Protocol for detecting rare and common genetic associations in whole-exome sequencing studies using MAGICpipeline

Jian Yuan; Kai Li; Hui Peng; Yue Zhang; Yinghao Yao; Myopia Associated Genetics and Intervention Consortium; Jia Qu; Jianzhong Su

doi:10.1016/j.xpro.2023.102806

Protocol for detecting rare and common genetic associations in whole-exome sequencing studies using MAGICpipeline

STAR Protoc. 2024 Mar 15;5(1):102806. doi: 10.1016/j.xpro.2023.102806. Epub 2024 Jan 3.

Authors

Jian Yuan¹, Kai Li², Hui Peng¹, Yue Zhang¹, Yinghao Yao³; Myopia Associated Genetics and Intervention Consortium; Jia Qu⁴, Jianzhong Su⁵

Affiliations

¹ National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.
² Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China.
³ Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China.
⁴ National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China.
⁵ National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China. Electronic address: sujz@wmu.edu.cn.

Abstract

Whole-exome sequencing (WES) is a major approach to uncovering gene-disease associations and pinpointing effector genes. Here, we present a protocol for estimating genetic associations of rare and common variants in large-scale case-control WES studies using MAGICpipeline, an open-access analysis pipeline. We describe steps for assessing gene-based rare-variant association analyses by incorporating multiple variant pathogenic annotations and statistical techniques. We then detail procedures for identifying disease-related modules and hub genes using weighted correlation network analysis, a systems biology approach. For complete details on the use and execution of this protocol, please refer to Su et al. (2023).¹.

Keywords: Bioinformatics; Genetics; Systems biology.

MeSH terms

Case-Control Studies
Exome Sequencing
Exome* / genetics
Systems Biology*