Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics

BMC Bioinformatics

Table 4 Posterior probabilities of African ethnicity membership in 6 test populations obtained by a GTM model trained on African populations exclusively

Population (pop)	P(ESN\|pop)	P(YRI\|pop)	P(GWD\|pop)	P(LWK\|pop)	P(MSL\|pop)
ASW	0.24	0.37	0.11	0.13	0.14
ACB	0.29	0.42	0.07	0.07	0.15
EUR	0.04	0.10	0.21	0.62	0.04
EAS	0.09	0.19	0.21	0.44	0.07
AMR	0.07	0.15	0.23	0.49	0.06
SAS	0.06	0.13	0.21	0.53	0.05

NB: GTM classification models are restricted by an applicability domain defined by the training set. Here, the training set contains only African populations, excluding ASW and ACB subsets. These posterior probabilities should be considered as a similarity measure between test populations and populations used to build the map, and not as an absolute measure of population admixture. Abbreviations: ASW = Americans of African Ancestry in SW USA; ACB = African Caribbeans in Barbados; ESN = Esan in Nigeria; YRI = Yoruba in Ibadan; Nigeria; GWD = Gambian in Western Divisions in the Gambia; LWK = Luhya in Webuye, Kenya; MSL = Mende in Sierra Leone; EUR = Europeans; EAS = East Asians; AMR = Admixed Americans; SAS = South Asians

ISSN: 1471-2105