A deep population reference panel of tandem repeat variation

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 Joseph; Blessing Onyido; Jumoke Adeyemi; Mehrdad Bakhtiari; Jonghun Park; Sara Javadzadeh; Daudi Jjingo; Ezekiel Adebiyi; Vineet Bafna; Melissa Gymrek

doi:10.1038/s41467-023-42278-3

Nature Communications (Oct 2023)

A deep population reference panel of tandem repeat variation

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 Joseph,
Blessing Onyido,
Jumoke Adeyemi,
Mehrdad Bakhtiari,
Jonghun Park,
Sara Javadzadeh,
Daudi Jjingo,
Ezekiel Adebiyi,
Vineet Bafna,
Melissa Gymrek

Affiliations

Helyaneh Ziaei Jam: Department of Computer Science and Engineering, University of California San Diego
Yang Li: Department of Medicine, University of California San Diego
Ross DeVito: Department of Computer Science and Engineering, University of California San Diego
Nima Mousavi: Department of Electrical and Computer Engineering, University of California San Diego
Nichole Ma: Department of Medicine, University of California San Diego
Ibra Lujumba: The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University
Yagoub Adam: Covenant University Bioinformatics Research (CUBRe), Covenant University
Mikhail Maksimov: Department of Computer Science and Engineering, University of California San Diego
Bonnie Huang: Department of Bioengineering, University of California San Diego
Egor Dolzhenko: Illumina Incorporated
Yunjiang Qiu: Illumina Incorporated
Fredrick Elishama Kakembo: The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University
Habi Joseph: The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University
Blessing Onyido: Department of Computer & Information Sciences, Covenant University
Jumoke Adeyemi: Department of Computer & Information Sciences, Covenant University
Mehrdad Bakhtiari: Department of Computer Science and Engineering, University of California San Diego
Jonghun Park: Department of Computer Science and Engineering, University of California San Diego
Sara Javadzadeh: Department of Computer Science and Engineering, University of California San Diego
Daudi Jjingo: The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University
Ezekiel Adebiyi: Covenant University Bioinformatics Research (CUBRe), Covenant University
Vineet Bafna: Department of Computer Science and Engineering, University of California San Diego
Melissa Gymrek: Department of Computer Science and Engineering, University of California San Diego

DOI: https://doi.org/10.1038/s41467-023-42278-3
Journal volume & issue: Vol. 14, no. 1
pp. 1 – 15

Abstract

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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.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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