Table 8.

Top 5 CL/P SNPs from our PIX-LRT analysis and from Patel et al. (2013).

Our Top 5	Patel Top 5	Marker	Position	Gene	MAFb	Method	Comb. Z stat	RB	RG1
1	1	rs5981162	68318753	EFNB1,	0.076	PIX EM	−5.82	0.48	0.56
				PJA1a		SSX	−4.79	0.48	0.58
						Parent only	−3.09	0.45	0.51
2	–	rs5980788	68315938	EFNB1,	0.039	PIX EM	−4.26	0.49	0.54
				PJA1a		SSX	−4.01	0.45	0.53
						Parent only	−1.38	0.84	0.45
3	2	rs5928207	33244129	DMD	0.357	PIX EM	−3.90	0.73	0.87
						SSX	−4.72	0.67	0.74
						Parent only	−0.02	0.90	1.22
4	–	rs5930900	135296409	MAP7D3	0.370	PIX EM	3.69	1.22	1.30
						SSX	2.24	1.13	1.28
						Parent only	1.71	1.40	1
5	–	rs5905410	44584855	FUNDC1,	0.356	PIX EM	−3.69	0.81	0.72
				DUSP21a		SSX	−3.39	0.81	0.67
						Parent only	−1.99	0.77	0.72
–	3	rs5928208	33253904	DMD	0.390	PIX EM	−3.09	0.76	0.92
						SSX	−4.60	0.65	0.75
						Parent only	1.34	1.07	1.57
–	4	rs6631759	33239353	DMD	0.289	PIX EM	−3.17	0.75	0.90
						SSX	−4.45	0.66	0.73
						Parent only	0.55	0.99	1.33
–	5	rs5971698	33245234	DMD	0.366	PIX EM	−3.08	0.76	0.93
						SSX	−4.33	0.65	0.83
						Parent only	1.02	1.09	1.32

The top 5 from Patel et al. (2013), after excluding SNPs that raised genotyping concern. Parent informed X-LRT (PIX-LRT) with the EM, Sex stratified X-LRT (SSX-LRT) on complete data, and a parent only analysis on complete data are used to calculate relative risk for CL/P in the combined Asian and Caucasian families. Combined Z statistics are used as opposed to LRT statistics to show direction of effect and are calculated from the sex-stratified analysis, as mentioned in the methods section.

^aThis marker lies in the intergenic region between the genes shown.

^bThe minor allele frequency calculated from the parents in the population, not stratified by cleft type.