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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Vydáno v:Molecular biology and evolution Ročník 37; číslo 1; s. 2 - 10
Hlavní autoři: Anderson-Trocmé, Luke, Farouni, Rick, Bourgey, Mathieu, Kamatani, Yoichiro, Higasa, Koichiro, Seo, Jeong-Sun, Kim, Changhoon, Matsuda, Fumihiko, Gravel, Simon
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Oxford University Press 01.01.2020
Témata:
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
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Abstract 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.
AbstractList 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.
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.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.
Author Kim, Changhoon
Farouni, Rick
Gravel, Simon
Matsuda, Fumihiko
Bourgey, Mathieu
Higasa, Koichiro
Anderson-Trocmé, Luke
Seo, Jeong-Sun
Kamatani, Yoichiro
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Copyright The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2019
The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Copyright_xml – notice: The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2019
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Keywords batch effect
population genetics
statistical genetics
imputation
reference cohorts
mutational signature
Language English
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Snippet Recent reports have identified differences in the mutational spectra across human populations. Although some of these reports have been replicated in other...
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SubjectTerms Consortia
Genetics
Genome-Wide Association Study
Genomes
Genomics
Human Genome Project
Human populations
Humans
Japan
Mutation
Stratification
Title Legacy Data Confound Genomics Studies
URI https://www.ncbi.nlm.nih.gov/pubmed/31504792
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Volume 37
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