Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin

Table 3 Validation of eight PyroAssays performed in the independent set of B-lymphocyte cell lines

PyroAssay number_ position of CpG in the assay	CEU (n)	CHB (n)	CEU.mean	CHB.mean	CEU.var	CHB.var	CEU.mean - CHB.mean	padj_beta	*Pop_diff* potential
1_CpG1	34	34	0.800	0.759	0.008	0.006	0.040	0.032	1
2_CpG1	34	34	0.243	0.252	0.052	0.040	−0.008	0.723	0
3_CpG1	34	34	0.246	0.222	0.069	0.051	0.024	0.828	0
3_CpG2	34	34	0.203	0.168	0.044	0.031	0.035	0.696	0
5_CpG1	34	34	0.718	0.594	0.057	0.041	0.124	0.049	1
5_CpG2	34	34	0.561	0.420	0.046	0.046	0.141	0.040	1
5_CpG3	34	34	0.522	0.448	0.064	0.049	0.074	0.319	0
6_CpG1	34	34	0.132	0.242	0.017	0.029	−0.110	0.007	1
6_CpG2	34	34	0.236	0.343	0.036	0.031	−0.107	0.018	1
8_CpG1	35	35	0.481	0.180	0.111	0.039	0.301	0.000	1
8_CpG2	35	35	0.492	0.166	0.125	0.050	0.325	0.000	1
8_CpG3	35	35	0.459	0.193	0.108	0.050	0.267	0.002	1
9_CpG1	34	34	0.713	0.806	0.042	0.035	−0.093	0.075	0
9_CpG2	34	34	0.632	0.772	0.035	0.021	−0.140	0.001	1
9_CpG3	34	34	0.657	0.784	0.049	0.030	−0.127	0.017	1
10_CpG1	30	31	0.146	0.561	0.035	0.055	−0.415	0.000	1
10_CpG2	30	31	0.171	0.640	0.043	0.062	−0.469	0.000	1

CpG sites characterized by statistically significant inter-population differences in their methylation level are bolded. padj_beta: p-value after Benjamin Hochberg correction; pop-diff potential: differentiation potential of individual sites: 0-non-differentiating; 1-differentiating

ISSN: 1471-2164