ArticleAmerican journal of human genetics2022
Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries.
Article in American journal of human genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 36 citations in OpenAlex.
- Characterizing breed-shared and breed-specific genetic regulatory effects of gene expression across three pig breeds.Journal of animal science and biotechnology · 2026Article
- Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans.PLoS genetics · 2026Article
- Admixture influences the genetic architecture of DNA methylation in a wild primate hybrid zone.Genome biology · 2026Article
- Methodological opportunities in genomic data analysis to advance health equity.Nature reviews. Genetics · 2025Review
- Archaic hominin admixture and its consequences for modern humans.Current opinion in genetics & development · 2025Review
- Whole blood transcriptomics analysis of Indonesians reveals translocated and pathogenic microbiota in blood.PloS one · 2025Article
- A scoping review of statistical methods to investigate colocalization between genetic associations and microRNA expression in osteoarthritis.Osteoarthritis and cartilage open · 2024Article
- Profiling genetically driven alternative splicing across the Indonesian archipelago.American journal of human genetics · 2024Article
- Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- More than a decade of genetic research on the Denisovans.Nature reviews. Genetics · 2024Review
- Exploring Genetic Variants and Platinum Chemotherapy Response in Indonesian Non-Small Cell Lung Cancer Patients: Insights fromOncoTargets and therapy · 2024Article
- Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population.BMC genomics · 2023Article
- Synthetic biology in Indonesia: Potential and projection in a country with mega biodiversity.Biotechnology notes (Amsterdam, Netherlands) · 2023Review
- Denisovan introgression has shaped the immune system of present-day Papuans.PLoS genetics · 2022Article
- The contribution of Neanderthal introgression to modern human traits.Current biology : CB · 2022Review
- Predicted gene expression in ancestrally diverse populations leads to discovery of susceptibility loci for lifestyle and cardiometabolic traits.American journal of human genetics · 2022Article
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 7 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 in the region. In a comparison with European datasets, we identify eQTLs shared between Indonesia and Europe as well as population-specific eQTLs that exhibit differences in allele frequencies and/or overall expression levels between populations. By combining local ancestry and archaic introgression inference with 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, and further comparison with European datasets reflects the poor overall transferability of GWAS statistics across diverse populations. Our findings illustrate how population-specific genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations and highlight the need for performing association studies on non-European populations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.