EGAS00001005373-sc-2021-07-01T08:32:01Z - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001007815 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Genes & Health is a cohort of British Bangladeshi and British Pakistani individuals. In the Feb2020 data freeze, 28,022 individuals were genotyped on the Illumina Infinium Global Screening Array v3 chip (with the additional Multi-Disease variants). Imputation was performed using the Michigan Imputation Server with the GenomeAsia pilot reference panel, which contains 1,739 genomes and 642 from them are from South Asian groups. This dataset contains imputed SNPs with imputation accuracy >0.3 and MAF >0.1%.
| EGAS00001005373 | EGA
Project description:This data set contains whole exome sequences of individuals from 8086 (mostly British Pakistani/British Bangladeshi, mostly self-reported parentally related) individuals from the following studies:
1. 5236 British Pakistani/British Bangladeshi adults from East London Genes & Health, now known as Genes & Health
2. 2624 British South Asian mothers from Born in Bradford (mostly Pakistani)
3. 1061 British South Asian adults from Birmingham (mostly Pakistani)
This dataset contains all the exome sequence data available for this study on 2022-04-26
| EGAD00001008736 | EGA
Project description:A population and admixture analysis of Mesoamerican Totonacs and South American Bolivians. A panel of highly informative ancestry informative markers (AIMs) for New World populations is identified. Regions coinciding with AIMs are have moderate signatures of selection. Population structure and differentiation were assessed with a genome-wide panel of 815,377 autosomal markers, Y-chromosome STR and SNPs, and mtDNA sequence data.
2011-06-09 | E-GEOD-29851 | biostudies-arrayexpress
Project description:Only a few scattered groups with oral traditions of Khoe-San hunter-gatherer ancestry remain in southeastern Africa. We investigate genomic variation of remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published datasets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu-speakers. Specifically, we found that the Lake Chrissie San are closely related to current southern San groups (i.e. the Karretjie People). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. Samples were genotyped on the Illumina Omni2.5M (HumanOmni25-8v1-2_A1) SNP chip. Results were analyzed using the software GenomeStudio 2011.1 and the data were exported to Plink format, aligned to Human Genome build version 37.
2016-09-21 | E-MTAB-5119 | biostudies-arrayexpress
Project description:Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped using Illumina technology. To investigate variations of continental ancestry between different Hispanic/Latino groups (using self-reported country-specific identification of individual, both parents, and all four grandparents) and within them from healthy controls represented in the New York Health Project Biorepository. Genotyped on the Illumina 610-Quad, which is identical to HumanHap550-v3 SNPs plus an additional ~60,000 SNPs for CNV, no CNV data is provided or was analyzed.
2010-04-07 | E-GEOD-21248 | biostudies-arrayexpress
Project description:This includes variant calls (single nucleotide variants and small insertions/deletions) from 8086 (mostly British Pakistani/British Bangladeshi) individuals from the following studies:
1. 3781 British Pakistani/British Bangladeshi adults from East London Genes and Health
2. 2791 British South Asian mothers from Born in Bradford
3. 1428 British South Asian adults from Birmingham
4. 86 individuals (mixed ancestries) from families with rare diseases, from Queen Mary University London
All of the Birmingham and most of the Born in Bradford samples were previously sequenced as part of PMID: 26940866.
Mapping was done with bwa-mem and variant calling was carried out with GATK HaplotypeCaller. We removed variant sites for which the following was true:
SNPs: "QD < 2.0 || FS > 30 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"
Indels: "QD < 2.0 || FS > 30 || ReadPosRankSum < -20.0"
| EGAD00001004581 | EGA
Project description:Background: Mortality from preeclampsia (PE) and PE-associated morbidities are 3-to 5-fold higher in persons of African ancestry than in those of Asian and European ancestries. The placenta is central to the etiology of PE. However, how and to what extent the placenta contributes to worse PE outcomes in persons of African ancestry is yet to be fully elucidated. Objective: We aimed to identify molecular pathways that are unique or enriched in placentas of parturient persons of African ancestry with PE with severe features (sPE) compared to those of Asian and European ancestry with sPE. Study design: Bulk RNA sequencing was performed on 50 placentas from parturient persons with sPE of African (n=9), Asian (n=18) and European (n=23) ancestries and 73 normotensive controls of African (n=9), Asian (n=15) and European (n=49) ancestries. Results: Metabolism, hormone regulation and hypoxia/angiogenesis genes, previously described to be upregulated in PE, including: LEP, PAPPA2, INHA, FSTL3, FLT1, PHYHIP and ENG, were upregulated in sPE across ancestries, with high expression of FSTL3 being additionally associated with intrauterine growth restriction (p<.0001). Notably, LEP, FLT1 and PHYHIP were more highly upregulated in sPE placentas from parturient persons of African versus Asian ancestry. Genes associated with allograft rejection and adaptive immune response were selectively upregulated in placentas from African ancestry parturitions and not in those of Asian and European ancestries. Among the allograft rejection/adaptive immune response genes, IL3RA was of particular interest because the patient with the highest placental IL3RA level, a woman of African ancestry with IL3RA levels 4.5-fold above the average for African ancestry parturitions with sPE, developed postpartum cardiomyopathy, and was the only patient out of 123, that developed this condition. Interestingly, the sPE patients of Asian and European ancestries with the highest IL3RA levels for their ancestries developed unexplained tachycardia peripartum, necessitating echocardiography in the European ancestry patient. The association between elevated placental IL3RA levels and unexplained tachycardia or peripartum cardiomyopathy was found to be significant in the 50 sPE patients (p=.0005). Conclusions: African ancestry parturitions are associated with higher placental upregulation of metabolism (LEP) and hypoxia/angiogenesis (FLT1) genes, and selective upregulation of allograft rejection/adaptive immune response genes, including IL3RA. High placental expression of IL3RA may predict worse maternal cardiovascular outcomes, including peripartum cardiomyopathy. Studies evaluating placental IL3RA levels in peripartum cardiomyopathy cohorts are therefore warranted, as are broader studies evaluating placental factors in maternal cardiovascular outcomes postpartum.
2023-11-09 | GSE234729 | GEO
Project description:Exome sequences of three unrelated individuals of south Asian ancestry from the EXCEED study
| EGAD00001007649 | EGA
Project description:48 ǂKhomani San living in the South African Kalahari were genotyped using the Illumina OmniExpress, OmniExpress Plus, and HumanHap550 arrays
2017-05-20 | GSE99090 | GEO
Project description:Previously developed gene expression signatures had high predictive accuracy at distinguishing viral and bacterial infection in a South Asian cohort with ARI caused by typical and atypical pathogens.
2020-07-06 | GSE149947 | GEO