Tatsiana Vaitsiakhovich1, Dmitriy Drichel2, Christine Herold2, André Lacour2, Tim Becker1. 1. Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn and German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 25, D-53105 Bonn, Germany Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn and German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 25, D-53105 Bonn, Germany. 2. Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn and German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 25, D-53105 Bonn, Germany.
Abstract
MOTIVATION: Meta-analysis of summary statistics is an essential approach to guarantee the success of genome-wide association studies (GWAS). Application of the fixed or random effects model to single-marker association tests is a standard practice. More complex methods of meta-analysis involving multiple parameters have not been used frequently, a gap that could be explained by the lack of a respective meta-analysis pipeline. Meta-analysis based on combining p-values can be applied to any association test. However, to be powerful, meta-analysis methods for high-dimensional models should incorporate additional information such as study-specific properties of parameter estimates, their effect directions, standard errors and covariance structure. RESULTS: We modified 'method for the synthesis of linear regression slopes' recently proposed in the educational sciences to the case of multiple logistic regression, and implemented it in a meta-analysis tool called METAINTER. The software handles models with an arbitrary number of parameters, and can directly be applied to analyze the results of single-SNP tests, global haplotype tests, tests for and under gene-gene or gene-environment interaction. Via simulations for two-single nucleotide polymorphisms (SNP) models we have shown that the proposed meta-analysis method has correct type I error rate. Moreover, power estimates come close to that of the joint analysis of the entire sample. We conducted a real data analysis of six GWAS of type 2 diabetes, available from dbGaP (http://www.ncbi.nlm.nih.gov/gap). For each study, a genome-wide interaction analysis of all SNP pairs was performed by logistic regression tests. The results were then meta-analyzed with METAINTER. AVAILABILITY: The software is freely available and distributed under the conditions specified on http://metainter.meb.uni-bonn.de. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Meta-analysis of summary statistics is an essential approach to guarantee the success of genome-wide association studies (GWAS). Application of the fixed or random effects model to single-marker association tests is a standard practice. More complex methods of meta-analysis involving multiple parameters have not been used frequently, a gap that could be explained by the lack of a respective meta-analysis pipeline. Meta-analysis based on combining p-values can be applied to any association test. However, to be powerful, meta-analysis methods for high-dimensional models should incorporate additional information such as study-specific properties of parameter estimates, their effect directions, standard errors and covariance structure. RESULTS: We modified 'method for the synthesis of linear regression slopes' recently proposed in the educational sciences to the case of multiple logistic regression, and implemented it in a meta-analysis tool called METAINTER. The software handles models with an arbitrary number of parameters, and can directly be applied to analyze the results of single-SNP tests, global haplotype tests, tests for and under gene-gene or gene-environment interaction. Via simulations for two-single nucleotide polymorphisms (SNP) models we have shown that the proposed meta-analysis method has correct type I error rate. Moreover, power estimates come close to that of the joint analysis of the entire sample. We conducted a real data analysis of six GWAS of type 2 diabetes, available from dbGaP (http://www.ncbi.nlm.nih.gov/gap). For each study, a genome-wide interaction analysis of all SNP pairs was performed by logistic regression tests. The results were then meta-analyzed with METAINTER. AVAILABILITY: The software is freely available and distributed under the conditions specified on http://metainter.meb.uni-bonn.de. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Rosanna Asselta; Elvezia M Paraboschi; Alessio Gerussi; Heather J Cordell; George F Mells; Richard N Sandford; David E Jones; Minoru Nakamura; Kazuko Ueno; Yuki Hitomi; Minae Kawashima; Nao Nishida; Katsushi Tokunaga; Masao Nagasaki; Atsushi Tanaka; Ruqi Tang; Zhiqiang Li; Yongyong Shi; Xiangdong Liu; Ma Xiong; Gideon Hirschfield; Katherine A Siminovitch; Marco Carbone; Giulia Cardamone; Stefano Duga; M Eric Gershwin; Michael F Seldin; Pietro Invernizzi Journal: Gastroenterology Date: 2021-03-04 Impact factor: 33.883