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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
general
A deep population reference panel of tandem repeat variation
Nature Communications, Volume 14, No. 1, Article 6711, Year 2023
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Description
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. © 2023, Springer Nature Limited.
Authors & Co-Authors
Lujumba, Ibra
Uganda, Kampala
Makerere University
Adam, Yagoub
Nigeria, Ota
Covenant University
Kakembo, Fredrick Elishama
Uganda, Kampala
Makerere University
Onyido, Blessing Chioma
Nigeria, Ota
Covenant University
Jjingo, Daudi
Uganda, Kampala
Makerere University
Adebiyi, Ezekiel Femi
Nigeria, Ota
Covenant University
Germany, Heidelberg
German Cancer Research Center
Bafna, Vineet
United States, La Jolla
University of California, San Diego
Gymrek, Melissa
United States, La Jolla
University of California, San Diego
Statistics
Citations: 1
Authors: 8
Affiliations: 5
Identifiers
Doi:
10.1038/s41467-023-42278-3
ISSN:
20411723
Research Areas
Genetics And Genomics
Health System And Policy
Study Design
Cross Sectional Study
Cohort Study