Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa

Bains, Ripudaman K; Kovacevic, Mirna; Plaster, Christopher A; Tarekegn, Ayele; Bekele, Endashaw; Bradman, Neil N; Thomas, Mark G

doi:10.1186/1471-2156-14-34

BMC Genomic Data

Table 1 Genotype and allele frequencies and tests for deviation from Hardy-Weinberg Equilibrium (χ ² p -values given)

From: Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa

Region	Country	Population	CYP3A51/CYP3A53						CYP3A56*						CYP3A57*
			AA	AG	GG	Total	G [*3]	HWE	GG	GA	AA	Total	A [*6]	HWE	−/−	-/T	T/T	Total	T [*7]	HWE
Europe	Armenia	Southern Armenians	0	10	90	100	0.95	1.00	100	0	0	100	0.00	N/A	100	0	0	100	0.00	N/A
	Turkey	Anatolian Turks	2	10	62	74	0.91	0.11	74	0	0	74	0.00	N/A	74	0	0	74	0.00	N/A
Arabian	Yemen	Yemeni from Hadramaut	2	21	59	82	0.85	1.00	77	5	0	82	0.03	1.00	80	2	0	82	0.01	1.00
Peninsula		Yemeni from Sena and Msila	7	17	13	37	0.58	0.74	29	7	1	37	0.12	0.42	35	2	0	37	0.03	1.00
North Africa	Algeria	Northern Algerians	9	42	108	159	0.81	0.12	146	15	0	161	0.05	1.00	159	2	0	161	0.01	1.00
	Morocco	Berbers	3	28	54	85	0.80	1.00	79	7	0	86	0.04	1.00	85	1	0	86	0.01	1.00
	Sudan	Northern Sudanese	24	58	51	133	0.60	0.29	104	28	0	132	0.11	0.36	135	1	0	136	0.00	1.00
		Sudanese from Kordofan	11	11	8	30	0.45	0.16	19	10	1	30	0.20	1.00	29	1	0	30	0.02	N/A
East Africa	Ethiopia	Afar	10	31	32	73	0.65	0.61	47	26	0	73	0.18	0.11	73	0	0	73	0.00	N/A
		Amhara	14	22	40	76	0.67	0.004	55	19	2	76	0.15	0.67	76	0	0	76	0.00	N/A
		Anuak	38	32	6	76	0.29	1.00	44	25	7	76	0.26	0.23	75	1	0	76	0.01	1.00
		Maale	20	36	19	75	0.49	0.82	53	22	0	75	0.15	0.34	74	1	0	75	0.01	1.00
		Oromo	12	28	34	74	0.65	0.20	55	19	1	75	0.14	1.00	75	0	0	75	0.00	N/A
	Republic of South Sudan	Southern Sudanese	74	42	9	125	0.24	0.46	58	50	15	123	0.33	0.42	117	8	0	125	0.03	1.00
	Tanzania	Chagga	28	18	4	50	0.26	0.71	36	14	0	50	0.14	0.57	41	9	0	50	0.09	1.00
	Uganda	Bantu speakers from Ssese	36	3	0	39	0.04	1.00	22	17	0	39	0.22	0.16	23	16	0	39	0.21	0.31
West Africa	Ghana	Asante	27	8	0	35	0.11	1.00	20	13	1	34	0.22	1.00	29	5	0	34	0.07	1.00
		Bulsa	58	29	3	90	0.19	1.00	61	28	0	89	0.16	0.11	69	19	2	90	0.13	0.62
		Kasena	28	17	2	47	0.22	1.00	31	16	0	47	0.17	0.32	35	12	0	47	0.13	1.00
	Senegal	Manjak	57	29	4	90	0.21	1.00	59	24	9	92	0.23	0.02	81	13	0	94	0.07	1.00
		Wolof	55	31	8	94	0.25	0.27	58	31	1	90	0.18	0.29	78	15	1	94	0.09	0.55
West Central	Cameroon	Kotoko	18	21	0	39	0.27	0.04	23	16	1	40	0.23	0.65	36	4	0	40	0.05	1.00
Africa		Shewa Arabs	26	31	12	69	0.40	0.62	42	24	3	69	0.22	1.00	60	9	0	69	0.07	1.00
		Mayo Darle	66	38	13	117	0.27	0.06	71	33	13	117	0.25	0.01	102	15	0	117	0.06	1.00
		Somie, Cameroonian Grassfields	36	28	1	65	0.23	0.16	44	19	2	65	0.18	1.00	52	13	0	65	0.10	1.00
	Congo	Congolese from Brazzaville	35	18	2	55	0.20	1.00	43	11	1	55	0.12	0.55	45	10	0	55	0.09	1.00
	Nigeria	Igbo	64	23	0	87	0.13	0.35	60	24	4	88	0.18	0.47	73	12	2	87	0.09	0.14
South East	Malawi	Chewa	66	25	1	92	0.15	1.00	66	23	3	92	0.16	0.69	60	31	0	91	0.17	0.06
Africa		Lomwe	13	4	1	18	0.17	N/A	10	8	0	18	0.22	N/A	14	4	0	18	0.11	N/A
		Ngoni	15	2	1	18	0.11	N/A	9	6	3	18	0.33	N/A	16	2	0	18	0.06	N/A
		Tumbuka	44	18	0	62	0.15	0.34	40	17	5	62	0.22	0.14	45	17	0	62	0.14	0.59
		Yao	37	18	1	56	0.18	0.67	43	12	1	56	0.13	1.00	46	10	0	56	0.09	1.00
	Mozambique	Sena	58	21	3	82	0.16	0.44	51	28	5	84	0.23	0.75	59	25	1	85	0.16	0.68
	South Africa	Bantu speakers	22	17	2	41	0.26	1.00	29	9	3	41	0.18	0.10	34	4	2	40	0.10	0.03
	Zimbabwe	Lemba	17	6	0	23	0.13	1.00	13	10	1	24	0.25	1.00	17	7	0	24	0.15	1.00
		Zimbabweans from Mposi	36	7	4	47	0.16	0.008	36	10	3	49	0.16	0.09	34	16	2	52	0.19	1.00

HWE could not be calculated for the Lomwe and Ngoni as both populations had fewer than 50 chromosomes meaning that the test had insufficient power. No population deviated from Hardy-Weinberg equilibrium, following Bonferonni correction (for CYP3A5*3: adjusted p value = 0.00139; correction for 36 tests, for CYP3A5*6: adjusted p value=0.0015; correction for 34 tests, for CYP3A5*7: adjusted p value=0.0017; correction for 30 tests). Deviations from HWE cannot be calculated for monomorphic loci: labeled “N/A” on the Table. “Total” refers to the number of individuals, from a given population, successfully genotyped at each locus. Population refers to the grouping of individuals either by self-declared ethnicity or geography/place collected.

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