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A deep population reference panel of tandem repeat variation

Author

Listed:
  • Helyaneh Ziaei Jam

    (University of California San Diego)

  • Yang Li

    (University of California San Diego)

  • Ross DeVito

    (University of California San Diego)

  • Nima Mousavi

    (University of California San Diego)

  • Nichole Ma

    (University of California San Diego)

  • Ibra Lujumba

    (Makerere University)

  • Yagoub Adam

    (Covenant University Bioinformatics Research (CUBRe), Covenant University)

  • Mikhail Maksimov

    (University of California San Diego)

  • Bonnie Huang

    (University of California San Diego)

  • Egor Dolzhenko

    (Illumina Incorporated)

  • Yunjiang Qiu

    (Illumina Incorporated)

  • Fredrick Elishama Kakembo

    (Makerere University)

  • Habi Joseph

    (Makerere University)

  • Blessing Onyido

    (Covenant University
    Covenant University)

  • Jumoke Adeyemi

    (Covenant University
    Covenant University)

  • Mehrdad Bakhtiari

    (University of California San Diego)

  • Jonghun Park

    (University of California San Diego)

  • Sara Javadzadeh

    (University of California San Diego)

  • Daudi Jjingo

    (Makerere University
    Makerere University)

  • Ezekiel Adebiyi

    (Covenant University Bioinformatics Research (CUBRe), Covenant University
    Covenant University
    Covenant University
    German Cancer Research Center (DKFZ))

  • Vineet Bafna

    (University of California San Diego)

  • Melissa Gymrek

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

Abstract

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

Suggested Citation

  • Helyaneh Ziaei Jam & Yang Li & Ross DeVito & Nima Mousavi & Nichole Ma & Ibra Lujumba & Yagoub Adam & Mikhail Maksimov & Bonnie Huang & Egor Dolzhenko & Yunjiang Qiu & Fredrick Elishama Kakembo & Habi, 2023. "A deep population reference panel of tandem repeat variation," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42278-3
    DOI: 10.1038/s41467-023-42278-3
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    References listed on IDEAS

    as
    1. Swapan Mallick & Heng Li & Mark Lipson & Iain Mathieson & Melissa Gymrek & Fernando Racimo & Mengyao Zhao & Niru Chennagiri & Susanne Nordenfelt & Arti Tandon & Pontus Skoglund & Iosif Lazaridis & Sri, 2016. "The Simons Genome Diversity Project: 300 genomes from 142 diverse populations," Nature, Nature, vol. 538(7624), pages 201-206, October.
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