Meta-analysis of SNP-environment interaction with heterogeneity for overlapping data

Abstract Meta-analysis is a popular method used in genome-wide association studies, by which the results of multiple studies are combined to identify associations. This process generates heterogeneity. Recently, we proposed a random effect model meta-regression method (MR) to study the effect of sin...

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Autores principales:	Qinqin Jin, Gang Shi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a3c0f19e76dc41238ef7f5772413a003
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id	oai:doaj.org-article:a3c0f19e76dc41238ef7f5772413a003
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spelling	oai:doaj.org-article:a3c0f19e76dc41238ef7f5772413a0032021-12-02T14:16:42ZMeta-analysis of SNP-environment interaction with heterogeneity for overlapping data10.1038/s41598-021-82336-82045-2322https://doaj.org/article/a3c0f19e76dc41238ef7f5772413a0032021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82336-8https://doaj.org/toc/2045-2322Abstract Meta-analysis is a popular method used in genome-wide association studies, by which the results of multiple studies are combined to identify associations. This process generates heterogeneity. Recently, we proposed a random effect model meta-regression method (MR) to study the effect of single nucleotide polymorphism (SNP)-environment interactions. This method takes heterogeneity into account and produces high power. We also proposed a fixed effect model overlapping MR in which the overlapping data is taken into account. In the present study, a random effect model overlapping MR that simultaneously considers heterogeneity and overlapping data is proposed. This method is based on the random effect model MR and the fixed effect model overlapping MR. A new way of solving the logarithm of the determinant of covariance matrices in likelihood functions is also provided. Tests for the likelihood ratio statistic of the SNP-environment interaction effect and the SNP and SNP-environment joint effects are given. In our simulations, null distributions and type I error rates were proposed to verify the suitability of our method, and powers were applied to evaluate the superiority of our method. Our findings indicate that this method is effective in cases of overlapping data with a high heterogeneity.Qinqin JinGang ShiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qinqin Jin Gang Shi Meta-analysis of SNP-environment interaction with heterogeneity for overlapping data
description	Abstract Meta-analysis is a popular method used in genome-wide association studies, by which the results of multiple studies are combined to identify associations. This process generates heterogeneity. Recently, we proposed a random effect model meta-regression method (MR) to study the effect of single nucleotide polymorphism (SNP)-environment interactions. This method takes heterogeneity into account and produces high power. We also proposed a fixed effect model overlapping MR in which the overlapping data is taken into account. In the present study, a random effect model overlapping MR that simultaneously considers heterogeneity and overlapping data is proposed. This method is based on the random effect model MR and the fixed effect model overlapping MR. A new way of solving the logarithm of the determinant of covariance matrices in likelihood functions is also provided. Tests for the likelihood ratio statistic of the SNP-environment interaction effect and the SNP and SNP-environment joint effects are given. In our simulations, null distributions and type I error rates were proposed to verify the suitability of our method, and powers were applied to evaluate the superiority of our method. Our findings indicate that this method is effective in cases of overlapping data with a high heterogeneity.
format	article
author	Qinqin Jin Gang Shi
author_facet	Qinqin Jin Gang Shi
author_sort	Qinqin Jin
title	Meta-analysis of SNP-environment interaction with heterogeneity for overlapping data
title_short	Meta-analysis of SNP-environment interaction with heterogeneity for overlapping data
title_full	Meta-analysis of SNP-environment interaction with heterogeneity for overlapping data
title_fullStr	Meta-analysis of SNP-environment interaction with heterogeneity for overlapping data
title_full_unstemmed	Meta-analysis of SNP-environment interaction with heterogeneity for overlapping data
title_sort	meta-analysis of snp-environment interaction with heterogeneity for overlapping data
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/a3c0f19e76dc41238ef7f5772413a003
work_keys_str_mv	AT qinqinjin metaanalysisofsnpenvironmentinteractionwithheterogeneityforoverlappingdata AT gangshi metaanalysisofsnpenvironmentinteractionwithheterogeneityforoverlappingdata
_version_	1718391684499243008

Meta-analysis of SNP-environment interaction with heterogeneity for overlapping data

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