Table 4.

Gene-based analysis stratified by histologic subtype

Seminoma cases (N=4,529) vs. controls (N=27,693)			Non-seminomatous cases (N=4,630) vs. controls (N=27,693)
GENE	perm-p#	q-value§	GENE	perm-p#	q-value§
MTHFR	1×10−5	2.8×10−4	DNMT1	7.9×10−3	0.22
AHCY	0.02	0.2	MTRR	0.02	0.35
DNMT3L	0.02	0.2	MBD3	0.05	0.48
SHMT1	0.05	0.34	MBD3L1	0.09	0.64
ZBTB38	0.06	0.36	MTHFR	0.2	0.70
ZBTB4	0.07	0.40	ZBTB4	0.26	0.70
MAT1A	0.10	0.40	DNMT3B	0.26	0.70
MBD3L1	0.12	0.41	MAT1A	0.27	0.70
MECP2	0.13	0.41	TET1	0.28	0.70
CBS	0.20	0.55	CBS	0.30	0.70
MAT2A	0.27	0.61	BHMT	0.32	0.70
MTRR	0.28	0.61	MECP2	0.37	0.70
TET1	0.28	0.61	UHRF1	0.38	0.70
MBD1	0.38	0.76	MBD1	0.39	0.70
DNMT3B	0.41	0.77	MAT2B	0.39	0.70
UHRF1	0.46	0.77	AHCY	0.40	0.70
MBD3	0.47	0.77	SHMT1	0.48	0.75
MAT2B	0.51	0.79	DNMT3L	0.48	0.75
TET3	0.56	0.83	TET3	0.57	0.84
MBD2	0.61	0.84	MTR	0.61	0.84
DNMT1	0.67	0.84	TET2	0.63	0.84
BHMT	0.68	0.84	DNMT3A	0.68	0.87
TET2	0.69	0.84	ZBTB38	0.72	0.88
GADD45b	0.76	0.86	CTCF	0.78	0.91
DNMT3A	0.77	0.86	MAT2A	0.85	0.95
MBD4	0.88	0.94	MBD2	0.95	0.99
MTR	0.90	0.94	MBD4	0.95	0.99
CTCF	0.96	0.96	GADD45b	0.99	0.99

^#Gene level p-value computed by MAGMA after 100,000 permutations

^§Gene level q-value on permutation p-value