PT  - JOURNAL ARTICLE
AU  - Luke Anderson-Trocmé
AU  - Rick Farouni
AU  - Mathieu Bourgey
AU  - Yoichiro Kamatani
AU  - Koichiro Higasa
AU  - Jeong-Sun Seo
AU  - Changhoon Kim
AU  - Fumihiko Matsuda
AU  - Simon Gravel
TI  - Legacy Data Confounds Genomics Studies
AID  - 10.1101/624908
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 624908
4099  - http://biorxiv.org/content/early/2019/05/03/624908.short
4100  - http://biorxiv.org/content/early/2019/05/03/624908.full
AB  - Recent reports have identified differences in the mutational spectra across human populations. While 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 is used extensively, we find that the batch effects also lead to incorrect imputation by leading imputation servers and suspicious GWAS associations. Lower-quality data from the early phases of the 1kGP thus continues to contaminate modern studies in hidden ways. It may be time to retire or upgrade such legacy sequencing data.