RT Journal Article
SR Electronic
T1 Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with local ancestry and archaic introgression
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.25.313726
DO 10.1101/2020.09.25.313726
A1 Heini M. Natri
A1 Georgi Hudjashov
A1 Guy Jacobs
A1 Pradiptajati Kusuma
A1 Lauri Saag
A1 Chelzie Crenna Darusallam
A1 Mait Metspalu
A1 Herawati Sudoyo
A1 Murray P. Cox
A1 Irene Gallego Romero
A1 Nicholas E. Banovich
YR 2020
UL http://biorxiv.org/content/early/2020/09/29/2020.09.25.313726.abstract
AB Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity on the region. In a comparison with a European dataset, we identify 166 uniquely Indonesia-specific eQTLs, highlighting the benefits of performing association studies on non-European populations. By combining local ancestry and archaic introgression inference eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits. Our findings illustrate how local ancestry and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations.Competing Interest StatementThe authors have declared no competing interest.