1
|
Adkins AE, Hack LM, Bigdeli TB, Williamson VS, McMichael GO, Mamdani M, Edwards AC, Aliev F, Chan RF, Bhandari P, Raabe RC, Alaimo JT, Blackwell GG, Moscati A, Poland RS, Rood B, Patterson DG, Walsh D, Whitfield JB, Zhu G, Montgomery GW, Henders AK, Martin NG, Heath AC, Madden PAF, Frank J, Ridinger M, Wodarz N, Soyka M, Zill P, Ising M, Nöthen MM, Kiefer F, Rietschel M, Gelernter J, Sherva R, Koesterer R, Almasy L, Zhao H, Kranzler HR, Farrer LA, Maher BS, Prescott CA, Dick DM, Bacanu SA, Mathies LD, Davies AG, Vladimirov VI, Grotewiel M, Bowers MS, Bettinger JC, Webb BT, Miles MF, Kendler KS, Riley BP. Genomewide Association Study of Alcohol Dependence Identifies Risk Loci Altering Ethanol-Response Behaviors in Model Organisms. Alcohol Clin Exp Res 2017; 41:911-928. [PMID: 28226201 DOI: 10.1111/acer.13362] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 02/16/2017] [Indexed: 01/23/2023]
Abstract
BACKGROUND Alcohol dependence (AD) shows evidence for genetic liability, but genes influencing risk remain largely unidentified. METHODS We conducted a genomewide association study in 706 related AD cases and 1,748 unscreened population controls from Ireland. We sought replication in 15,496 samples of European descent. We used model organisms (MOs) to assess the role of orthologous genes in ethanol (EtOH)-response behaviors. We tested 1 primate-specific gene for expression differences in case/control postmortem brain tissue. RESULTS We detected significant association in COL6A3 and suggestive association in 2 previously implicated loci, KLF12 and RYR3. None of these signals are significant in replication. A suggestive signal in the long noncoding RNA LOC339975 is significant in case:control meta-analysis, but not in a population sample. Knockdown of a COL6A3 ortholog in Caenorhabditis elegans reduced EtOH sensitivity. Col6a3 expression correlated with handling-induced convulsions in mice. Loss of function of the KLF12 ortholog in C. elegans impaired development of acute functional tolerance (AFT). Klf12 expression correlated with locomotor activation following EtOH injection in mice. Loss of function of the RYR3 ortholog reduced EtOH sensitivity in C. elegans and rapid tolerance in Drosophila. The ryanodine receptor antagonist dantrolene reduced motivation to self-administer EtOH in rats. Expression of LOC339975 does not differ between cases and controls but is reduced in carriers of the associated rs11726136 allele in nucleus accumbens (NAc). CONCLUSIONS We detect association between AD and COL6A3, KLF12, RYR3, and LOC339975. Despite nonreplication of COL6A3, KLF12, and RYR3 signals, orthologs of these genes influence behavioral response to EtOH in MOs, suggesting potential involvement in human EtOH response and AD liability. The associated LOC339975 allele may influence gene expression in human NAc. Although the functions of long noncoding RNAs are poorly understood, there is mounting evidence implicating these genes in multiple brain functions and disorders.
Collapse
Affiliation(s)
- Amy E Adkins
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Laura M Hack
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Tim B Bigdeli
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Vernell S Williamson
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - G Omari McMichael
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Mohammed Mamdani
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Alexis C Edwards
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Fazil Aliev
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Robin F Chan
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Poonam Bhandari
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Richard C Raabe
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Joseph T Alaimo
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - GinaMari G Blackwell
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Arden Moscati
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Ryan S Poland
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Benjamin Rood
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | | | | | | | - John B Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Gu Zhu
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Grant W Montgomery
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Anjali K Henders
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Monika Ridinger
- Department of Psychiatry, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Norbert Wodarz
- Department of Psychiatry, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Michael Soyka
- Privatklinik Meiringen, Meiringen, Switzerland.,Department of Psychiatry and Psychotherapy, University of Munich, Munich, Germany
| | - Peter Zill
- Department of Psychiatry and Psychotherapy, University of Munich, Munich, Germany
| | - Marcus Ising
- Department of Molecular Psychology, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | | | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.,Department of Neurobiology, Yale University School of Medicine, New Haven, Connecticut.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,Department of Psychiatry, VA CT Healthcare Center, West Haven, Connecticut
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
| | - Ryan Koesterer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
| | - Laura Almasy
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,Department of Biostatistics, Yale University School of Medicine, New Haven, Connecticut
| | - Henry R Kranzler
- Department of Psychiatry, Treatment Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Philadelphia VA Medical Center, VISN 4 MIRECC, Philadelphia, Pennsylvania
| | - Lindsay A Farrer
- Department of Psychiatry, VA CT Healthcare Center, West Haven, Connecticut.,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts.,Department of Neurology, Boston University School of Medicine, Boston, Massachusetts.,Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts.,Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts.,Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Brion S Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Carol A Prescott
- Department of Psychology, University of Southern California, Los Angeles, California
| | - Danielle M Dick
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Silviu A Bacanu
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Laura D Mathies
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Andrew G Davies
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Vladimir I Vladimirov
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, Maryland.,Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Mike Grotewiel
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - M Scott Bowers
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Jill C Bettinger
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Bradley T Webb
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Michael F Miles
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia.,Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Kenneth S Kendler
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Brien P Riley
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| |
Collapse
|
2
|
Webb BT, Edwards AC, Wolen AR, Salvatore JE, Aliev F, Riley BP, Sun C, Williamson VS, Kitchens JN, Pedersen K, Adkins A, Cooke ME, Savage JE, Neale Z, Cho SB, Dick DM, Kendler KS. Molecular Genetic Influences on Normative and Problematic Alcohol Use in a Population-Based Sample of College Students. Front Genet 2017; 8:30. [PMID: 28360924 PMCID: PMC5350109 DOI: 10.3389/fgene.2017.00030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
Background: Genetic factors impact alcohol use behaviors and these factors may become increasingly evident during emerging adulthood. Examination of the effects of individual variants as well as aggregate genetic variation can clarify mechanisms underlying risk. Methods: We conducted genome-wide association studies (GWAS) in an ethnically diverse sample of college students for three quantitative outcomes including typical monthly alcohol consumption, alcohol problems, and maximum number of drinks in 24 h. Heritability based on common genetic variants (h2SNP) was assessed. We also evaluated whether risk variants in aggregate were associated with alcohol use outcomes in an independent sample of young adults. Results: Two genome-wide significant markers were observed: rs11201929 in GRID1 for maximum drinks in 24 h, with supportive evidence across all ancestry groups; and rs73317305 in SAMD12 (alcohol problems), tested only in the African ancestry group. The h2SNP estimate was 0.19 (SE = 0.11) for consumption, and was non-significant for other outcomes. Genome-wide polygenic scores were significantly associated with alcohol outcomes in an independent sample. Conclusions: These results robustly identify genetic risk for alcohol use outcomes at the variant level and in aggregate. We confirm prior evidence that genetic variation in GRID1 impacts alcohol use, and identify novel loci of interest for multiple alcohol outcomes in emerging adults. These findings indicate that genetic variation influencing normative and problematic alcohol use is, to some extent, convergent across ancestry groups. Studying college populations represents a promising avenue by which to obtain large, diverse samples for gene identification.
Collapse
Affiliation(s)
- Bradley T Webb
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Psychiatry, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Human and Molecular Genetics, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Alexis C Edwards
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Psychiatry, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Aaron R Wolen
- Center for Clinical and Translational Research, Virginia Commonwealth University Richmond, VA, USA
| | - Jessica E Salvatore
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Psychology, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Fazil Aliev
- Department of African-American Studies, Virginia Commonwealth UniversityRichmond, VA, USA; Faculty of Business, Karabuk UniversityKarabuk, Turkey; College Behavioral and Emotional Health Institute, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Brien P Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Psychiatry, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Human and Molecular Genetics, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Cuie Sun
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Psychiatry, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Vernell S Williamson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University Richmond, VA, USA
| | - James N Kitchens
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University Richmond, VA, USA
| | - Kimberly Pedersen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Psychiatry, Virginia Commonwealth UniversityRichmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Amy Adkins
- Department of Psychology, Virginia Commonwealth UniversityRichmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Megan E Cooke
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Jeanne E Savage
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Zoe Neale
- Department of Psychology, Virginia Commonwealth UniversityRichmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Seung B Cho
- Department of Psychology, Virginia Commonwealth UniversityRichmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Danielle M Dick
- Department of Human and Molecular Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Psychology, Virginia Commonwealth UniversityRichmond, VA, USA; Department of African-American Studies, Virginia Commonwealth UniversityRichmond, VA, USA; College Behavioral and Emotional Health Institute, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmond, VA, USA; Department of Psychiatry, Virginia Commonwealth UniversityRichmond, VA, USA
| |
Collapse
|
4
|
Lee D, Bigdeli TB, Williamson VS, Vladimirov VI, Riley BP, Fanous AH, Bacanu SA. DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts. Bioinformatics 2015; 31:3099-104. [PMID: 26059716 PMCID: PMC4576696 DOI: 10.1093/bioinformatics/btv348] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 05/29/2015] [Indexed: 01/09/2023] Open
Abstract
Motivation: To increase the signal resolution for large-scale meta-analyses of genome-wide association studies, genotypes at unmeasured single nucleotide polymorphisms (SNPs) are commonly imputed using large multi-ethnic reference panels. However, the ever increasing size and ethnic diversity of both reference panels and cohorts makes genotype imputation computationally challenging for moderately sized computer clusters. Moreover, genotype imputation requires subject-level genetic data, which unlike summary statistics provided by virtually all studies, is not publicly available. While there are much less demanding methods which avoid the genotype imputation step by directly imputing SNP statistics, e.g. Directly Imputing summary STatistics (DIST) proposed by our group, their implicit assumptions make them applicable only to ethnically homogeneous cohorts. Results: To decrease computational and access requirements for the analysis of cosmopolitan cohorts, we propose DISTMIX, which extends DIST capabilities to the analysis of mixed ethnicity cohorts. The method uses a relevant reference panel to directly impute unmeasured SNP statistics based only on statistics at measured SNPs and estimated/user-specified ethnic proportions. Simulations show that the proposed method adequately controls the Type I error rates. The 1000 Genomes panel imputation of summary statistics from the ethnically diverse Psychiatric Genetic Consortium Schizophrenia Phase 2 suggests that, when compared to genotype imputation methods, DISTMIX offers comparable imputation accuracy for only a fraction of computational resources. Availability and implementation: DISTMIX software, its reference population data, and usage examples are publicly available at http://code.google.com/p/distmix. Contact:dlee4@vcu.edu Supplementary information:Supplementary Data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Donghyung Lee
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA, Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - T Bernard Bigdeli
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Vernell S Williamson
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Vladimir I Vladimirov
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Brien P Riley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ayman H Fanous
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Silviu-Alin Bacanu
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| |
Collapse
|
5
|
Lee D, Williamson VS, Bigdeli TB, Riley BP, Fanous AH, Vladimirov VI, Bacanu SA. JEPEG: a summary statistics based tool for gene-level joint testing of functional variants. ACTA ACUST UNITED AC 2014; 31:1176-82. [PMID: 25505091 PMCID: PMC4393522 DOI: 10.1093/bioinformatics/btu816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 12/07/2014] [Indexed: 01/03/2023]
Abstract
MOTIVATION Gene expression is influenced by variants commonly known as expression quantitative trait loci (eQTL). On the basis of this fact, researchers proposed to use eQTL/functional information univariately for prioritizing single nucleotide polymorphisms (SNPs) signals from genome-wide association studies (GWAS). However, most genes are influenced by multiple eQTLs which, thus, jointly affect any downstream phenotype. Therefore, when compared with the univariate prioritization approach, a joint modeling of eQTL action on phenotypes has the potential to substantially increase signal detection power. Nonetheless, a joint eQTL analysis is impeded by (i) not measuring all eQTLs in a gene and/or (ii) lack of access to individual genotypes. RESULTS We propose joint effect on phenotype of eQTL/functional SNPs associated with a gene (JEPEG), a novel software tool which uses only GWAS summary statistics to (i) impute the summary statistics at unmeasured eQTLs and (ii) test for the joint effect of all measured and imputed eQTLs in a gene. We illustrate the behavior/performance of the developed tool by analysing the GWAS meta-analysis summary statistics from the Psychiatric Genomics Consortium Stage 1 and the Genetic Consortium for Anorexia Nervosa. CONCLUSIONS Applied analyses results suggest that JEPEG complements commonly used univariate GWAS tools by: (i) increasing signal detection power via uncovering (a) novel genes or (b) known associated genes in smaller cohorts and (ii) assisting in fine-mapping of challenging regions, e.g. major histocompatibility complex for schizophrenia. AVAILABILITY AND IMPLEMENTATION JEPEG, its associated database of eQTL SNPs and usage examples are publicly available at http://code.google.com/p/jepeg/. CONTACT dlee4@vcu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Donghyung Lee
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Vernell S Williamson
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| | - T Bernard Bigdeli
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Brien P Riley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ayman H Fanous
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Vladimir I Vladimirov
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Silviu-Alin Bacanu
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Center for Biomarker Research & Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA and Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| |
Collapse
|