ArticleHuman genome variation2025
High-coverage whole-genome sequencing of a Jakun individual from the "Orang Asli" Proto-Malay subtribe from Peninsular Malaysia.
Article in Human genome variation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Jakun, a Proto-Malay subtribe from Peninsular Malaysia, is believed to have inhabited the Malay Archipelago during the period of agricultural expansion approximately 4 thousand years ago (kya). However, their genetic structure and population history remain inconclusive. In this study, we report the genome structure of a Jakun female, based on whole-genome sequencing, which yielded an average coverage of 35.97-fold. We identified approximately 3.6 million single-nucleotide variations (SNVs) and 517,784 small insertions/deletions (indels). Of these, 39,916 SNVs were novel (referencing dbSNP151), and 10,167 were nonsynonymous (nsSNVs), spanning 5674 genes. Principal Component Analysis (PCA) revealed that the Jakun genome sequence closely clustered with the genomes of the Cambodians (CAM) and the Metropolitan Malays from Singapore (SG_MAS). The ADMIXTURE analysis further revealed potential admixture from the EA and North Borneo populations, as corroborated by the results from the F3, F4, and TreeMix analyses. Mitochondrial DNA analysis revealed that the Jakun genome carried the N21a haplogroup (estimated to have occurred ~19 kya), which is commonly found among Malays from Malaysia and Indonesia. From the whole-genome sequence data, we identified 825 damaging and deleterious nonsynonymous single-nucleotide polymorphisms (nsSNVs) affecting 720 genes. Some of these variants are associated with age-related macular degeneration, atrial fibrillation, and HDL cholesterol level. Additionally, we located a total of 3310 variants on 32 core adsorption, distribution, metabolism, and elimination (ADME) genes. Of these, 193 variants are listed in PharmGKB, and 21 are nsSNVs. In summary, the genetic structure identified in the Jakun individual could enhance the mapping of genetic variants for disease-based population studies and further our understanding of the human migration history in Southeast Asia.
Identifiers
What OpenQuestion holds
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.