Legacy Data Confound Genomics Studies

Recent reports have identified differences in the mutational spectra across human populations. Although some of these reports have been replicated in other cohorts, most have been reported only in the 1000 Genomes Project (1kGP) data. While investigating an intriguing putative population stratificat...

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Bibliographic Details
Published in:Molecular biology and evolution Vol. 37; no. 1; pp. 2 - 10
Main Authors: Anderson-Trocmé, Luke, Farouni, Rick, Bourgey, Mathieu, Kamatani, Yoichiro, Higasa, Koichiro, Seo, Jeong-Sun, Kim, Changhoon, Matsuda, Fumihiko, Gravel, Simon
Format: Journal Article
Language:English
Published: United States Oxford University Press 01.01.2020
Subjects:
Consortia
Genetics
Genome-Wide Association Study
Genomes
Genomics
Human Genome Project
Human populations
Humans
Japan
Mutation
Stratification
Japan
batch effect
population genetics
statistical genetics
imputation
reference cohorts
mutational signature
ISSN:0737-4038, 1537-1719, 1537-1719
Online Access:Get full text
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Summary:Recent reports have identified differences in the mutational spectra across human populations. Although some of these reports have been replicated in other cohorts, most have been reported only in the 1000 Genomes Project (1kGP) data. While investigating an intriguing putative population stratification within the Japanese population, we identified a previously unreported batch effect leading to spurious mutation calls in the 1kGP data and to the apparent population stratification. Because the 1kGP data are used extensively, we find that the batch effects also lead to incorrect imputation by leading imputation servers and a small number of suspicious GWAS associations. Lower quality data from the early phases of the 1kGP thus continue to contaminate modern studies in hidden ways. It may be time to retire or upgrade such legacy sequencing data.
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ISSN:0737-4038
1537-1719
1537-1719
DOI:10.1093/molbev/msz201