Table 1. Association analysis (TDT), both allelic and haplotype, between NSCL/P and IRF6 SNPs rs642961 (G>A) and rs2235371 (V274I) in Norwegian, Danish, European and Filipino families as calculated in the full dataset (including intact extended kindreds).
Statistically significant P-values (i.e. P-values ≤ 0.0016) for positive associations are in bold, and for negative associations are in italics
| Population (N families) | TDT results | Haplotype TDT P-value (haplotype frequency) | |||||
|---|---|---|---|---|---|---|---|
| rs2235371 (V274I) | rs642961 | Overall | V-G | V-A | I-G | I-A | |
| P-value (inf fam, V freq a) | P-value (inf fam, A freq a) | P-value | P-value | P-value | P-value | P-value | |
| Norway (314) | 0.09 (22, 98%) | 0.005 (130, 26%) | 0.01 | 0.01 (72%) d | 0.004 (26%) | 0.35 (2%) | NA e |
| Denmark (360) | NA (8, 98%) | 1e-04 (165, 24%) | 0.003 | 5e-04 (73%) d | 3e-04 (25%) | 0.76 (2%) | NA ( <1%) e |
| EUROCRAN b (453) | 0.64 (17, 98%) | 0.003 (233, 25%) | 0.02 | 0.003 (74%) d | 0.003 (25%) | 0.72 (1%) | NA (<1%) e |
| Europec (1127) | 0.49 (47, 98%) | 3e-08 (528, 24%) | 3e-06 | 4e-07 (73%) d | 2e-07 (25%) | 0.87 (2%) | NA (<1%) e |
| Philippines (657) | 6e-12 (337, 75%) | 6e-06 (359, 32%) | 7e-11 | 0.38 (47%) | 1e-06 (31%) | 1e-09 (21%) d | 0.007(0.5%) d |
| TOTAL CL/P(1784) | 1e-11 (384, 88%) | 1e-11 (887, 27%) | 9e-16 | 0.005 (61%) d | 8e-13 (30%) | 4e-09 (11%) d | 0.004 (<1%) d |
| SUBSETS: | |||||||
| TOTAL CL(743) | 1e-07 (162, 89%) | 1e-11 (399, 30%) | 1e-11 | 0.001(58%) d | 5e-11(30%) | 1e-06 (12%) d | NA (<1%) e |
| TOTAL CLP(1041) | 1e-05 (222, 89%) | 8e-04 (488, 25%) | 3e-05 | 0.43 (63%) | 4e-04 (26%) | 5e-04 (11%) d | NA (<1%) e |
| TOTAL PALATE(N=419) | 0.78 (42, 97%) | 0.67 (179, 22%) | 0.95 | 0.76 (73%) | 0.79 (21%) | 0.89 (5%) | NA (<1%) e |
V freq: frequency of associated V allele of rs223537 (V274I) and A freq: frequency of associated A allele of rs642961. Frequencies are estimated from the founders in the family data using FBAT program.
EUROCRAN are trios from the Netherlands (CL/P=274, PALATE=63), United Kingdom (CL/P=114, PALATE=67) and Italy (CL/P=64, PALATE=23) combined.
Europe is the combination of data from EUROCRAN Project , Norway (CL/P=314, PALATE=118) and Denmark (CL/P=360, PALATE=119).
Negative association of haplotype.
NA: Not Applicable: the haplotype I-A does not exist or exists with frequency <1% and/or in less than 10 informative families.