Identification of population substructure among Jews using STR markers and dependence on reference populations included

Listman, Jennifer B; Hasin, Deborah; Kranzler, Henry R; Malison, Robert T; Mutirangura, Apiwat; Sughondhabirom, Atapol; Aharonovich, Efrat; Spivak, Baruch; Gelernter, Joel

doi:10.1186/1471-2156-11-48

Table 2 average, variance, and standard deviation of percent assignment value per cluster when K = 4

From: Identification of population substructure among Jews using STR markers and dependence on reference populations included

average, variance, and standard deviation of percent assignment value per cluster when K = 4
N		Southern cluster			Northern cluster			Asian cluster			African cluster
	grandparental world region of origin (GRO)	ave	var	sd	ave	var	sd	ave	var	sd	ave	var	sd
49	Asia	0.652	0.106	0.326	0.273	0.086	0.294	0.057	0.026	0.160	0.018	0.000	0.017
119	Africa (except South Africa, including North Africa)	0.621	0.077	0.278	0.311	0.077	0.277	0.022	0.001	0.023	0.047	0.011	0.105
44	Middle East (including Turkey)	0.606	0.087	0.296	0.341	0.087	0.296	0.025	0.001	0.027	0.028	0.003	0.054
8	Balkans (Greece, former Yugoslavia, Bulgaria)	0.493	0.133	0.365	0.474	0.138	0.372	0.021	0.000	0.017	0.012	0.000	0.013
34	Former Soviet Union	0.326	0.118	0.344	0.623	0.126	0.355	0.033	0.002	0.046	0.018	0.001	0.032
9	North America, Australia, or South Africa	0.283	0.088	0.297	0.671	0.088	0.296	0.024	0.001	0.032	0.022	0.000	0.008
115	Western, Central, or Eastern Europe	0.244	0.070	0.264	0.723	0.070	0.265	0.019	0.000	0.022	0.015	0.000	0.017
grandparental group affiliation
230	Non-Ashkenazi	*0.602*	0.090	0.300	*0.334*	0.088	0.296	*0.031*	0.006	0.079	*0.033*	0.004	0.061
136	Ashkenazi	*0.233*	0.067	0.260	*0.729*	0.069	0.263	*0.023*	0.001	0.032	*0.014*	0.000	0.016
grandparental country of birth (GCB)
46	Yemen	0.793	0.051	0.226	0.157	0.049	0.220	0.023	0.001	0.031	0.026	0.003	0.052
5	Afghanistan/Uzbekistan	0.716	0.079	0.281	0.243	0.075	0.274	0.023	0.001	0.023	0.017	0.000	0.008
4	Egypt	0.661	0.049	0.221	0.280	0.053	0.231	0.026	0.001	0.023	0.033	0.000	0.017
4	Bulgaria (included on Fig. 2 with Balkan)	0.629	0.105	0.324	0.329	0.109	0.330	0.029	0.000	0.019	0.013	0.000	0.008
13	Iran	0.613	0.119	0.345	0.345	0.107	0.327	0.018	0.001	0.023	0.024	0.001	0.031
29	Iraq	0.603	0.087	0.295	0.353	0.085	0.292	0.025	0.001	0.025	0.019	0.000	0.022
14	Libya	0.585	0.055	0.234	0.334	0.071	0.266	0.010	0.000	0.005	0.071	0.012	0.109
47	Morocco	0.578	0.089	0.298	0.368	0.089	0.298	0.024	0.001	0.022	0.030	0.002	0.039
10	Tunisia	0.541	0.039	0.198	0.355	0.043	0.208	0.018	0.000	0.008	0.086	0.007	0.083
6	India	0.537	0.158	0.398	0.091	0.015	0.121	0.357	0.119	0.346	0.014	0.000	0.008
5	Turkey	0.511	0.086	0.293	0.434	0.105	0.324	0.030	0.001	0.024	0.025	0.000	0.017
42	Ethiopian Jews	0.325	0.074	0.272	0.078	0.008	0.089	0.046	0.004	0.064	0.552	0.097	0.312
7	Belorus/Lithuania/Latvia/Ukraine	0.291	0.145	0.381	0.678	0.145	0.381	0.019	0.000	0.014	0.012	0.000	0.009
31	Poland	0.250	0.090	0.299	0.719	0.090	0.300	0.018	0.000	0.020	0.013	0.000	0.010
18	Romania	0.249	0.058	0.240	0.724	0.058	0.240	0.014	0.000	0.012	0.014	0.000	0.014
6	Czech/Hungary/Austria	0.231	0.056	0.237	0.737	0.056	0.237	0.018	0.000	0.016	0.014	0.000	0.005
7	Russia	0.165	0.077	0.277	0.801	0.085	0.292	0.025	0.000	0.018	0.010	0.000	0.008
6	Ukraine	0.120	0.003	0.055	0.834	0.005	0.073	0.024	0.001	0.032	0.021	0.000	0.015
6	Germany	0.075	0.005	0.068	0.865	0.005	0.067	0.050	0.002	0.048	0.010	0.000	0.002

Shown, for a given subset of individuals, are average, variance, and s.d. of assignment values from STRUCTURE results when K = 4. Differences in assignment values for Northern, Southern, Asian, and African clusters (italicized and in bold) were found to be significant between Non-Ashkenazi and Ashkenazi Jews based on 10000 permutations of assignment values. Variance of Northern and Southern assignment values was high within a subset based on grandparental country of birth (GCB), with the exception of Ukraine and Germany (italicized). For GCB, in four instances, individuals were combined into a subset when GCBs were adjoining geographically and had a history of border shifts and periods of unification or division (ex: Czech/Hungary/Austria), such that the town or city in which a grandparent was born might currently lie in one of the neighboring countries rather than the stated GCB.

Back to article page

ISSN: 2730-6844

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Genomic Data

Contact us