Dataset Information

Ethiopia Genome Project low coverage

ABSTRACT: The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity. This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum. The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.

PROVIDER: EGAS00001000238 | EGA |

REPOSITORIES: EGA

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Publications

Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.

Pagani Luca L Schiffels Stephan S Gurdasani Deepti D Danecek Petr P Scally Aylwyn A Chen Yuan Y Xue Yali Y Haber Marc M Ekong Rosemary R Oljira Tamiru T Mekonnen Ephrem E Luiselli Donata D Bradman Neil N Bekele Endashaw E Zalloua Pierre P Durbin Richard R Kivisild Toomas T Tyler-Smith Chris C

American journal of human genetics 20150528 6

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were incre ...[more]

PMID: 26027499

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Project description:Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical, and cultural traditions1,2. Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa, and Asia - in what is termed the Jewish Diaspora3-5. This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people6. While many genetic studies have shed light on Jewish diseases and origins, including those focusing on uniparentally- and biparentally-inherited markers7-16, genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbors have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities, and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not been previously reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and North Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight sub-cluster that overlies Druze and Cypriot samples, but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Bene Israel Indian Jews cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively; despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant. 466 samples are analysed on three different Illumina platforms.

Dataset Information

Ethiopia Genome Project low coverage

Publications

Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.

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