 29801418 DOI: 10.1146/annurev-genom-083117-021641] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome-wide association studies (GWASs) have revolutionized human disease genetics by discovering tens of thousands of associations between common variants and complex diseases. In parallel, huge technological advances in DNA sequencing have made it possible to measure and analyze rare variation in populations. This review considers these two stories and how they have come together. We first review the history of GWASs and sequencing. We then consider how to understand the biological mechanisms that drive signals of strong association in the absence of rare-variant studies. We describe how rare-variant studies complement these approaches and highlight both data generation and statistical challenges in their interpretation. Finally, we consider how certain special study designs, such as those for families and isolated populations, fit in this paradigm.
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Affiliation(s)
- A Sazonovs
- Wellcome Sanger Institute, Cambridge CB10 1HH, United Kingdom;
| | - J C Barrett
- Wellcome Sanger Institute, Cambridge CB10 1HH, United Kingdom;
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