Table 4.
GORs for heterozygotes and homozygotes for two-, three-, and four-SNP haplotypes consisting of SNPs increasing risk in 146 Taiwanese CL/P case-parent trios
| Diplotype | Na (%) | GOR (95% CI) | Diplotype | Na (%) | GOR (95% CI) |
|---|---|---|---|---|---|
| rs599021-rs2235373 (P = 1 × 10−4)b n = 556 | rs2235373-rs2235371 (P < 10−4) n = 548 | ||||
| AA/AA | 140 (25.2) | Reference | AT/AT | 100 (18.3) | Reference |
| AA/AG | 153 (27.5) | 1.35 (0.69–2.66) | AT/AC | 31 (5.7) | 0.18 (0.04–0.90) |
| AA/CG | 103 (18.5) | 1.62 (0.75–3.50) | AT/GC | 221 (40.3) | 0.85 (0.44–1.66) |
| AG/AG | 61 (11.0) | 5.10 (2.08–12.48) | AC/GC | 31 (5.7) | 1.47 (0.52–4.16) |
| AG/CG | 68 (12.2) | 5.95 (2.53–13.99) | GC/ GC | 152 (27.7) | 3.51 (1.66–7.42) |
| CG/CG | 25 (4.5) | 3.96 (1.40–11.24) | 4 types (<4%) | 13 (2.4) | 0.61 (0.05–7.01) |
| 3 types (<4%) | 6 (3.3) | 1.91 (0.15–24.12) | |||
| rs599021-rs2235371 (P = 2 × 10−4) n = 548 | rs2235373-rs2013162 (P = 1 × 10−4) n = 548 | ||||
| AT/AT | 101 (18.4) | Reference | AA/AA | 137 (25.0) | Reference |
| AT/AC | 164 (29.9) | 0.70 (034–1.43) | AA/GA | 39 (7.1) | 1.64 (0.60–4.52) |
| AT/CC | 91 (16.6) | 0.97 (0.43–2.19) | AA/GC | 212 (38.7) | 1.34 (0.73–2.47) |
| AC/AC | 81 (14.8) | 2.29 (1.01–5.20) | GA/GC | 41 (7.5) | 3.94 (1.48–10.46) |
| AC/CC | 82 (15.0) | 3.27 (1.46–7.31) | GC/ GC | 103 (18.8) | 5.01 (2.35–10.66) |
| CC/CC | 25 (4.6) | 3.05 (1.08–8.63) | 4 types (<4%) | 16 (2.9) | 1.26 (0.18–8.61) |
| 3 types (<4%) | 4 (0.7) | 2.04 (0.11–36.83) | |||
| rs599021-rs2013162 (P = 3.7 × 10−3) n = 548 | rs2235371-rs2013162 (P < 10−4) n = 544 | ||||
| AA/AA | 182 (33.2) | Reference | TA/TA | 98 (18.0) | Reference |
| AA/AC | 135 (24.6) | 1.14 (0.63–2.08) | TA/CA | 68 (12.5) | 0.57 (0.23–1.38) |
| AA/CC | 121 (22.1) | 1.44 (0.74–2.79) | TA/CC | 182 (33.5) | 0.78 (0.40–1.55) |
| AC/AC | 29 (5.3) | 3.71 (1.27–10.85) | CA/CC | 68 (12.5) | 2.17 (0.95–5.00) |
| AC/CC | 50 (9.1) | 4.84 (2.05–11.44) | CC/CC | 102 (18.8) | 3.62 (1.64–7.97) |
| CC/CC | 25 (4.6) | 3.16 (1.18–8.47) | 4 types (<4%) | 26 (4.8) | 0.37 (0.08–1.79) |
| 3 types (<4%) | 6 (1.1) | 1.45 (0.11–18.71) | |||
| rs599021-rs2235373-rs2235371 (P < 10−4) n = 548 | rs599021-rs2235371-rs2013162 (P = 1 × 10−4) n = 544 | ||||
| AAT/AAT | 99 (18.1) | Reference | ATA/ATA | 97 (17.8) | Reference |
| AAT/AAC | 31 (5.7) | 0.19 (0.04–0.93) | ATA/ACA | 68 (12.5) | 0.57 (0.23–1.40) |
| AAT/AGC | 128 (23.4) | 0.79 (0.36–1.72) | ATA/ACC | 89 (16.4) | 0.61 (0.26–1.42) |
| AAT/CGC | 90 (16.4) | 0.88 (0.38–2.03) | ATA/CCC | 90 (16.5) | 0.95 (0.41–2.19) |
| AGC/AGC | 59 (10.8) | 3.98 (1.56–10.14) | ACA/ACC | 37 (6.8) | 2.13 (0.79–5.72) |
| AGC/CGC | 68 (12.4) | 4.14 (1.72–9.96) | ACA/CCC | 31 (5.7) | 2.34 (0.84–6.53) |
| CGC/CGC | 25 (4.6) | 2.56 (0.90–7.29) | ACC/ACC | 27 (5.0) | 4.12 (1.26–13.51) |
| 11 types (<4%) | 48 (8.8) | 1.48 (0.54–4.07) | ACC/CCC | 50 (9.2) | 4.59 (1.76–11.97) |
| CCC/CCC | 25 (4.6) | 2.80 (0.97–8.05) | |||
| 8 types (<4%) | 30 (5.5) | 0.53 (0.12–2.30) | |||
| rs599021-rs2235373-rs2013162 (P = 5 × 10−4) n = 548 | rs2235373-rs2235371-rs2013162 (P < 10−4) n = 548 | ||||
| AAA/AAA | 135 (24.6) | Reference | ATA/ATA | 98 (18.0) | Reference |
| AAA/AGA | 39 (7.1) | 1.72 (0.63–4.70) | ATA/ACA | 31 (5.7) | 0.17 (0.04–0.84) |
| AAA/AGC | 105 (19.2) | 1.15 (0.55–2.39) | ATA/GCA | 36 (6.6) | 1.15 (0.41–3.25) |
| AAA/CGC | 103 (18.8) | 1.57 (0.73–3.41) | ATA/GCC | 181 (33.3) | 0.79 (0.39–1.56) |
| AGA/AGC | 23 (4.2) | 5.18 (1.61–16.67) | ACA/GCC | 26 (4.8) | 2.03 (0.68–6.02) |
| AGC/AGC | 28 (5.1) | 5.76 (1.83–18.16) | GCA/GCC | 41 (7.5) | 2.65 (0.98–7.19) |
| AGC/CGC | 50 (9.1) | 6.99 (2.70–18.06) | GCC/GCC | 102 (18.8) | 3.71 (1.67–8.23) |
| CGC/CGC | 25 (4.6) | 3.70 (1.31–10.46) | 12 types (<4%) | 29 (5.3) | 0.40 (0.07–2.15) |
| 8 types (<4%) | 40 (7.3) | 2.57 (0.83–7.97) | |||
| rs599021-rs2235373-rs2235371-rs2013162 (P < 10−4) n = 544 | |||||
| AATA/AATA | 97 (17.8) | Reference | AGCA/AGCC | 23 (4.2) | 3.55 (1.09–11.59) |
| AATA/AACA | 31 (5.7) | 0.19 (0.04–0.93) | AGCC/AGCC | 27 (5.0) | 4.58 (1.39–15.09) |
| AATA/AGCA | 36 (6.6) | 1.31 (0.46–3.72) | AGCC/CGCC | 50 (9.2) | 4.90 (1.85–12.97) |
| AATA/AGCC | 88 (16.2) | 0.63 (0.26–1.50) | CGCC/CGCC | 25 (4.6) | 2.53 (0.89–7.20) |
| AATA/CGCC | 90 (16.5) | 0.91 (0.39–2.10) | 20 types (<4%) | 77 (14.2) | 1.68 (0.07–2.15) |
a
N and n refer to the number of subjects carrying the genotype (including both cases and pseudosibs) and the number of case/pseudocontrol sets.
b
Global P value for the conditional logistic model.
GORs, genotypic odds ratios; SNP, single nucleotide polymorphism; CL/P, cleft lip with or without cleft palate.