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A landscape of complex tandem repeats within individual human genomes

Author

Listed:
  • Kazuki Ichikawa

    (The University of Tokyo)

  • Riki Kawahara

    (The University of Tokyo)

  • Takeshi Asano

    (The University of Tokyo)

  • Shinichi Morishita

    (The University of Tokyo)

Abstract

Markedly expanded tandem repeats (TRs) have been correlated with ~60 diseases. TR diversity has been considered a clue toward understanding missing heritability. However, haplotype-resolved long TRs remain mostly hidden or blacked out because their complex structures (TRs composed of various units and minisatellites containing >10-bp units) make them difficult to determine accurately with existing methods. Here, using a high-precision algorithm to determine complex TR structures from long, accurate reads of PacBio HiFi, an investigation of 270 Japanese control samples yields several genome-wide findings. Approximately 322,000 TRs are difficult to impute from the surrounding single-nucleotide variants. Greater genetic divergence of TR loci is significantly correlated with more events of younger replication slippage. Complex TRs are more abundant than single-unit TRs, and a tendency for complex TRs to consist of 100b longer than the mode) contain several known disease-associated TRs and are considered candidates for association with disorders. Overall, complex TRs and minisatellites are found to be abundant and diverse, even in genetically small Japanese populations, yielding insights into the landscape of long TRs.

Suggested Citation

  • Kazuki Ichikawa & Riki Kawahara & Takeshi Asano & Shinichi Morishita, 2023. "A landscape of complex tandem repeats within individual human genomes," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41262-1
    DOI: 10.1038/s41467-023-41262-1
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    1. Aaron R. Haeusler & Christopher J. Donnelly & Goran Periz & Eric A. J. Simko & Patrick G. Shaw & Min-Sik Kim & Nicholas J. Maragakis & Juan C. Troncoso & Akhilesh Pandey & Rita Sattler & Jeffrey D. Ro, 2014. "C9orf72 nucleotide repeat structures initiate molecular cascades of disease," Nature, Nature, vol. 507(7491), pages 195-200, March.
    2. Ileena Mitra & Bonnie Huang & Nima Mousavi & Nichole Ma & Michael Lamkin & Richard Yanicky & Sharona Shleizer-Burko & Kirk E. Lohmueller & Melissa Gymrek, 2021. "Patterns of de novo tandem repeat mutations and their role in autism," Nature, Nature, vol. 589(7841), pages 246-250, January.
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