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Bager CL, Blair JPM, Tang MHE, Mortensen JH, Bay-Jensen AC, Frederiksen P, Leeming D, Christiansen C, Karsdal MA. Citrullinated and MMP-degraded vimentin is associated with chronic pulmonary diseases and genetic variants in PADI3/PADI4 and CFH in postmenopausal women. Sci Rep 2023; 13:23039. [PMID: 38155185 PMCID: PMC10754934 DOI: 10.1038/s41598-023-50313-y] [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: 01/03/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Citrullinated vimentin has been linked to several chronic and autoimmune diseases, but how citrullinated vimentin is associated with disease prevalence and genetic variants in a clinical setting remains unknown. The aim of this study was to obtain a better understanding of the genetic variants and pathologies associated with citrullinated and MMP-degraded vimentin. Patient Registry data, serum samples and genotypes were collected for a total of 4369 Danish post-menopausal women enrolled in the Prospective Epidemiologic and Risk Factor study (PERF). Circulating citrullinated and MMP-degraded vimentin (VICM) was measured. Genome-wide association studies (GWAS) and phenome wide association studies (PheWAS) with levels of VICM were performed. High levels of VICM were significantly associated with the prevalence of chronic pulmonary diseases and death from respiratory and cardiovascular diseases (CVD). GWAS identified 33 single nucleotide polymorphisms (SNPs) with a significant association with VICM. These variants were in the peptidylarginine deiminase 3/4 (PADI3/PADI4) and Complement Factor H (CFH)/KCNT2 gene loci on chromosome 1. Serum levels of VICM, a marker of citrullinated and MMP-degraded vimentin, were associated with chronic pulmonary diseases and genetic variance in PADI3/PADI4 and CFH/ KCNT2. This points to the potential for VICM to be used as an activity marker of both citrullination and inflammation, identifying responders to targeted treatment and patients likely to experience disease progression.
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Affiliation(s)
- Cecilie Liv Bager
- Nordic Bioscience, Biomarkers and Research, Hovedgade 205-207, 2730, Herlev, Denmark.
| | - Joseph P M Blair
- Nordic Bioscience, Biomarkers and Research, Hovedgade 205-207, 2730, Herlev, Denmark
| | - Man-Hung Eric Tang
- Nordic Bioscience, Biomarkers and Research, Hovedgade 205-207, 2730, Herlev, Denmark
| | - Joachim Høg Mortensen
- Nordic Bioscience, Biomarkers and Research, Hovedgade 205-207, 2730, Herlev, Denmark
| | | | - Peder Frederiksen
- Nordic Bioscience, Biomarkers and Research, Hovedgade 205-207, 2730, Herlev, Denmark
| | - Diana Leeming
- Nordic Bioscience, Biomarkers and Research, Hovedgade 205-207, 2730, Herlev, Denmark
| | - Claus Christiansen
- Nordic Bioscience, Biomarkers and Research, Hovedgade 205-207, 2730, Herlev, Denmark
| | - Morten Asser Karsdal
- Nordic Bioscience, Biomarkers and Research, Hovedgade 205-207, 2730, Herlev, Denmark
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Waksmunski AR, Grunin M, Kinzy TG, Igo RP, Haines JL, Cooke Bailey JN. Statistical driver genes as a means to uncover missing heritability for age-related macular degeneration. BMC Med Genomics 2020; 13:95. [PMID: 32631374 PMCID: PMC7336430 DOI: 10.1186/s12920-020-00747-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/22/2020] [Indexed: 11/26/2022] Open
Abstract
Background Age-related macular degeneration (AMD) is a progressive retinal disease contributing to blindness worldwide. Multiple estimates for AMD heritability (h2) exist; however, a substantial proportion of h2 is not attributable to known genomic loci. The International AMD Genomics Consortium (IAMDGC) gathered the largest dataset of advanced AMD (ADV) cases and controls available and identified 34 loci containing 52 independent risk variants defining known AMD h2. To better define AMD heterogeneity, we used Pathway Analysis by Randomization Incorporating Structure (PARIS) on the IAMDGC data and identified 8 statistical driver genes (SDGs), including 2 novel SDGs not discovered by the IAMDGC. We chose to further investigate these pathway-based risk genes and determine their contribution to ADV h2, as well as the differential ADV subtype h2. Methods We performed genomic-relatedness-based restricted maximum-likelihood (GREML) analyses on ADV, geographic atrophy (GA), and choroidal neovascularization (CNV) subtypes to investigate the h2 of genotyped variants on the full DNA array chip, 34 risk loci (n = 2758 common variants), 52 variants from the IAMDGC 2016 GWAS, and the 8 SDGs, specifically the novel 2 SDGs, PPARA and PLCG2. Results Via GREML, full chip h2 was 44.05% for ADV, 46.37% for GA, and 62.03% for CNV. The lead 52 variants’ h2 (ADV: 14.52%, GA: 8.02%, CNV: 13.62%) and 34 loci h2 (ADV: 13.73%, GA: 8.81%, CNV: 12.89%) indicate that known variants contribute ~ 14% to ADV h2. SDG variants account for a small percentage of ADV, GA, and CNV heritability, but estimates based on the combination of SDGs and the 34 known loci are similar to those calculated for known loci alone. We identified modest epistatic interactions among variants in the 2 SDGs and the 52 IAMDGC variants, including modest interactions between variants in PPARA and PLCG2. Conclusions Pathway analyses, which leverage biological relationships among genes in a pathway, may be useful in identifying additional loci that contribute to the heritability of complex disorders in a non-additive manner. Heritability analyses of these loci, especially amongst disease subtypes, may provide clues to the importance of specific genes to the genetic architecture of AMD.
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Affiliation(s)
- Andrea R Waksmunski
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Michelle Grunin
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Tyler G Kinzy
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jonathan L Haines
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jessica N Cooke Bailey
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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4
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Waksmunski AR, Grunin M, Kinzy TG, Igo RP, Haines JL, Cooke Bailey JN. Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci 2019; 60:4041-4051. [PMID: 31560769 PMCID: PMC6779289 DOI: 10.1167/iovs.19-27827] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/14/2019] [Indexed: 11/24/2022] Open
Abstract
Purpose Age-related macular degeneration (AMD) is the worldwide leading cause of blindness among the elderly. Although genome-wide association studies (GWAS) have identified AMD risk variants, their roles in disease etiology are not well-characterized, and they only explain a portion of AMD heritability. Methods We performed pathway analyses using summary statistics from the International AMD Genomics Consortium's 2016 GWAS and multiple pathway databases to identify biological pathways wherein genetic association signals for AMD may be aggregating. We determined which genes contributed most to significant pathway signals across the databases. We characterized these genes by constructing protein-protein interaction networks and performing motif analysis. Results We determined that eight genes (C2, C3, LIPC, MICA, NOTCH4, PLCG2, PPARA, and RAD51B) "drive" the statistical signals observed across pathways curated in the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and Gene Ontology (GO) databases. We further refined our definition of statistical driver gene to identify PLCG2 as a candidate gene for AMD due to its significant gene-level signals (P < 0.0001) across KEGG, Reactome, GO, and NetPath pathways. Conclusions We performed pathway analyses on the largest available collection of advanced AMD cases and controls in the world. Eight genes strongly contributed to significant pathways from the three larger databases, and one gene (PLCG2) was central to significant pathways from all four databases. This is, to our knowledge, the first study to identify PLCG2 as a candidate gene for AMD based solely on genetic burden. Our findings reinforce the utility of integrating in silico genetic and biological pathway data to investigate the genetic architecture of AMD.
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Affiliation(s)
- Andrea R. Waksmunski
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Michelle Grunin
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Tyler G. Kinzy
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Jonathan L. Haines
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Jessica N. Cooke Bailey
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - for the International Age-Related Macular Degeneration Genomics Consortium
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
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5
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White MJ, Yaspan BL, Veatch OJ, Goddard P, Risse-Adams OS, Contreras MG. Strategies for Pathway Analysis Using GWAS and WGS Data. ACTA ACUST UNITED AC 2018; 100:e79. [PMID: 30387919 DOI: 10.1002/cphg.79] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-allele study designs, commonly used in genome-wide association studies (GWAS) as well as the more recently developed whole genome sequencing (WGS) studies, are a standard approach for investigating the relationship of common variation within the human genome to a given phenotype of interest. However, single-allele association results published for many GWAS studies represent only the tip of the iceberg for the information that can be extracted from these datasets. The primary analysis strategy for GWAS entails association analysis in which only the single nucleotide polymorphisms (SNPs) with the strongest p-values are declared statistically significant due to issues arising from multiple testing and type I errors. Factors such as locus heterogeneity, epistasis, and multiple genes conferring small effects contribute to the complexity of the genetic models underlying phenotype expression. Thus, many biologically meaningful associations having lower effect sizes at individual genes are overlooked, making it difficult to separate true associations from a sea of false-positive associations. Organizing these individual SNPs into biologically meaningful groups to look at the overall effects of minor perturbations to genes and pathways is desirable. This pathway-based approach provides researchers with insight into the functional foundations of the phenotype being studied and allows testing of various genetic scenarios. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marquitta J White
- Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California
| | | | - Olivia J Veatch
- Center for Sleep and Circadian Neurobiology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Pagé Goddard
- Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California
| | - Oona S Risse-Adams
- Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California
| | - Maria G Contreras
- Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California.,MARC, San Francisco State University, San Francisco, California
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6
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Bailey JNC, Gharahkhani P, Kang JH, Butkiewicz M, Sullivan DA, Weinreb RN, Aschard H, Allingham RR, Ashley-Koch A, Lee RK, Moroi SE, Brilliant MH, Wollstein G, Schuman JS, Fingert JH, Budenz DL, Realini T, Gaasterland T, Scott WK, Singh K, Sit AJ, Igo RP, Song YE, Hark L, Ritch R, Rhee DJ, Vollrath D, Zack DJ, Medeiros F, Vajaranant TS, Chasman DI, Christen WG, Pericak-Vance MA, Liu Y, Kraft P, Richards JE, Rosner BA, Hauser MA, Craig JE, Burdon KP, Hewitt AW, Mackey DA, Haines JL, MacGregor S, Wiggs JL, Pasquale LR. Testosterone Pathway Genetic Polymorphisms in Relation to Primary Open-Angle Glaucoma: An Analysis in Two Large Datasets. Invest Ophthalmol Vis Sci 2018; 59:629-636. [PMID: 29392307 PMCID: PMC5795896 DOI: 10.1167/iovs.17-22708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Sex hormones may be associated with primary open-angle glaucoma (POAG), although the mechanisms are unclear. We previously observed that gene variants involved with estrogen metabolism were collectively associated with POAG in women but not men; here we assessed gene variants related to testosterone metabolism collectively and POAG risk. Methods We used two datasets: one from the United States (3853 cases and 33,480 controls) and another from Australia (1155 cases and 1992 controls). Both datasets contained densely called genotypes imputed to the 1000 Genomes reference panel. We used pathway- and gene-based approaches with Pathway Analysis by Randomization Incorporating Structure (PARIS) software to assess the overall association between a panel of single nucleotide polymorphisms (SNPs) in testosterone metabolism genes and POAG. In sex-stratified analyses, we evaluated POAG overall and POAG subtypes defined by maximum IOP (high-tension [HTG] or normal tension glaucoma [NTG]). Results In the US dataset, the SNP panel was not associated with POAG (permuted P = 0.77), although there was an association in the Australian sample (permuted P = 0.018). In both datasets, the SNP panel was associated with POAG in men (permuted P ≤ 0.033) and not women (permuted P ≥ 0.42), but in gene-based analyses, there was no consistency on the main genes responsible for these findings. In both datasets, the testosterone pathway association with HTG was significant (permuted P ≤ 0.011), but again, gene-based analyses showed no consistent driver gene associations. Conclusions Collectively, testosterone metabolism pathway SNPs were consistently associated with the high-tension subtype of POAG in two datasets.
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Affiliation(s)
- Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Mariusz Butkiewicz
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - David A Sullivan
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Robert N Weinreb
- Department of Ophthalmology, Hamilton Glaucoma Center and Shiley Eye Institute, University of California at San Diego, La Jolla, California, United States
| | - Hugues Aschard
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States
| | - Gadi Wollstein
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, New York, United States
| | - Joel S Schuman
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, New York, United States
| | - John H Fingert
- Departments of Ophthalmology and Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City, Iowa, United States
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Tony Realini
- Department of Ophthalmology, WVU Eye Institute, Morgantown, West Virginia, United States
| | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, California, United States
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Lisa Hark
- Wills Eye Hospital, Glaucoma Research Center, Philadelphia, Pennsylvania, United States
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York, United States
| | - Douglas J Rhee
- Department of Ophthalmology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Douglas Vollrath
- Department of Genetics, Stanford University, Palo Alto, California, United States
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, United States
| | - Felipe Medeiros
- Department of Ophthalmology, Hamilton Glaucoma Center and Shiley Eye Institute, University of California at San Diego, La Jolla, California, United States
| | - Thasarat S Vajaranant
- Department of Ophthalmology, University of Illinois College of Medicine at Chicago, Chicago, Illinois, United States
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - William G Christen
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Margaret A Pericak-Vance
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Peter Kraft
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Bernard A Rosner
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Kathryn P Burdon
- School of Medicine, Menzies Research Institute of Tasmania, Hobart, Australia
| | - Alex W Hewitt
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - David A Mackey
- School of Medicine, Menzies Research Institute of Tasmania, Hobart, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - Janey L Wiggs
- Department of Ophthalmology, Mass Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Louis R Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States.,Department of Ophthalmology, Mass Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
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7
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Hoppmann AS, Schlosser P, Backofen R, Lausch E, Köttgen A. GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS. PLoS One 2016; 11:e0162466. [PMID: 27612175 PMCID: PMC5017755 DOI: 10.1371/journal.pone.0162466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/23/2016] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association studies (GWAS) evaluate associations between genetic variants and a trait or disease of interest free of prior biological hypotheses. GWAS require stringent correction for multiple testing, with genome-wide significance typically defined as association p-value <5*10-8. This study presents a new tool that uses external information about genes to prioritize SNP associations (GenToS). For a given list of candidate genes, GenToS calculates an appropriate statistical significance threshold and then searches for trait-associated variants in summary statistics from human GWAS. It thereby allows for identifying trait-associated genetic variants that do not meet genome-wide significance. The program additionally tests for enrichment of significant candidate gene associations in the human GWAS data compared to the number expected by chance. As proof of principle, this report used external information from a comprehensive resource of genetically manipulated and systematically phenotyped mice. Based on selected murine phenotypes for which human GWAS data for corresponding traits were publicly available, several candidate gene input lists were derived. Using GenToS for the investigation of candidate genes underlying murine skeletal phenotypes in data from a large human discovery GWAS meta-analysis of bone mineral density resulted in the identification of significantly associated variants in 29 genes. Index variants in 28 of these loci were subsequently replicated in an independent GWAS replication step, highlighting that they are true positive associations. One signal, COL11A1, has not been discovered through GWAS so far and represents a novel human candidate gene for altered bone mineral density. The number of observed genes that contained significant SNP associations in human GWAS based on murine candidate gene input lists was much greater than the number expected by chance across several complex human traits (enrichment p-value as low as 10-10). GenToS can be used with any candidate gene list, any GWAS summary file, runs on a desktop computer and is freely available.
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Affiliation(s)
- Anselm S. Hoppmann
- Dept. of Pediatric Genetics, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Division of Genetic Epidemiology, Institute for Medical Biometry and Statistics, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pascal Schlosser
- Institute for Medical Biometry and Statistics, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Ekkehart Lausch
- Dept. of Pediatric Genetics, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Division of Genetic Epidemiology, Institute for Medical Biometry and Statistics, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- * E-mail:
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