Ontology highlight
ABSTRACT:
PROVIDER: PRJNA681146 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:<p>Due to a unique adaptation to high altitude, the Tibetan Plateau population has been the subject of much research interest. In this study, we conducted whole genome sequencing of 27 Tibetan individuals. Through our analysis, we inferred a detailed history of demography and revealed the natural selection of Tibetan population. We provided evidence of genetic separation between the two subpopulations of Han and Tibetans as early as 44 to 58 thousand years ago, replicated previously reported high altitude adaptation genes, including <i>EPAS1</i> and <i>EGLN1</i>, and reported three new candidate genes, including <i>PTGIS</i>, <i>VDR</i>, and <i>KCTD12</i>.</p>
| phs001338 | dbGaP
Project description:Since their arrival in the Tibetan Plateau during the Neolithic Age, Tibetans have been well-adapted to extreme environmental conditions and possess genetic variation that reflect their living environment and migratory history. To investigate the origin of Tibetans and the genetic basis of adaptation in a rigorous environment, we genotyped 30 Tibetan individuals with more than one million SNP markers. Our findings suggested that Tibetans, together with the Yi people, were descendants of Tibeto-Burmans who diverged from ancient settlers of East Asia. The valleys of the Hengduan Mountain range may be a major migration route. We also identified a set of positively-selected genes that belong to functional classes of the embryonic, female gonad, and blood vessel developments, as well as response to hypoxia. Most of these genes were highly correlated with population-specific and beneficial phenotypes, such as high infant survival rate and the absence of chronic mountain sickness. Genetic features of Tibetans have been broadly investigated, but the properties of copy number variation (CNV) have not been well examined. To get a preliminary view of CNV in Tibetans, we scanned 29 Tibetan genomes with the Illumina Human-1 M high-resolution genotyping microarray and identified 139 putative copy number variable regions (CNVRs), consisting of 70 deletions, 61 duplications, and 8 multi-allelic loci. Thirty-four of the 139 CNVRs showed differential allele frequencies versus other East-Asian populations, with P values ,0.0001. These results indicated a distinct pattern of CNVR allele frequency distribution in Tibetans. The Tibetan CNVRs are enriched for genes in the disease class of human reproduction (such as genes from the DAZ, BPY2, CDY, and HLA-DQ and -DR gene clusters) and biological process categories of ‘‘response to DNA damage stimulus’’ and ‘‘DNA repair’’ (such as RAD51, RAD52, and MRE11A). These genes are related to the adaptive traits of high infant birth weight and darker skin tone of Tibetans, and may be attributed to recent local adaptation. Our results provide a different view of genetic diversity in Tibetans and new insights into their high-altitude adaptation.
2016-11-08 | GSE89635 | GEO
Project description:To revisit and address four major unresolved issues regarding prehistory, especially the Neolithic history of Sherpas and Tibetans and their hypoxic adaptation: (i) whether they are two genetically different ethnic groups; (ii) whether population substructures exist in either of the two groups; (iii) how long they have diverged from their ancestral group and when the two separated groups started to re-contact by population admixture; and (iv) whether the two groups share major high-altitude adaptation mechanisms. The careful and systematical analysis of these newly sequenced genomes, together with available genotyping data can provide further insight into the genetic origins of Sherpas and Tibetans and uncover their different adaptive mechanisms.
2017-03-01 | GSE93037 | GEO
Project description:Understanding molecular mechanism associated with high altitude exposure during acclimatization/adaptation/maladaptation. Data reveals specific components of the complex molecular circuitry underlying high altitude pulmonary edema. Individualized outcome prediction were constructed through expression profiling of 39400 genes in sea level sojourners who were acclimatized to high altitude and grouped as controls (n=14), high altitude natives (n=14) and individuals who developed high altitude pulmonary edema within 48-72 hours after air induction to high altitude (n=17).
2013-12-18 | E-GEOD-52209 | biostudies-arrayexpress
Project description:Understanding molecular mechanism associated with high altitude exposure during acclimatization/adaptation/maladaptation. Data reveals specific components of the complex molecular circuitry underlying high altitude pulmonary edema.
2013-12-18 | GSE52209 | GEO
Project description:This study evaluates genetic and phenotypic variation in the intermediate altitude Calchaquí population living in the Calchaquí Valleys of the Argentinean Andes in the town of Cachi at 2300 m. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to moderate hypoxia at a intermediate altitude.
2014-04-05 | GSE56518 | GEO
Project description:This study evaluates genetic and phenotypic variation in the intermediate altitude Calchaquà population living in the Calchaquà Valleys of the Argentinean Andes in the town of Cachi at 2300 m. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to moderate hypoxia at a intermediate altitude. DNA from 24 saliva samples of CalchaquÃes living at 2300 m in Cachi in the Province of Salta in Argentina was genotyped.
2014-04-05 | E-GEOD-56518 | biostudies-arrayexpress
Project description:Tibetan's adaptation to high-altitude environment at the Qinghai-Tibetan plateau represents a remarkable case of natural selection during recent human evolution. We generated time series paired RNAseq, ATACseq and Hi-C data in Tibetan and Han Chinese's umbilical endothelial cells from normoxia to hypoxia condition. Our results provide a broad resource of genome-wide hypoxia regulatory network to characterize the effect of genetic variation in high-altitude adaptation, and indicates large-scale maps of variants need proper cell types to understand its act on gene regulation.
2020-07-15 | GSE145774 | GEO
Project description:Tibetan adaptation to high-altitude hypoxia remains a classic example of Darwinian selection in humans. Amongst Tibetans, alleles in the EPAS1 gene - whose protein product, Hif-2α, is a central regulator of the hypoxia response - have repeatedly been shown to carry some of the strongest signals of positive selection in humans and to influence several adaptive phenotypes. We recently showed that the selected haplotype at this locus spans a hypoxia-dependent enhancer (ENH5) that contributes to the regulation of EPAS1 in a variety of cell types. However, selective sweep signals alone may account for only part of the phenotypes that differentiate Tibetans from closely related lowlanders. Therefore, there is a pressing need to functionally probe adaptive alleles and their impact at the genome-wide level and across cell types to uncover the full range of beneficial traits. To cast a wider net, we established a library of induced pluripotent stem cells (iPSCs) derived from Tibetan and Han Chinese individuals, a robust model system allowing precise exploration of both locus-specific and genome-wide effects on transcriptional responses. We harness this system by differentiating the iPSC library into vascular endothelium and investigating the locus-specific effects of the ENH5 enhancer in this cellular context. In addition, we use it to explore Tibetan-specific transcriptome-wide responses and find evidence that energy metabolism and immune pathways have been shaped by natural selection in Tibetans. Finally, to aid with the interpretation of the transcriptional differences between populations, we test for polygenic adaptations as a complementary in silico approach for the identification of beneficial Tibetan phenotypes.
2025-01-12 | GSE280017 | GEO