Analysis of pharmacogenetic traits in two distinct South African populations

Ikediobi, Ogechi; Aouizerat, Bradley; Xiao, Yuanyuan; Gandhi, Monica; Gebhardt, Stefan; Warnich, Louise

doi:10.1186/1479-7364-5-4-265

Human Genomics

Table 3 Minor allele frequencies (MAFs) of clinically associated single nucleotide polymorphisms in African, US and Asian populations.

From: Analysis of pharmacogenetic traits in two distinct South African populations

					MAF
	Gene	rsID	Minor allele	Polymorphism (NTpos; AA change)	Xhosa (n= 109)	CMA (n= 67)	Yoruba (n= 60)	Luhya (n= 89)	Maasai (n= 143)	Caucasian (n= 60)	Chinese (n= 45)	Hispanic (n= 23)	AAm (n= 24)
ABC transporters	ABCB1	rs2229109	A	1199G > A;S400N	0.0	0.0	0.0	NA	0.0	0.03	0.0	0.0	0.0
	ABCB1	rs9282564	G	61A > G; N21D	0.0	0.0	0.0	NA	NA	0.1	0.0	0.07	0.0
	ABCB1	rs1045642	C	3435C > T	0.89	0.8	0.88	NA	0.84	0.43	0.58	0.45	0.84
	ABCB1	rs4148740	G	12386379A > G	0.14	0.17	0.13	NA	NA	0.1	0.02	NA	0.15
	ABCB1	rs7787082	A	12391327G > A	0.69	0.61	0.68	0.71	0.62	0.18	0.46	NA	0.56
	ABCB1	rs2032583	G	12394837A > G	0.14	0.18	0.25	0.25	0.23	0.16	0.03	0.04	0.15
	ABCB1	rs3789243	G	12455162A > G	0.63	0.61	0.41	0.58	0.44	0.43	0.72	NA	0.6
	ABCB1	rs1128503	T	1236C > T	0.13	0.23	0.12	0.11	0.14	0.39	0.68	0.54	0.06
	ABCB1	rs10248420	G	12399262A > G	0.59	0.56	0.59	0.64	0.56	0.17	0.48	0.12	0.53
	ABCB1	rs2235041	A	12400010G > A	0.12	0.07	0.12	0.1	0.1	0.0	0.0	0.0	0.14
	ABCC2	rs8187707	T	4488C > T;H1496H	0.08	0.08	0.0	0.06	0.09	0.04	0.0	0.0	0.02
	ABCC2	rs2273697	A	1249G > A;V417I	0.11	0.18	0.21	0.2	0.23	0.23	0.07	0.15	0.23
	ABCC2	rs717620	T	-24C > T	0.03	0.04	0.04	0.02	0.04	0.18	0.22	0.23	0.06
Phase I	CYP2B6	rs3745274	T	516G > T;Q172H, *6	0.2	0.23	0.45	0.31	0.37	0.25	0.15	0.27	0.46
	CYP2B6	rs28399499	C	983T > C;I328T, *18	0.17	0.09	0.04	0.07	0.02	0.0	0.0	0.0	0.03
	CYP2B6	rs36079186	C	593T > C; M198T, *27	0.0	0.0	NA	NA	NA	NA	NA	NA	NA
	CYP2C18	rs7896133	A	15213256G > A	0.2	0.2	0.12	0.11	0.16	0.07	0.08	NA	0.1
	CYP2C18	rs2860840	T	15243758C > T	0.0	0.09	0	0.01	0.06	0.35	0.23	0.28	0.09
	CYP2C18	rs10509675	A	15237414G > A	0.15	0.09	0.27	0.18	0.17	0.21	0.02	NA	0.13
	CYP2C19	rs4917623	C	15358094T > C	0.11	0.2	0.18	0.16	0.29	0.49	0.6	NA	0.1
	CYP2C19	rs12248560	T	-806C > T, *17	0.15	0.09	0.27	NA	NA	0.21	0.02	NA	0.15
	CYP2C19	rs4244285	A	681G > A, *2	0.22	0.2	0.16	NA	NA	0.15	0.26	0.16	0.17
	CYP2D6	rs3892097	A	1846G > A, *4	0.0	0.01	NA	NA	NA	0.5	NA	NA	NA
	CYP3A4	rs4986910	C	1334T > C;M445T, *3	0.0	0.0	0.0	NA	NA	0.0	0.0	0.0	0.03
	CYP3A4	rs4986909	T	1247C > T; P416L, *13	0.0	0.0	0.0	NA	NA	0.0	0.0	NA	NA
	CYP3A4	rs28371759	C	878T > C; L293P, *18	0.0	0.0	NA	NA	NA	NA	NA	NA	NA
	CYP3A4	rs4986907	A	485G > A; R162Q, *15A	0.01	0.0	0.0	NA	NA	0.0	0.0	0.0	0.03
	CYP3A4	rs4987161	C	566T > C; F189S, *17	0.0	0.0	0.0	NA	NA	0.0	0.0	NA	NA
	CYP3A4	rs2740574	G	-392A > G, *1B	0.77	0.58	0.75	NA	NA	0.03	0.0	0.11	0.68
	CYP3A5	rs4646450	T	-1630 T > C	0.97	0.83	1.0	0.98	0.85	0.13	0.34	NA	NA
	CYP3A5	rs10264272	A	711G > A;K208K, *6	0.2	0.17	0.15	0.25	0.14	0.0	0.0	0.02	0.11
	CYP3A7	rs10211	G	129 A > G	0.35	0.52	0.75	0.72	0.44	0.06	0.34	0.19	0.58
Phase II	UGT1A1	rs4148323	A	211G > A;G71R, *6	0.0	0.0	0.0	NA	NA	0.0	0.2	0.03	0.0
	UGT1A1	rs887829	T	601324 C > T	0.35	0.36	0.55	NA	NA	0.28	0.08	0.35	0.57
	UGT1A1	rs10929302	A	598536 G > A, *93	0.25	0.29	0.36	NA	NA	0.26	0.08	NA	NA

MAF data for non-South African populations were obtained from the National Center for Biotechnology Information (NCBI) dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP)
Abbreviations: AA, amino acid; AAm, African American; N = total number of samples per population; NA, no data available in the NCBI dbSNP database; NTpos, nucleotide position; Phase I, Phase I drug metabolising enzymes; Phase II, Phase II I drug metabolising enzymes; CMA, Cape Mixed Ancestry; MAF, minor allele frequency
N.B. HapMap Caucasian minor alleles and MAFs are used as the reference in this table.

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ISSN: 1479-7364

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