A deep population reference panel of tandem repeat variation.

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

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

Afiliación

Jam HZ; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Li Y; Department of Medicine, University of California San Diego, La Jolla, CA.
DeVito R; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Mousavi N; Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA.
Ma N; Department of Medicine, University of California San Diego, La Jolla, CA.
Lujumba I; The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala-Uganda.
Adam Y; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria.
Maksimov M; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Huang B; Department of Bioengineering, University of California San Diego, La Jolla, CA.
Dolzhenko E; Illumina Incorporated, San Diego, California 92122, USA.
Qiu Y; Illumina Incorporated, San Diego, California 92122, USA.
Kakembo FE; The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala-Uganda.
Joseph H; The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala-Uganda.
Onyido B; Department of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria.
Adeyemi J; Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun, 112233, Nigeria.
Bakhtiari M; Department of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria.
Park J; Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun, 112233, Nigeria.
Javadzadeh S; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Jjingo D; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Adebiyi E; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA.
Bafna V; The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala-Uganda.
Gymrek M; Department of Computer Science, Makerere University, Kampala, Uganda.

bioRxiv ; 2023 Mar 12.

Article en En | MEDLINE | ID: mdl-36945429

RESUMEN

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 3,550 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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article