Polymorphism analysis of six selenoprotein genes: support for a selective sweep at the glutathione peroxidase 1 locus (3p21) in Asian populations

Table 2 Sequence Diversity and Evolutionary Analysis of 6 Selenoprotein Loci Stratified by Estimated Population

Gene	Ethnic Group	SNPs	Singletons	SYN	NSYN	π × 10-4	Θ × 10-4	D_TTajima's	D_F	F
GPX1
202	Total	38	14	1	3	5.2	8.7	-1.16256	-2.49532*	-2.31912*
48	AA	23	6	1	3	6.5	7.0	-0.25380	-0.23160	-0.28398
62	CA	15	3	0	2	5.3	4.3	0.69670	0.119874	0.38011
46	HI	20	10	0	2	5.1	6.2	-0.55642	-1.92897**	-1.72989
46	PR	15	6	0	2	2.0	4.7	-1.75961**	-1.12837	-1.58364
GPX2
204	Total	47	11	0	0	8.2	8.7	-0.18534	-0.85302	-0.67535
48	AA	27	7			8.1	6.7	0.69919	-0.22648	0.11635
62	CA	33	7			6.7	7.7	-0.43521	0.03790	-0.16317
46	HI	32	8			8.7	8.0	0.31148	-0.13732	0.02421
48	PR	30	8			6.6	7.4	-0.36659	-0.28952	-0.37648
GPX3
204	Total	52	6	1	0	11.0	10.4	0.18669	0.76044	0.60998
48	AA	42	4	1		13.9	11.1	0.84504	1.12623	1.22113
62	CA	30	2	0		8.6	7.5	0.47394	1.29418	1.18465
46	HI	38	8	1		10.1	10.2	-0.03486	0.17869	0.12254
48	PR	37	10	1		9.5	9.8	-0.11667	-0.32911	-0.30155
GPX4
204	Total	31	7	1	0	10.4	7.7	0.99362	-0.65746	0.03750
48	AA	24	6	0		9.9	7.9	0.85392	-0.15103	0.23582
62	CA	21	3	0		10.2	6.5	1.77252**	0.57981	1.19930
46	HI	18	3	0		10.2	6.0	2.24912*	0.46442	1.26672
48	PR	19	3	1		10.0	6.3	1.88377**	0.53274	1.17584
TXNRD1
204	Total	43	10	3	0	3.7	5.2	-0.84233	-0.81317	-0.99372
48	AA	28	5	2		4.4	4.5	-0.09852	0.40341	0.26989
62	CA	22	3	1		3.8	3.4	0.44241	0.64623	0.68209
46	HI	24	7	1		3.9	3.9	-0.02622	-0.44254	-0.35427
48	PR	20	7	2		2.3	3.2	-0.96694	-0.87634	-1.07578
SEPP1
204	Total	24	5	0	2	4.8	3.3	1.25024	-0.41307	0.31238
48	AA	17	3		1	3.8	3.1	0.73630	0.37764	0.59147
62	CA	18	2		1	5.2	3.1	2.05607*	0.80818	1.48364**
46	HI	17	2		2	5.0	3.1	1.83966**	0.79897	1.36158
48	PR	16	0		1	4.5	2.9	1.66728	1.59572*	1.91681*

Single nucleotide polymorphisms (SNPs) were identified by re-sequencing 6 selenoprotein gene regions in a 102 member control population. Nucleotide diversity (π) and the population mutation parameter (Θ) were calculated using the most probable PHASED haplotypes. To determine whether variation was consistent with the expectations of the neutral equilibrium model, neutrality was tested using Tajima's (D_T) and Fu and Li's (D_F and F) statistics. D_T, D_F and F were computed using S, the number of segregating sites, in DNASP.
*Statistical significance: P < 0.05
**Statistical significance: P < 0.10, P > 0.05

ISSN: 2730-6844