publication . Article . Other literature type . 2018

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation.

Farhad Hormozdiari; Farhad Hormozdiari; Ayellet V. Segrè; Ayellet V. Segrè; Halit Ongen; Halit Ongen; Dan L. Nicolae; Nancy J. Cox; Anuar Konkashbaev; Hualin S. Xi; ...
Open Access English
  • Published: 28 Jun 2018 Journal: Nature Genetics, volume 50, issue 7 (issn: 1061-4036, eissn: 1546-1718, Copyright policy)
Abstract
National Institutes of Health (U.S.) (Contract HHSN268201000029C)
Subjects
free text keywords: Genetics, Article, Heritability, Expression quantitative trait loci, Locus (genetics), Genome-wide association study, Trait, Linkage disequilibrium, Biology, Regulation of gene expression, Functional genomics, ddc:576.5, ddc:590, ddc:025.063/570
Funded by
NIH| Automated Storage and Retrieval of Biological Systems
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1S10RR025141-01
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
,
NIH| Genetic Susceptibility and Biomarkers of Platinum-related Toxicities
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01CA157823-01A1
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Discovering Biology for Neuropsychiatric Diseases Through Omics Studies on Comorbidities
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3R01MH113362-02S1
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
,
NIH| VESPA: Vanderbilt Electronic Systems for Pharmacogenomic Assessment
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5RC2GM092618-02
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| Computational and statistical models for human genetics
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG007022-04
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
57 references, page 1 of 4

The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013; 45: 580-5 [OpenAIRE] [PubMed]

Genetic effects on gene expression across human tissues. Nature. 2017; 550: 204-213 [OpenAIRE] [PubMed]

Ongen, H, Buil, A, Brown, AA, Dermitzakis, ET, Delaneau, O. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics. 2016; 32: 1479-85 [OpenAIRE] [PubMed]

Han, B, Eskin, E. Random-effects model aimed at discovering associations in meta-analysis of genome-wide association studies. Am J Hum Genet. 2011; 88: 586-98 [OpenAIRE] [PubMed]

Sudlow, C. UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med. 2015; 12 [OpenAIRE]

Denny, JC. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat Biotechnol. 2013; 31: 1102-10 [OpenAIRE] [PubMed]

Wood, AR. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet. 2014; 46: 1173-86 [OpenAIRE] [PubMed]

Dupuis, J. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet. 2010; 42: 105-16 [OpenAIRE] [PubMed]

Wen, X. Molecular QTL Discovery Incorporating Genomic Annotations using Bayesian False Discovery Rate Control. Annals of Applied Statistics. 2016

Wen, X, Lee, Y, Luca, F, Pique-Regi, R. Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. Am J Hum Genet. 2016; 98: 1114-29 [OpenAIRE] [PubMed]

Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015; 348: 648-60 [OpenAIRE] [PubMed]

Pandey, GK. The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. Cancer Cell. 2014; 26: 722-37 [PubMed]

Nica, AC. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet. 2010; 6: e1000895 [OpenAIRE] [PubMed]

Ongen, H. Estimating the causal tissues for complex traits and diseases. Nat Genet. 2017; 49: 1676-1683 [OpenAIRE] [PubMed]

Hormozdiari, F. Colocalization of GWAS and eQTL Signals Detects Target Genes. Am J Hum Genet. 2016; 99: 1245-1260 [OpenAIRE] [PubMed]

57 references, page 1 of 4
Abstract
National Institutes of Health (U.S.) (Contract HHSN268201000029C)
Subjects
free text keywords: Genetics, Article, Heritability, Expression quantitative trait loci, Locus (genetics), Genome-wide association study, Trait, Linkage disequilibrium, Biology, Regulation of gene expression, Functional genomics, ddc:576.5, ddc:590, ddc:025.063/570
Funded by
NIH| Automated Storage and Retrieval of Biological Systems
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1S10RR025141-01
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
,
NIH| Genetic Susceptibility and Biomarkers of Platinum-related Toxicities
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01CA157823-01A1
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Discovering Biology for Neuropsychiatric Diseases Through Omics Studies on Comorbidities
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3R01MH113362-02S1
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
,
NIH| VESPA: Vanderbilt Electronic Systems for Pharmacogenomic Assessment
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5RC2GM092618-02
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| Computational and statistical models for human genetics
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG007022-04
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
57 references, page 1 of 4

The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013; 45: 580-5 [OpenAIRE] [PubMed]

Genetic effects on gene expression across human tissues. Nature. 2017; 550: 204-213 [OpenAIRE] [PubMed]

Ongen, H, Buil, A, Brown, AA, Dermitzakis, ET, Delaneau, O. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics. 2016; 32: 1479-85 [OpenAIRE] [PubMed]

Han, B, Eskin, E. Random-effects model aimed at discovering associations in meta-analysis of genome-wide association studies. Am J Hum Genet. 2011; 88: 586-98 [OpenAIRE] [PubMed]

Sudlow, C. UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med. 2015; 12 [OpenAIRE]

Denny, JC. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat Biotechnol. 2013; 31: 1102-10 [OpenAIRE] [PubMed]

Wood, AR. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet. 2014; 46: 1173-86 [OpenAIRE] [PubMed]

Dupuis, J. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet. 2010; 42: 105-16 [OpenAIRE] [PubMed]

Wen, X. Molecular QTL Discovery Incorporating Genomic Annotations using Bayesian False Discovery Rate Control. Annals of Applied Statistics. 2016

Wen, X, Lee, Y, Luca, F, Pique-Regi, R. Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. Am J Hum Genet. 2016; 98: 1114-29 [OpenAIRE] [PubMed]

Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015; 348: 648-60 [OpenAIRE] [PubMed]

Pandey, GK. The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. Cancer Cell. 2014; 26: 722-37 [PubMed]

Nica, AC. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet. 2010; 6: e1000895 [OpenAIRE] [PubMed]

Ongen, H. Estimating the causal tissues for complex traits and diseases. Nat Genet. 2017; 49: 1676-1683 [OpenAIRE] [PubMed]

Hormozdiari, F. Colocalization of GWAS and eQTL Signals Detects Target Genes. Am J Hum Genet. 2016; 99: 1245-1260 [OpenAIRE] [PubMed]

57 references, page 1 of 4
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