Table 1.
Association Results
| Population Origin (in Collaboration with) | Genotyped SNPs (Major/Minor allele) | Cleft Type | Number of Individuals (T = 7597) | Number of Affected Individuals | Associated SNP (Associated Allele) | Familial History | TDT p Value rs1149795 | TDT p Value rs3827730 | Relative risk of CPO Conferred by TT Genotype of rs3827730; p value |
|---|---|---|---|---|---|---|---|---|---|
| Belgium | rs6588392 (C/G), rs11205768 (T/C), rs17387761(G/A), rs3827730 (T/C) | mixed | 1072 | 421 | rs3827730 (T) | S | N/A | 0.004 | |
| CPO | 325 | 126 | rs3827730 (T) | S | N/A | 0.001 | 2.72 (1.49-4.98); p = 0.001 | ||
| CL | 227 | 94 | none | S | N/A | 0.23 | |||
| CLP | 520 | 202 | none | S | N/A | 0.45 | |||
| CL/P | 747 | 296 | none | S | N/A | 0.15 | |||
| European descent- Iowa, USA (J. Murray) | rs11205760 (C/T), rs1149795 (T/C), rs3827730 (C/T), rs2784143 (C/T), rs2455636 (G/A) | mixed | 981 | 350 | rs1149795 (C) | F + S | 0.006 | 0.16 | |
| CPO | 246 | 90 | rs1149795 (C) | F + S | 0.02 | 0.34 | 1.23 (0.6–2.53); p = 0.569 | ||
| CL | 275 | 91 | none | F + S | 0.67 | 0.78 | |||
| CLP | 412 | 146 | none | F + S | 0.61 | 0.34 | |||
| CL/P | 42 | 22 | none | F + S | 0.1 | 0.65 | |||
| European descent- Texas, USA (J. Hecht) | rs3827730 (T/C) | CL/P | 499 | N/A | rs3827730 (T) | F + S | N/A | 0.38 | |
| Mexican Hispanics- Texas, USA (J. Hecht) | rs3827730 (T/C) | CL/P | 177 | N/A | rs3827730 (T) | F + S | N/A | 0.14 | |
| Philippines (J. Murray) | rs11205760 (C/T), rs1149795 (T/C), rs3827730 (T/C), rs2784143 (C/T), rs2455636 (G/A) | mixed | 2511 | 570 | none | F | 0.73 | 0.62 | |
| CPO | 22 | 4 | none | F | NI | 0.52 | |||
| CL | 429 | 98 | none | F | 1 | 0.93 | |||
| CLP | 1203 | 246 | none | F | 0.86 | 0.78 | |||
| CL/P | 823 | 212 | none | F | 0.51 | 0.29 | |||
| Germany (E. Mangold) | rs11205760 (C/T), rs17387761 (G/A), rs11587909 (C/T), rs17382596 (T/G), rs3827730 (T/C) | mixed | 1514 | 679 | none | N/A | N/A | 0.16 | |
| CPO | 242 | 99 | none | N/A | N/A | 0.78 | 1.17 (0.63-2.17); p = 0.624 | ||
| CL | 225 | 99 | none | N/A | N/A | 1 | |||
| CLP | 1047 | 481 | none | N/A | N/A | 0.12 | |||
| CL/P | 1272 | 580 | none | N/A | N/A | 0.16 | |||
| Eurocran and Italcleft: IT, NL, UK, HU, SL, ET, SK, and BU (M. Rubini) | rs1149795 (T/C), rs3827730 (C/T), rs17382596 (T/G) | CPO | 843 | 281 | rs3827730 (T) | S | 0.67 | 0.007 | 1.38 (1.02-1.87); p = 0.036 |
| NL | CPO | 165 | 55 | none | S | N/A | 0.42 | 1.02 (0.51-2.05); p = 0.955 | |
| IT | CPO | 183 | 61 | rs3827730 (T) | S | N/A | 0.02 | 2.04 (1.06-3.96); p = 0.034 | |
| UK | CPO | 201 | 67 | none | S | N/A | 0.43 | 1.44 (0.77-2.70); p = 0.252 | |
| Eurocran Western Europe (NL + IT + UK) | CPO | 549 | 183 | rs3827730 (T) | S | N/A | 0.03 | 1.43 (0.98- 2.08); p = 0.064 | |
| Eurocran Eastern Europe (HU, SL, ET, SK, BU) | CPO | 294 | 98 | none | S | N/A | 0.09 | 1.38 (0.82-2.30); p = 0.224 | |
| Belgium + Germany + Eurocran and Italcleft | rs3827730 (C/T) | CPO | 1410 | 506 | rs3827730 (T) | S+N/A | N/A | 0.0007 | 1.51 (1.18-1.93); p = 0.001 |
| Belgium + Germany + Eurocran and Italcleft + Iowa | rs3827730 (C/T) | CPO | 1656 | 596 | rs3827730 (T) | F+S | N/A | 0.0003 | 1.47 (1.17-1.86); p = 0.001 |
TDT was done with the FBAT program for all populations except the European-descent cohort from Texas (APL). Notations are as follows: mixed, all cleft types together (CPO + CL + CLP); CPO, cleft palate only; CL, cleft lip; CLP, cleft lip and palate; CL/P, ceft lip with or without cleft palate; F, familial; S, sporadic; N/A, not available; NI, not informative; T, total; IT, Italy; NL, The Nerherlands; UK, The United Kingdom; HU Hungary; SL Slovenia; ET, Estonia; SK, Slovakia; and BU, Bulgaria. Note that in the CPO cohort from Belgium, 38 patients had isolated PRS (CPO + retrognatia), all others had CPO.