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

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 AdebiyiVineet Bafna, Melissa Gymrek

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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.

Original language	English
Article number	6711
Journal	Nature communications
Volume	14
Issue number	1
DOIs	https://doi.org/10.1038/s41467-023-42278-3
State	Published - Dec 2023

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Ziaei Jam, H., Li, Y., DeVito, R., Mousavi, N., Ma, N., Lujumba, I., Adam, Y., Maksimov, M., Huang, B., Dolzhenko, E., Qiu, Y., Kakembo, F. E., Joseph, H., Onyido, B., Adeyemi, J., Bakhtiari, M., Park, J., Javadzadeh, S., Jjingo, D., ... Gymrek, M. (2023). A deep population reference panel of tandem repeat variation. Nature communications, 14(1), Article 6711. https://doi.org/10.1038/s41467-023-42278-3

@article{47d8e9350eba41a28a81bd14a5c13949,

title = "A deep population reference panel of tandem repeat variation",

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.",

author = "{Ziaei Jam}, Helyaneh and Yang Li and Ross DeVito and Nima Mousavi and Nichole Ma and Ibra Lujumba and Yagoub Adam and Mikhail Maksimov and Bonnie Huang and Egor Dolzhenko and Yunjiang Qiu and Kakembo, {Fredrick Elishama} and Habi Joseph and Blessing Onyido and Jumoke Adeyemi and Mehrdad Bakhtiari and Jonghun Park and Sara Javadzadeh and Daudi Jjingo and Ezekiel Adebiyi and Vineet Bafna and Melissa Gymrek",

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year = "2023",

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doi = "10.1038/s41467-023-42278-3",

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Ziaei Jam, H, Li, Y, DeVito, R, Mousavi, N, Ma, N, Lujumba, I, Adam, Y, Maksimov, M, Huang, B, Dolzhenko, E, Qiu, Y, Kakembo, FE, Joseph, H, Onyido, B, Adeyemi, J, Bakhtiari, M, Park, J, Javadzadeh, S, Jjingo, D, Adebiyi, E, Bafna, V & Gymrek, M 2023, 'A deep population reference panel of tandem repeat variation', Nature communications, vol. 14, no. 1, 6711. https://doi.org/10.1038/s41467-023-42278-3

TY - JOUR

T1 - A deep population reference panel of tandem repeat variation

AU - Ziaei Jam, Helyaneh

AU - Li, Yang

AU - DeVito, Ross

AU - Mousavi, Nima

AU - Ma, Nichole

AU - Lujumba, Ibra

AU - Adam, Yagoub

AU - Maksimov, Mikhail

AU - Huang, Bonnie

AU - Dolzhenko, Egor

AU - Qiu, Yunjiang

AU - Kakembo, Fredrick Elishama

AU - Joseph, Habi

AU - Onyido, Blessing

AU - Adeyemi, Jumoke

AU - Bakhtiari, Mehrdad

AU - Park, Jonghun

AU - Javadzadeh, Sara

AU - Jjingo, Daudi

AU - Adebiyi, Ezekiel

AU - Bafna, Vineet

AU - Gymrek, Melissa

PY - 2023/12

Y1 - 2023/12

N2 - 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.

AB - 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.

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SN - 2041-1723

VL - 14

JO - Nature communications

JF - Nature communications

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ER -

A deep population reference panel of tandem repeat variation

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