Two consortia contributed to this study. The first, from the GENEVA consortium, used a family-based design and included 461 case-parent trios with cleft lip (CL), 1,143 case-parent trios with cleft lip and palate (CLP), and 451 case-parent trios with CP, respectively, from populations in Europe (Denmark and Norway), the United States, and Asia (Singapore, Taiwan, Philippines, Korea, and China). The specifics of this study have been described previously (Beaty et al., 2010 (
link); Leslie, Carlson, et al., 2016 (
link); Leslie, Liu, et al., 2016 (
link)). Briefly, samples were genotyped for 589,945 SNPs on the Illumina Human610-Quadv.1_B BeadChip, genetic data were phased using SHAPEIT, and imputation was performed with IMPUTE2 software to the 1000 Genomes Phase 1 release (June 2011) reference panel. Genotype probabilities were converted to most-likely genotype calls with the GTOOL software (
http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html).
The second consortium included samples from the Pittsburgh Orofacial Cleft (POFC) study, comprising 179 cases and 271 case-parent trios with CL, 644 cases and 1,048 trios with CLP, 78 cases and 165 trios with CP, and 1,700 unaffected controls with no history of craniofacial anomalies. Participants were recruited from 13 countries in North America (United States), Central or South America (Guatemala, Argentina, Colombia, Puerto Rico), Asia (China, Philippines), Europe (Denmark, Turkey, Spain), and Africa (Ethiopia, Nigeria). Additional details on recruitment, genotyping, and quality controls were previously described (Leslie, Carlson, et al., 2016 (
link); Leslie, Liu, et al., 2016 (
link)). Briefly, these samples were genotyped for 539,473 SNPs on the Illumina HumanCore+Exome array. Data were phased with SHAPEIT2 and imputed using IMPUTE2 to the 1000 Genomes Phase 3 release (September 2014) reference panel. The most-likely genotypes (i.e. genotypes with the highest probability [Q]) were selected for statistical analysis only if the genotype with the highest probability was greater than 0.9.
A total of 412 individuals were in both the GENEVA OFC and POFC studies, so we excluded these participants from the GENEVA study for this analysis. Informed consent was obtained for all participants and all sites had both local IRB approval and approval at the University of Pittsburgh, the University of Iowa, or Johns Hopkins University. Individual level genotype and phenotype data for the GENEVA and POFC studies are available from dbGaP: phs000774.v1.p1 and phs000094.v1.p1.
Carlson J.C., Anand D., Butali A., Buxo C.J., Christensen K., Deleyiannis F., Hecht J.T., Moreno L.M., Orioli I.M., Padilla C., Shaffer J.R., Vieira A.R., Wehby G.L., Weinberg S.M., Murray J.C., Beaty T.H., Saadi I., Lachke S.A., Marazita M.L., Feingold E, & Leslie E.J. (2019). A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals. Genetic epidemiology, 43(6), 704-716.