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Peruvian Genome Project - Whole Genome Sequencing

ABSTRACT: In this study, we sequence 150 genomes to high coverage from Native American and mestizo populations in Peru. The majority of our samples possess greater than 90% Native American ancestry, which makes this the most extensive Native American sequencing project to date.

PROVIDER: EGAS00001004995 | EGA |

REPOSITORIES: EGA

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654f9e22-c4f6-4eb2-8671-6a6de6800f8f - samples

Project description:Through the Peruvian Genome Project we generate and analyze the high coverage genomes of 150 individuals where the majority have >90% Native American ancestry and explore questions at the interface of evolutionary genetics, history, anthropology, and medicine. This is the most extensive sampling of high-coverage Native American and mestizo whole genomes to date. Reference: https://doi.org/10.1073/pnas.1720798115

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Genome-wide Patterns of Population Structure and Admixture among Hispanic/Latino Populations

2010-04-08 | GSE21248 | GEO

Genome-wide Patterns of Population Structure and Admixture among Hispanic/Latino Populations

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

Population genetics context of ancient human genome sequence of an extinct Palaeo-Eskimo

Project description:To study the population genetics context of the Saqqaq individual we carried out Illumina Bead-Array-based genotyping on four native North American and twelve north Asian populations.

2010-11-30 | GSE22494 | GEO

Hispanic Lupus GWAS_HISPSLEI Study

Project description:<p>The study comprises SLE patients recruited from specialist rheumatology clinics from the United States, Mexico, Argentina, Chile and Peru. Two strategies were used to enrich samples for Native American ancestry: a. previously genotyped Hispanic and Latin American and US Native American individuals were selected according to their ancestry based on 253 ancestry informative markers as part of the Lupus Large Association 2 Study. The approximate 35% of the samples were primarily of European and Native American admixture was selected; b. the recruitment of patients took place primarily in countries with little African admixture. All samples were genotyped on the HumanOmni1-Quad BeadChip using manifest H at the Oklahoma Medical Research Foundation. The Illumina clustering algorithm with GenomeStudio v2011.1 was used. </p>

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Native American Population Genetics

Project description:Native American Population Genetics

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Genetic analysis of ancestry, admixture, and selection in Bolivian and Totonac populations of the New World

Project description:The genetic structure of some native Bolivians has been substantially influenced by admixture from Europeans, which we estimate to have occurred approximately 360 – 384 years ago. Consistent with historical accounts of male admixture, Y-chromosome haplogroups typical of Europeans were found in 39% of our Bolivian samples. No evidence of African admixture was found in native Bolivians. The Mesoamerican Totonacs have little evidence of European or African admixture. Our analysis indicates that some admixed Bolivians have Native American mtDNA and Y-chromosomes but harbor up to 30% European autosomal ancestry, demonstrating the need for autosomal markers to assess ancestry in admixed populations. From a dense genome-wide panel of 815,377 markers, we developed a set of 324 AIMs, specific for Native American ancestry. As few a 40-50 of these markers successfully predict New World ancestry in the ascertainment panel of Bolivians and Totonacs. The markers easily distinguish New World from Old World ancestry, even for populations more closely related to the Americas such as central and eastern Asians, and were effective for New World vs. Old World comparisons in five other geographically and culturally distinct populations of the Americas. SNPs demonstrating very high divergence between the two Native American populations and major Old World populations are found on haplotypes that are shared and occur at similar frequencies in other indigenous low-admixture American populations examined here (i.e. Pima, Maya, Colombian, Karitiana, and Surui). After excluding the possibility of recent relatedness, our results indicate that native Bolivians and Totonacs share ancestry with other American populations through a substantial contribution from a common founding population, population bottlenecks, and possible natural selection on functional variation.

2011-06-09 | GSE29851 | GEO

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