PT  - JOURNAL ARTICLE
AU  - Heini M. Natri
AU  - Georgi Hudjashov
AU  - Guy Jacobs
AU  - Pradiptajati Kusuma
AU  - Lauri Saag
AU  - Chelzie Crenna Darusallam
AU  - Mait Metspalu
AU  - Herawati Sudoyo
AU  - Murray P. Cox
AU  - Irene Gallego Romero
AU  - Nicholas E. Banovich
TI  - Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with local ancestry and archaic introgression
AID  - 10.1101/2020.09.25.313726
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.09.25.313726
4099  - http://biorxiv.org/content/early/2020/09/29/2020.09.25.313726.short
4100  - http://biorxiv.org/content/early/2020/09/29/2020.09.25.313726.full
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.