TableA1 Summary of TDT for SNPs and haplotypes in 64 candidate genes for non‐syndromic oral cleft in 58 trios, and gene expression in eight structures relevant to craniofacial development.
| Gene | SNP (n) | TDT (p value) | Expression | ||||||
|---|---|---|---|---|---|---|---|---|---|
| 58 Trios* | 40 Trios with CL/P† | Palate lineage | Lip lineage | ||||||
| SNP | Haplotype | SNP | Haplotype | Affy‡ | SAGE§ | Affy‡ | SAGE§ | ||
| Chromosome 2q37 (26 genes/115 SNPs) | |||||||||
| SP110 | 3 | <0.05 | <0.05 | A | A | A | A | ||
| SP100 | 5 | <0.05 | <0.05 | <0.05 | 4 | A | A | A | |
| SPATA3 | 3 | NA | 2 | NA | A | ||||
| FLJ12584 | 4 | <0.05 | NA | 1, 2 | NA | 5, 6 | |||
| PDE6D | 3 | A | A | 6 | 5, 6 | ||||
| EIF4EL3 | 3 | NA | 1, 2 | NA | 6 | ||||
| TNRC15 | 3 | 2 | 1, 2 | 6, 7 | 6 | ||||
| NGEF | 4 | NA | A | NA | A | ||||
| DGKD | 6 | <0.1 | 1–3 | 1, 2 | 6, 7 | 6 | |||
| USP40 | 4 | <0.1 | <0.1 | NA | A | NA | A | ||
| TRPM8 | 6 | NA | A | NA | A | ||||
| CENTG2 | 9 | 1, 2 | 2 | 6 | A | ||||
| ASB18 | 4 | NA | NA | NA | NA | ||||
| IQCA | 4 | NA | A | NA | A | ||||
| COL6A3 | 3 | <0.1 | <0.1 | 1–3 | 1, 2 | 6–8 | 5, 6 | ||
| MLPH | 3 | <0.05 | <0.05 | <0.05 | NA | 2 | NA | A | |
| LRRFIP1 | 4 | <0.1 | <0.1 | 2 | A | 6 | A | ||
| FLJ40411 | 4 | NA | NA | NA | NA | ||||
| NCE2 | 3 | NA | 2 | NA | 5, 6 | ||||
| ASB1 | 4 | A | 1 | A | 5 | ||||
| LOC151171 | 3 | NA | NA | NA | NA | ||||
| HDAC4 | 13 | <0.05 | <0.01 | <0.05 | <0.05 | 1–3 | 1, 2 | 6 | 5, 6 |
| GPC1 | 3 | 1–3 | A | 5–7 | 6 | ||||
| KIF1A | 3 | A | A | A | A | ||||
| PASK | 3 | <0.1 | 1–4 | A | 6 | A | |||
| FARP2 | 8 | A | A | A | A | ||||
| Chromosome 4q21–q25 (7 genes/29 SNPs) | |||||||||
| MGC46496 | 3 | NA | NA | NA | NA | ||||
| ADH1A | 3 | 1, 2 | A | A | A | ||||
| ADH1B | 3 | A | A | 6 | A | ||||
| ADH1C | 8 | <0.01 | <0.001 | <0.05 | <0.05 | A | A | A | A |
| SLC39A8 | 3 | 1–3 | A | 6 | A | ||||
| UBE2D3 | 3 | 1–3 | A | 5–7 | 4 | ||||
| LEF1 | 6 | <0.05 | <0.05 | <0.1 | <0.1 | A | 2 | 5, 6 | 4 |
| Chromosome 6p23–p25 (6 genes/20 SNPs) | |||||||||
| SEC5L1 | 3 | NA | A | NA | A | ||||
| GMDS | 3 | A | 1 | 8 | A | ||||
| BMP6 | 3 | A | A | A | A | ||||
| C6orf105 | 3 | <0.05 | <0.05 | <0.05 | <0.1 | 2 | A | A | A |
| EDN1 | 4 | NA | NA | NA | NA | ||||
| JARID2 | 4 | 1–3 | 1, 2 | 5–7 | 3, 4 | ||||
| Chromosome 11p11–p13 (6 genes/22 SNPs) | |||||||||
| C11orf8 | 3 | 2, 3 | A | 6, 7 | 3, 4 | ||||
| ABTB2 | 3 | 3 | 2 | 6 | 3 | ||||
| CD44 | 4 | <0.1 | <0.05 | <0.05 | <0.05 | 1–4 | 1, 2 | 6, 8 | 3, 4 |
| ALX4 | 4 | <0.05 | <0.05 | NA | A | NA | A | ||
| LOC220074 | 5 | NA | 1 | NA | A | ||||
| WNT11 | 3 | <0.1 | <0.05 | <0.1 | A | A | 7 | A | |
| Chromosome 11q23–q25 (5 genes/29 SNPs) | |||||||||
| KIAA1959 | 5 | <0.1 | <0.1 | NA | NA | NA | NA | ||
| KIAA1201 | 9 | A | A | A | A | ||||
| SCN3B | 8 | <0.01 | <0.001 | <0.01 | NA | A | A | A | |
| ZNF202 | 4 | <0.05 | 1–4 | A | 5, 6 | A | |||
| LOC338661 | 3 | NA | NA | NA | NA | ||||
| Chromosome 17q21–q25 (14 genes/59 SNPs) | |||||||||
| CRHR1 | 5 | <0.05 | <0.05 | 1–4 | NA | 5–8 | NA | ||
| IMP5 | 2 | <0.1 | <0.05 | NA | A | NA | A | ||
| MAPT | 9 | <0.05 | 2, 4 | A | 8 | A | |||
| LOC284058 | 5 | NA | 1, 2 | NA | 4 | ||||
| NSF | 3 | <0.1 | <0.1 | 1–3 | A | 5, 6 | A | ||
| WNT3 | 5 | <0.1 | NA | A | NA | A | |||
| WNT9B | 3 | NA | NA | NA | NA | ||||
| ITGB3 | 5 | 1 | A | A | A | ||||
| DLX4 | 3 | 2 | A | A | A | ||||
| KCNJ16 | 5 | NA | NA | NA | NA | ||||
| KCNJ2 | 4 | 2 | A | A | A | ||||
| LOC400618 | 3 | NA | NA | NA | NA | ||||
| USP36 | 4 | <0.1 | NA | 1, 2 | NA | 3, 4 | |||
| TIMP2 | 3 | A | 1, 2 | A | 3, 4 | ||||
*58 trios including four African American, one Filipino American, and two inter‐racial families; †40 trios with CL/P; ‡for Affymetrix GeneChip analysis (Affy), the structures analyzed are: 1) 4th week pharyngeal arch 1, 2) 5th week pharyngeal arch 1, 3) 6th week maxilla, 4) 8.5th week palatine shelves, 5) 4th week frontonasal prominence, 6) 5th week frontonasal prominence, 7) 6th week median nasal prominence, and 8) 8.5th week upper lip; A, absent call; NA, not available because no probe sets were on the chip; §for Serial Analysis of Gene Expression (SAGE), the structures analyzed are: 1) 4th week pharyngeal arch 1, 2) 5th week pharyngeal arch 1, 3) 4th week frontonasal prominence, 4) 5th week frontonasal prominence; A, absent; NA, not available because appropriate tag sequence information was omitted.