Population Genomics of Peruvian Natives Americans
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39874 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Peruvian Native American individuals were genotyped as part of the Peruvian Genome Project (PGP). This data was used to infer population structure, demographic history and natural selection. We addressed question about gene flow across the Andes and Natural Selection in Andes and Amazon
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Project description:Using genome-wide information of Native Americans from Andes and Amazon we addressed questions about : the Andes-Amazon dichotomy, the Andean homogenization and how cultural and socioeconomic interactions revealed by archaeology were accompanied by gene flow, specifically in northern Peru. Moreover, this demographic history allowed for cases of positive natural selection in the high and arid Andes vs. the low Amazon tropical forest
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Project description:In this study, we sought to analyze the effects of genetic variants on gene expression levels in relation to the history of infectious disease and cell type. To do this, we focused on a Peruvian human cohort that had been previously genotyped who either progressed to active tuberculosis (TB) disease (cases) or did not progress to TB (controls). We isolated monocytes from PBMC samples of these individuals and differentiated in vitro to dendritic cells (DCs) and macrophages (MPs). We performed RNA-seq for each sample using a modified Smart-seq protocol for low-input RNA-sequencing. We measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified cell-type-specific eQTL genes as well as five genes that showed an interaction between eQTL variants and TB progression status in dendritic cells. We found that the top eQTL interaction with disease history was associated with a gene involved in tyrosine catabolism.
2024-06-04 | GSE269009 | GEO
Project description:Genomic insights reveal a shared demographic history of differentiated Atlantic and Indo-Pacific yellowfin tuna (Thunnus albacares) populations
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Project description:Here we fully characterize the genomes of 14 Plasmodium falciparum patient isolates taken recently from the Iquitos regions using genome-scanning, a microarray-based technique which delineates the majority of single-base changes, indels and copy number variants distinguishing the coding regions of two clones. We show that the parasite population in the Peruvian Amazon is highly structured with a limited number of genotypes and low recombination frequencies. Despite the essentially clonal nature of some isolates, we see high frequencies of mutations in subtelomeric highly variable genes and internal var genes indicating mutations arising during self-mating or mitotic replication. The data also reveal that 1 or 2 meioses separate different isolates showing that P. falciparum clones isolated from different individuals in defined geographical regions could be useful in linkage analyses or quantitative trait locus studies. Through pair-wise comparisons of different isolates we discovered point mutations in the apicoplast genome that are close to known mutations that confer clindamycin resistance in other species but which were hitherto unknown in malaria parasites. Subsequent drug sensitivity testing revealed over 100-fold increase clindamycin EC50 in strains harboring one of these mutations. This evidence of clindamycin resistant parasites in the Amazon suggests a shift should be made in health policy away from quinine+clindamycin therapy for malaria in pregnant women and infants and that the development of new lincosamide antibiotics for malaria should be reconsidered. Genome DNA from Peruvian Isolates vs. Reference 3D7
2010-08-04 | E-GEOD-22861 | biostudies-arrayexpress
Project description:Population genomics and evidence of clonal replacement of P. falciparum in the Peruvian Amazon
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Project description:Genome-wide data for 98 Native American individuals from Andes and Amazon
| EGAD00010001958 | EGA
Project description:The present study performed the proteomic and biological activities of Peruvian Crotalus durissus, an endangered species reported to cause neuro and myotoxic symptoms. Due to the severity of its envenomation and to its geographical location, Peruvian Crotalus durissus is considered of public health importance in Peru. Snakebite treatment depends on rapid administration of appropriate antivenom. In this sense, the recognition of Peruvian Crotalus durissus venom (PCdV) by Brazilian and Peruvian antivenoms was tested. The results of this study increase the scarce knowledge about PCdV composition and demonstrate antivenom recognition of PCdV proteins, indicating a possible efficiency of these antivenoms to treat Peruvian Crotalus durissus accidents
2021-12-06 | MSV000088524 | MassIVE
Project description:Most hepatocellular carcinomas in younger patients from Peru arise from non-cirrhotic livers. Histological examination of the non-tumor liver tissues highlights the presence of clear cell foci in a significant fraction of Peruvian patients with hepatocellular carcinoma. We used microarrays to compare gene expression between non-tumor liver tissues with and without clear cell foci and identified ontologies that are distinctively differentially expressed between subsets.
2018-08-29 | GSE111580 | GEO