Evaluation of common genetic variants in 82 candidate genes as risk factors for neural tube defects

BMC Medical Genetics

Table 4 The Ten Independent ^* Association Signals Exhibiting the Lowest Uncorrected p-values for Any Test of NTD Association

	Risk Allele Frequency^**	Cohort***	Model	OR	95% CI (LL)	95% CI (UL)	P
1 MFTC
rs17803441	0.07	Combined	LR CC Continuous	1.61	1.23	2.08	0.0003
MFTC
rs3134260	0.07	Combined	LR CC Continuous	1.56	1.22	2.04	0.0006
2 CDKN2A			LL Maternal effect,
rs3218009	0.13	Primary	Dominant	2.32	1.45	3.71	0.0004
3 ADA
rs2299686	0.45	Combined	LR MC Dominant	1.56	1.22	2.04	0.0005
ADA
rs406383	0.25	Combined	LR MC Continuous		1.12	1.58
ADA
rs427483	0.33	Combined	LR MC Continuous	1.28	1.10	1.52	0.0018
4 PEMT
rs1108579	0.52	Combined	TDT	1.47	1.18	1.82	0.0006
PEMT
rs11656215	0.49	Combined	LL Case effect, recessive	1.68	1.24	2.28	0.0008
PEMT
rs4646402	0.57	Combined	LL Case effect, dominant	1.67	1.25	2.17	0.0005
5 CUBN
rs7070148	0.90	Combined	LR MC Continuous	1.64	1.22	2.17	0.0010
CUBN
rs2273737	0.89	Combined	LR MC Continuous	1.54	1.18	2.04	0.0021
6 GART
rs2070388	0.91	Combined	TDT	1.89	1.28	2.78	0.0012
GART
rs2070388	0.91	Combined	LL Case effect, dominant	1.96	1.30	2.94	0.0012
7 ADA rs6031682	0.16	Combined	LR CC Dominant	1.49	1.16	1.92	0.0016
8 DNMT3A rs7560488	0.42	Primary	LL Case effect, recessive	2.10	1.31	3.38	0.0021
9 MTHFD1 rs2236225	0.40	Primary	LR MC Dominant	1.96	1.28	3.03	0.0022
10 T (Brachyury) rs10806845	0.51	Combined	LR MC Recessive	1.54	1.16	2.00	0.0023

^* LD between SNPs within an association signal are as follows: MFTC (D’ = 1, r² = 0.993), ADA (D’ > 0.822, r² > 0.394), PEMT (D’ > 0.693, r² > 0.428) and CUBN (D’ = 0.935, r² = 0.823). ADA rs6031682 was designated as an independent association signal because it shares very little LD (D’ < 0.206, r² < 0.016) with the other ADA SNPs (rs2299686, rs406383, rs427483).
^**Frequency of the risk allele was calculated using control sample genotypes.
^*** Primary: 320 triads, 341 controls. Combined: 570 triads, 999 controls.

ISSN: 1471-2350