Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix

doi:10.1089/cmb.2022.0067

	Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix
	Wang, Shijia 1; Ge, Shufei2 ; Sobkowiak, Benjamin 3; Wang, Liangliang 4; Grandjean, Louis 5; Colijn, Caroline 3; Elliott, Lloyd. T. T.4,6
	2022-11
发表期刊	JOURNAL OF COMPUTATIONAL BIOLOGY
ISSN	1066-5277
EISSN	1557-8666
发表状态	已发表
DOI	10.1089/cmb.2022.0067
摘要	Genome-wide association studies (GWASs) are often confounded by population stratification and structure. Linear mixed models (LMMs) are a powerful class of methods for uncovering genetic effects, while controlling for such confounding. LMMs include random effects for a genetic similarity matrix, and they assume that a true genetic similarity matrix is known. However, uncertainty about the phylogenetic structure of a study population may degrade the quality of LMM results. This may happen in bacterial studies in which the number of samples or loci is small, or in studies with low-quality genotyping. In this study, we develop methods for linear mixed models in which the genetic similarity matrix is unknown and is derived from Markov chain Monte Carlo estimates of the phylogeny. We apply our model to a GWAS of multidrug resistance in tuberculosis, and illustrate our methods on simulated data.
关键词	genome-wide association studies phylogenetics genetic similarity
URL	查看原文
收录类别	SCI ; SCIE ; SCOPUS
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000885118800001
出版者	MARY ANN LIEBERT, INC
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/251694
专题	数学科学研究所_PI研究组(P)_葛淑菲组
通讯作者	Elliott, Lloyd. T. T.
作者单位	1.Nankai Univ, LPMC & KLMDASR, Sch Stat & Data Sci, Tianjin, Peoples R China 2.ShanghaiTech Univ, Inst Math Sci, Shanghai, Peoples R China 3.Simon Fraser Univ, Dept Math, Burnaby, BC, Canada 4.Simon Fraser Univ, Dept Stat & Actuarial Sci, Burnaby, BC, Canada 5.UCL, Dept Infect Dis, London, England 6.Simon Fraser Univ, Dept Stat & Actuarial Sci, 8888 Univ Dr, Burnaby, BC V5A 1S6, Canada
推荐引用方式 GB/T 7714	Wang, Shijia,Ge, Shufei,Sobkowiak, Benjamin,et al. Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix[J]. JOURNAL OF COMPUTATIONAL BIOLOGY,2022.
APA	Wang, Shijia.,Ge, Shufei.,Sobkowiak, Benjamin.,Wang, Liangliang.,Grandjean, Louis.,...&Elliott, Lloyd. T. T..(2022).Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix.JOURNAL OF COMPUTATIONAL BIOLOGY.
MLA	Wang, Shijia,et al."Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix".JOURNAL OF COMPUTATIONAL BIOLOGY (2022).