Table 3.

P-values of association tests between SNPs and minimal residual disease in St. Jude and COG cohorts

	SJ				COG				Combined
SNP	LG	oLG	oPRB	SV	LG	oLG	oPRB	SV	LG	oLG	oPRB	SV
SNP_A-1709114	0.0086	0.0059	0.0055	0.006	0.0024	0.00171	0.00286	0.003	6.67×10−6	1.27×10−6	2.27×10−6	2.85×10−6
SNP_A-1793591	0.0015	0.0005	0.001	0.0012	0.0181	0.01411	0.01675	0.017	5.15×10−6	1.03×10−6	2.55×10−6	2.64×10−6
SNP_A-1794325	0.0006	0.0006	0.001	0.0011	0.0003	0.00017	0.00031	3×10−4	5.74×10−8	1.43×10−8	4.44×10−8	4.31×10−8
SNP_A-1807959	0.0119	0.0131	0.0186	0.0295	0.001	0.00128	0.00211	0.002	4.96×10−6	3.64×10−6	8.79×10−6	1.29×10−5
SNP_A-1892341	0.0045	0.0062	0.0157	0.018	0.0002	9.45×10−5	8.59×10−5	1×10−4	3.38×10−7	7.17×10−8	1.92×10−7	3.96×10−7
SNP_A-1918014	0.0022	0.0039	0.0107	0.0113	0.0081	0.00808	0.0086	0.011	4.70×10−5	8.23×10−5	0.00023	0.00028
SNP_A-1958136	0.0017	0.0023	0.0051	0.0053	0.0124	0.00993	0.00849	0.009	2.18×10−5	2.35×10−5	3.36×10−5	3.55×10−5
SNP_A-1980357	0.0104	0.0159	0.0414	0.0457	0.0073	0.00734	0.00995	0.018	7.26×10−5	0.00025	0.00123	0.00181
SNP_A-1988256	0.0003	0.0003	0.0008	0.0009	0.0274	0.01297	0.01552	0.017	3.47×10−5	1.96×10−5	6.82×10−5	8.78×10−5
SNP_A-2044445	0.0104	0.0051	0.0017	0.0019	0.0078	0.00226	0.00215	0.00195	0.00013	1.73×10−5	6.74×10−6	6.47×10−6
SNP_A-2062945	0.0006	0.0007	0.0017	0.0018	0.001	0.00216	0.00277	0.003	4.12×10−7	8.67×10−7	2.46×10−6	3.02×10−6
SNP_A-2105458	0.0015	0.0005	0.001	0.3138	0.0274	0.01297	0.01552	0.171	7.74×10−5	9.51×10−6	2.88×10−5	0.08431
SNP_A-2139851	0.005	0.0072	0.0154	0.0176	0.0031	0.00348	0.00562	0.007	1.26×10−5	1.39×10−5	4.85×10−5	7.62×10−5
SNP_A-2172039	0.0027	0.0023	0.0029	0.003	0.0335	0.00424	0.00186	0.0016	0.00059	0.0002	0.0001	9.40×10−5
SNP_A-2174556	0.0005	0.0007	0.002	0.0022	0.0045	0.00559	0.00844	0.009	2.37×10−6	3.93×10−6	1.47×10−5	1.96×10−5
SNP_A-2184177	0.0033	0.003	0.0029	0.0025	0.0056	0.00565	0.00564	0.006	2.85×10−5	2.28×10−5	2.29×10−5	1.99×10−5
SNP_A-2207718	0.0077	0.0036	0.0012	0.0014	0.0093	0.00256	0.00239	0.002	0.00011	1.32×10−5	5.23×10−6	5.18×10−6
SNP_A-2261153	0.0055	0.0049	0.0064	0.036	0.9885	0.00482	0.00319	0.278	0.00319	0.00244	0.00307	0.04401
SNP_A-2264953	0.0008	0.0008	0.0013	0.0026	0.0001	8.8×10−5	0.00016	1×10−4	2.77×10−8	7.47×10−9	2.24×10−7	3.27×10−8
SNP_A-4233826	0.0018	0.0019	0.0031	0.0032	0.0002	0.00032	0.00055	8×10−4	1.26×10−7	6.62×10−8	3.30×10−7	4.47×10−7
SNP_A-4234252	0.016	0.0207	0.0362	0.0403	0.9843	0.01177	0.0057	0.015	0.00079	0.00047	0.00069	0.00116
SNP_A-4236270	0.0013	0.001	0.0007	0.0008	0.0022	0.00348	0.0049	0.005	1.09×10−5	1.15×10−5	1.45×10−5	1.89×10−5
SNP_A-4244750	0.0051	0.0035	0.0032	0.0031	0.0134	0.00518	0.0055	0.006	0.00056	0.0003	0.00031	0.00032
SNP_A-4249789	0.0333	0.0335	0.0416	0.0415	0.0011	0.0007	0.00054	9×10−4	1.83×10−5	6.87×10−6	6.51×10−6	8.98×10−6
SNP_A-4272973	0.0029	0.0024	0.002	0.0019	0.0011	0.00041	0.00036	3×10−4	2.07×10−5	1.05×10−5	7.43×10−6	6.72×10−6

LG stands for logistic regression model on the regrouped binary outcome (recoding as 0 or greater than 0); SV stands for the set-valued method; oLG stands for ordered logistic regression method; oPRB is the usual probit model with IRWLS estimation algorithm. The p-values in bold showed statistically significant at a significance level of 0.002.