A protocol for applying a population-specific reference genome assembly to population genetics and medical studies

Lian Deng; Bo Xie; Yimin Wang; Xiaoxi Zhang; Shuhua Xu

doi:10.1016/j.xpro.2022.101440

A protocol for applying a population-specific reference genome assembly to population genetics and medical studies

STAR Protoc. 2022 May 27;3(2):101440. doi: 10.1016/j.xpro.2022.101440. eCollection 2022 Jun 17.

Authors

Lian Deng¹, Bo Xie², Yimin Wang², Xiaoxi Zhang³, Shuhua Xu^{1

2

3

4

5}

Affiliations

¹ State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China.
² Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
³ School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
⁴ Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China.
⁵ Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.

Abstract

With a growing number of available de novo sequenced genomes, protocols for their applications to population genetics will benefit our understanding of the human genome. Here we detail analytic steps to apply an example de novo reference genome to map and detect variants of short-read sequences from corresponding populations and to discover variants of disease-relevant genes. Using this protocol, we can improve variant discovery, better investigate population-specific genome properties, and evaluate the potential of sequenced genomes in medical studies. For complete details on the use and execution of this protocol, please refer to Lou et al. (2022).

Keywords: Bioinformatics; Genetics; Genomics; Health Sciences; Systems biology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Genetics, Population*
Genome, Human* / genetics
Humans
Metagenomics