Ethiopia_Genome_Project__low_coverage_ - EGA European Genome-Phenome Archive

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Dataset ID	Description	Technology	Samples
EGAD00001000598	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.	Illumina HiSeq 2000	120
EGAD00001003296	Integrated callset of low coverage Ethiopian and Egyptian genomes from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j.ajhg.2015.04.019)		220
EGAD00010001221	Illumina Omni 2.5M SNPchip data (build37) of Ethiopian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019)	Illumina HumanOmni2-5_8v1_A	124

Publications	Citations
Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Pagani L, Schiffels S, Gurdasani D, Danecek P, Scally A, Chen Y, Xue Y, Haber M, Ekong R, Oljira T, Mekonnen E, Luiselli D, Bradman N, Bekele E, Zalloua P, Durbin R, Kivisild T, Tyler-Smith C. Am J Hum Genet 96: 2015 986-991	84
Ancestry deconvolution and partial polygenic score can improve susceptibility predictions in recently admixed individuals. Marnetto D, Pärna K, Läll K, Molinaro L, Montinaro F, Haller T, Metspalu M, Mägi R, Fischer K, Pagani L. Nat Commun 11: 2020 1628	52
High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation. Mulindwa J, Noyes H, Ilboudo H, Pagani L, Nyangiri O, Kimuda MP, Ahouty B, Asina OF, Ofon E, Kamoto K, Kabore JW, Koffi M, Ngoyi DM, Simo G, Chisi J, Sidibe I, Enyaru J, Simuunza M, Alibu P, Jamonneau V, Camara M, Tait A, Hall N, Bucheton B, MacLeod A, Hertz-Fowler C, Matovu E, TrypanoGEN Research Group of the H3Africa Consortium. Am J Hum Genet 107: 2020 473-486	5
Positive selection in admixed populations from Ethiopia. Walsh S, Pagani L, Xue Y, Laayouni H, Tyler-Smith C, Bertranpetit J. BMC Genet 21: 2020 108	3
Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population. Walsh S, Izquierdo-Serra M, Acosta S, Edo A, Lloret M, Moret R, Bosch E, Oliva B, Bertranpetit J, Fernández-Fernández JM. Sci Rep 10: 2020 20999	2
The genomic history of the Middle East. Almarri MA, Haber M, Lootah RA, Hallast P, Al Turki S, Martin HC, Xue Y, Tyler-Smith C. Cell 184: 2021 4612-4625.e14	20
Predicting environmental and ecological drivers of human population structure. Pless E, Eckburg AM, Henn BM. Mol Biol Evol 40: 2023 msad094	0
The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal. Vallini L, Zampieri C, Shoaee MJ, Bortolini E, Marciani G, Aneli S, Pievani T, Benazzi S, Barausse A, Mezzavilla M, Petraglia MD, Pagani L. Nat Commun 15: 2024 1882	3