Characterization of genome-wide STR variation in 6487 human genomes

Yirong Shi, Yiwei Niu, Peng Zhang, Huaxia Luo, Shuai Liu, Sijia Zhang, Jiajia Wang, Yanyan Li, Xinyue Liu, Tingrui Song, Tao Xu () and Shunmin He ()
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Yirong Shi: Chinese Academy of Sciences
Yiwei Niu: Chinese Academy of Sciences
Peng Zhang: Chinese Academy of Sciences
Huaxia Luo: Chinese Academy of Sciences
Shuai Liu: Chinese Academy of Sciences
Sijia Zhang: Chinese Academy of Sciences
Jiajia Wang: Chinese Academy of Sciences
Yanyan Li: Chinese Academy of Sciences
Xinyue Liu: Chinese Academy of Sciences
Tingrui Song: Chinese Academy of Sciences
Tao Xu: Chinese Academy of Sciences
Shunmin He: Chinese Academy of Sciences

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract Short tandem repeats (STRs) are abundant and highly mutagenic in the human genome. Many STR loci have been associated with a range of human genetic disorders. However, most population-scale studies on STR variation in humans have focused on European ancestry cohorts or are limited by sequencing depth. Here, we depicted a comprehensive map of 366,013 polymorphic STRs (pSTRs) constructed from 6487 deeply sequenced genomes, comprising 3983 Chinese samples (~31.5x, NyuWa) and 2504 samples from the 1000 Genomes Project (~33.3x, 1KGP). We found that STR mutations were affected by motif length, chromosome context and epigenetic features. We identified 3273 and 1117 pSTRs whose repeat numbers were associated with gene expression and 3′UTR alternative polyadenylation, respectively. We also implemented population analysis, investigated population differentiated signatures, and genotyped 60 known disease-causing STRs. Overall, this study further extends the scale of STR variation in humans and propels our understanding of the semantics of STRs.

Date: 2023
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DOI: 10.1038/s41467-023-37690-8

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