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 and Melissa Gymrek ()
Additional contact information
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
Jumoke Adeyemi: 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
Ezekiel Adebiyi: Covenant University Bioinformatics Research (CUBRe), Covenant University
Vineet Bafna: University of California San Diego
Melissa Gymrek: University of California San Diego

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: 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.

Date: 2023
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42278-3

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DOI: 10.1038/s41467-023-42278-3

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