Protocol for a comprehensive pipeline to study ancient human genomes

Kongyang Zhu; Haifeng He; Le Tao; Hao Ma; Xiaomin Yang; Rui Wang; Jianxin Guo; Chuan-Chao Wang

doi:10.1016/j.xpro.2024.102985

Protocol for a comprehensive pipeline to study ancient human genomes

STAR Protoc. 2024 Jun 21;5(2):102985. doi: 10.1016/j.xpro.2024.102985. Epub 2024 Apr 30.

Authors

Kongyang Zhu¹, Haifeng He¹, Le Tao¹, Hao Ma¹, Xiaomin Yang², Rui Wang¹, Jianxin Guo³, Chuan-Chao Wang⁴

Affiliations

¹ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.
² Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China.
³ Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China. Electronic address: jxguo@xmu.edu.cn.
⁴ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen, Fujian 361005, China. Electronic address: wang@xmu.edu.cn.

Abstract

Ancient genomics has revolutionized our understanding of human evolution and migration history in recent years. Here, we present a protocol to prepare samples for ancient genomics research. We describe steps for releasing DNA from human remains, DNA library construction, hybridization capture, quantification, and sequencing. We then detail procedures for mapping sequence reads and population genetics analysis. This protocol also outlines challenges in extracting ancient DNA samples and authenticating ancient DNA to uncover the genetic history and diversity of ancient populations. For complete details on the use and execution of this protocol, please refer to Tao et al.¹.

Keywords: Genetics; Genomics; Sequence analysis; Sequencing.

MeSH terms

DNA, Ancient* / analysis
Gene Library
Genetics, Population / methods
Genome, Human* / genetics
Genomics* / methods
Humans
Sequence Analysis, DNA / methods

Substances

DNA, Ancient