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A reference haplotype panel for genome-wide imputation of short tandem repeats

Author

Listed:
  • Shubham Saini

    (University of California San Diego)

  • Ileena Mitra

    (University of California San Diego)

  • Nima Mousavi

    (University of California, San Diego)

  • Stephanie Feupe Fotsing

    (University of California San Diego
    University of California San Diego)

  • Melissa Gymrek

    (University of California San Diego
    University of California, San Diego)

Abstract

Short tandem repeats (STRs) are involved in dozens of Mendelian disorders and have been implicated in complex traits. However, genotyping arrays used in genome-wide association studies focus on single nucleotide polymorphisms (SNPs) and do not readily allow identification of STR associations. We leverage next-generation sequencing (NGS) from 479 families to create a SNP + STR reference haplotype panel. Our panel enables imputing STR genotypes into SNP array data when NGS is not available for directly genotyping STRs. Imputed genotypes achieve mean concordance of 97% with observed genotypes in an external dataset compared to 71% expected under a naive model. Performance varies widely across STRs, with near perfect concordance at bi-allelic STRs vs. 70% at highly polymorphic repeats. Imputation increases power over individual SNPs to detect STR associations with gene expression. Imputing STRs into existing SNP datasets will enable the first large-scale STR association studies across a range of complex traits.

Suggested Citation

  • Shubham Saini & Ileena Mitra & Nima Mousavi & Stephanie Feupe Fotsing & Melissa Gymrek, 2018. "A reference haplotype panel for genome-wide imputation of short tandem repeats," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06694-0
    DOI: 10.1038/s41467-018-06694-0
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    Cited by:

    1. Tsung-Yu Lu & Mark J. P. Chaisson, 2021. "Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. 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.

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