Table 1.
Subphenotypes, Sex, and Sample Types of Study Cohort That Passed Quality Control Checks and Were Included in Statistical Analyses.
| Cleft Subphenotype of Probands | Samples per Population, n |
|||
|---|---|---|---|---|
| Ghana | Ethiopia | Nigeria | Total | |
| Case-control cohort | ||||
| NSCL | 162 | 101 | 77 | 340 |
| NSCLP | 144 | 143 | 74 | 361 |
| NSCPO | 102 | 21 | 40 | 163 |
| Unrelated controls | 408 | 357 | 313 | 1078 |
| Case-parent trios | ||||
| NSCL | 52 | 2 | 20 | 74 |
| NSCLP | 48 | 3 | 26 | 77 |
| NSCPO | 34 | 1 | 7 | 42 |
| Case-parent dyads | ||||
| NSCL | 77 | 84 | 51 | 212 |
| NSCLP | 76 | 134 | 47 | 257 |
| NSCPO | 53 | 20 | 32 | 105 |
| Other trios | ||||
| NSCL | 18 | 0 | 0 | 18 |
| NSCLP | 14 | 0 | 0 | 14 |
| NSCPO | 11 | 0 | 0 | 11 |
| Other dyads | ||||
| NSCL | 8 | 0 | 0 | 8 |
| NSCLP | 3 | 0 | 0 | 3 |
| NSCPO | 3 | 0 | 0 | 3 |
| Singletons | ||||
| NSCL | 5 | 13 | 6 | 24 |
| NSCLP | 1 | 8 | 1 | 10 |
| NSCPO | 2 | 0 | 1 | 3 |
| Tetrads | ||||
| NSCLP | 2 | 0 | 0 | 2 |
| Pentads | ||||
| NSCLP | 1 | 0 | 0 | 1 |
Case probands consisted of 423 males and 441 females, whereas unrelated controls were made up of 441 males and 637 females. The probands in the case-control arm of the study are the same probands in the family-based studies. In some of the designated singletons, parental samples failed data cleaning and were dropped from statistical analyses—hence, the designation of such families as singletons. Singletons were informative in the case-control arm of our study but not the family-based studies. Tetrads and pentads were collected from families where 2 individuals were affected with clefts. “Other trios and dyads” largely refers to case-mother-maternal grandmother trios, case-mother-sibling trios, as well as case-siblings trios and dyads. Case-parent trios, tetrads, and pentads were employed in the transmission disequilibrium test, whereas all sample types, except singletons and unrelated controls, were used for analyses of the family-based association for disease traits. Only case probands and unrelated controls were included in the case-control analyses.
NSCL, nonsyndromic cleft lip; NSCL/P, nonsyndromic cleft lip with or without cleft palate; NSCLP, nonsyndromic cleft lip and palate; NSCPO, nonsyndromic cleft palate only.