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Characterization of genome-wide STR variation in 6487 human genomes

Author

Listed:
  • Yirong Shi

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yiwei Niu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Peng Zhang

    (Chinese Academy of Sciences)

  • Huaxia Luo

    (Chinese Academy of Sciences)

  • Shuai Liu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Sijia Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jiajia Wang

    (Chinese Academy of Sciences)

  • Yanyan Li

    (Chinese Academy of Sciences)

  • Xinyue Liu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Tingrui Song

    (Chinese Academy of Sciences)

  • Tao Xu

    (Chinese Academy of Sciences
    Shandong First Medical University & Shandong Academy of Medical Sciences)

  • Shunmin He

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

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.

Suggested Citation

  • Yirong Shi & Yiwei Niu & Peng Zhang & Huaxia Luo & Shuai Liu & Sijia Zhang & Jiajia Wang & Yanyan Li & Xinyue Liu & Tingrui Song & Tao Xu & Shunmin He, 2023. "Characterization of genome-wide STR variation in 6487 human genomes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37690-8
    DOI: 10.1038/s41467-023-37690-8
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