Table 5.
Tests of association between SNPs in 12 candidate genes and subgroups of isolated cleft lip with or without cleft palate: cleft lip only and cleft lip with cleft palate.
| SNPsa | Cleft Lip Only | Cleft Lip with Cleft Palate | ||||
|---|---|---|---|---|---|---|
| Case-Control OR (95% CI)b | TDT RR (95% CI)d | Case-Control OR (95% CI)b | TDT RR (95% CI)d | |||
| Heterozygotes | Homozygotesc | Heterozygotes | Homozygotesc | |||
| CLPTM1 | ||||||
| rs3786505 | 0.81 (0.56, 1.19) | 0.95 (0.52, 1.73) | 0.86 (0.58, 1.29) | 0.81 (0.61, 1.06) | 0.81 (0.51, 1.28) | 0.87 (0.65, 1.16) |
| rs204468 | 0.83 (0.57, 1.21) | 0.75 (0.43, 1.33) | 0.70 (0.47, 1.04) | 0.98 (0.74, 1.29) | 0.86 (0.57, 1.30) | 0.95 (0.72, 1.26) |
| rs7257610 | 0.68 (0.30, 1.51) | - | 0.57 (0.17, 1.95) | 0.84 (0.49, 1.42) | - | 0.71 (0.32, 1.61) |
| CRISPLD2 | ||||||
| rs12051468 | 0.94 (0.62, 1.43) | 0.94 (0.56, 1.58) | 0.94 (0.63, 1.40) | 0.97 (0.71, 1.33) | 1.07 (0.73, 1.56) | 1.33 (1.00, 1.77) |
| rs8061351 | 0.88 (0.60, 1.28) | 1.53 (0.76, 3.10) | 0.80 (0.53, 1.21) | 0.86 (0.66, 1.14) | 1.07 (0.60, 1.93) | 0.90 (0.66, 1.22) |
| rs721005 | 1.09 (0.74, 1.61) | 0.98 (0.57, 1.67) | 1.06 (0.73, 1.53) | 1.10 (0.83, 1.47) | 1.08(0.74, 1.60) | 1.08 (0.82, 1.41) |
| rs1546124 | 1.09 (0.75, 1.59) | 0.98 (0.53, 1.80) | 0.86 (0.60, 1.23) | 1.08 (0.82, 1.43) | 0.99 (0.63, 1.55) | 0.89 (0.68, 1.18) |
| rs16974880 | 0.87 (0.60, 1.27) | 0.82(0.44, 1.53) | 1.14 (0.76, 1.72) | 1.31 (0. 99, 1.73) | 1.32 (0.86, 2.04) | 1.39 (1.03, 1.87) |
| rs4783099 | 0.82 (0.56, 1.20) | 0.80 (0.46, 1.38) | 0.98 (0.66, 1.45) | 1.45 (1.07, 1.96) | 1.70 (1.15, 2.52) | 1.36 (1.02, 1.81) |
| FGFR2 | ||||||
| rs1047100 | 0.99 (0.67, 1.45) | 1.98 (0.91, 4.33) | 1.05 (0.69, 1.59) | 1.02 (0.77, 1.34) | 1.31 (0.67, 2.57) | 0.96 (0.71, 1.31) |
| GABRB3 | ||||||
| rs2017247 | 0.88 (0.60, 1.29) | 1.26 (0.67, 2.40) | 0.92 (0.59, 1.45) | 1.12 (0.85, 1.47) | 1.21 (0.74, 1.98) | 1.05 (0.78, 1.41) |
| rs11637141 | 0.73 (0.49, 1.09) | 2.34 (1.28, 4.29) | 0.98 (0.65, 1.47) | 1.12 (0.85, 1.46) | 0.68 (0.34, 1.38) | 0.88 (0.64, 1.21) |
| GLI2 | ||||||
| rs12711538 | 1.04 (0.72, 1.51) | 0.95 (0.48, 1.88) | 1.22 (0.79, 1.90) | 1.10 (0.83, 1.45) | 1.04 (0.63, 1.71) | 0.99 (0.74, 1.33) |
| IRF6 | ||||||
| rs2235371 | 0.48 (0.11, 2.06) | - | 0.33 (0.03, 3.20) | 0.22 (0.05, 0.95) | - | 1.00 (0.14, 7.10) |
| rs2013162 | 0.95 (0.66, 1.38) | 0.78 (0.42, 1.44) | 0.75 (0.50, 1.10) | 0.80 (0.61, 1.06) | 0.65 (0.41, 1.04) | 0.75 (0.57, 1.00) |
| rs7552506 | 0.98 (0.67, 1.42) | 0.89 (0.48, 1.65) | 0.79 (0.54, 1.15) | 0.92 (0.70, 1.21) | 0.84 (0.53, 1.33) | 0.82 (0.62, 1.09) |
| rs2235377 | 0.53 (0.12, 2.27) | - | 0.50 (0.05, 5.51) | 0.37 (0.11, 1.23) | - | 0.25 (0.03, 2.24) |
| PTCH1 | ||||||
| rs2066836 | 0.83 (0.56, 1.23) | 0.39 (0.12, 1.29) | 0.97 (0.59, 1.60) | 0.87 (0.66, 1.16) | 0.24 (0.08, 0.67) | 0.86 (0.60, 1.21) |
| rs357564 | 1.67 (1.14, 2.45) | 1.27 (0.69, 2.36) | 0.88 (0.60, 1.28) | 1.24 (0.94, 1.63) | 1.67 (1.13, 2.49)e | 1.06 (0.82, 1.38) |
| RARA | ||||||
| rs2229773 | 1.68 (0.90, 3.11) | - | 1.86 (0.74, 4.65) | 0.78 (0.43, 1.41) | - | 1.00 (0.46, 2.16) |
| RYK | ||||||
| rs1131262 | 0.96 (0.62, 1.50) | - | 0.64 (0.36, 1.16) | 1.16 (0.85, 1.58) | 0.22 (0.03, 1.72) | 1.04 (0.70, 1.54) |
| rs4470517 | 1.10 (0.74, 1.62) | 1.33 (0.78, 2.27) | 1.11 (0.74, 1.66) | 1.03 (0.77, 1.36) | 1.30 (0.88, 1.92) | 0.96 (0.74, 1.26) |
| SATB2 | ||||||
| rs4673313 | 1.31 (0.84, 2.04) | 0.43(0.06, 3.28) | 0.89 (0.51, 1.54) | 1.31 (0.95, 1.83) | 1.01 (0.36, 2.80) | 1.22 (0.79, 1.90) |
| rs17199393 | 1.25 (0.67, 2.32) | - | 0.64 (0.25, 1.64) | 1.14 (0.71, 1.82) | - | 0.94 (0.49, 1.83) |
| rs16831366 | 1.72 (1. 05, 2.80) | 1.37 (0.16, 11.86) | 1.00 (0.49, 2.05) | 1.36 (0.93, 2.00) | 1.19 (0.23, 6.17) | 0.96 (0.57, 1.64) |
| rs1446636 | 1.33 (0.88, 2.01) | 0.76 (0.17, 3.31) | 1.13 (0.65, 1.95) | 1.29 (0.94, 1.76) | 1.61 (0.71, 3.65) | 1.20 (0.82, 1.76) |
| rs4675475 | 1.41 (0.96, 2.06) | 0.91 (0.38, 2.20) | 0.97 (0.61, 1.56) | 1.24 (0.93, 1.65) | 1.25 (0.71, 2.20) | 1.11 (0.79, 1.56) |
| SUMO1 | ||||||
| rs3769817 | 1.20 (0.79, 1.84) | 1.29 (0.37, 4.53) | 1.00 (0.57, 1.74) | 1.45 (1.08, 1.96) | 0.61 (0.17, 2.11) | 1.10 (0.75, 1.60) |
| rs12470401 | 1.21 (0.79, 1.85) | 1.39 (0.39, 4.92) | 1.04 (0.61, 1.78) | 1.38 (1.02, 1.87) | 0.65 (0.18, 2.27) | 1.06 (0.73, 1.53) |
| TGFA | ||||||
| rs2166975 | 0.68 (0.46, 0.99) | 0.85 (0.39, 1.85) | 0.88 (0.56, 1.38) | 1.01 (0.77, 1.33) | 1.19 (0.69, 2.06) | 1.10 (0.80, 1.53) |
a
SNPs – single nucleotide polymorphisms
b
OR – odds ratio; CI – confidence interval; homozygous major allele was reference category
c
Homozygous for minor allele; homozygote odds ratios were not obtained when there were no cases and/or controls that were homozygous for the minor allele
d
TDT – transmission disequilibrium test; RR – risk ratio; CI – confidence interval
e
Significant difference for test of association, corrected P<0.05, after adjustment for multiple comparisons