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Background  Facial clefts are common birth defects with a strong genetic component. To identify fetal genetic risk factors for clefting, 1536 SNPs in 357 candidate genes were genotyped in two population-based samples from Scandinavia (Norway: 562 case-parent and 592 control-parent triads; Denmark: 235 case-parent triads).    Methodology/Principal Findings  We used two complementary statistical methods, TRIMM and HAPLIN, to look for associations across these two national samples. TRIMM tests for association in each gene by using multi-SNP genotypes from case-parent triads directly without the need to infer haplotypes. HAPLIN on the other hand estimates the full haplotype distribution over a set of SNPs and estimates relative risks associated with each haplotype. For isolated cleft lip with or without cleft palate (I-CL/P), TRIMM and HAPLIN both identified significant associations with  IRF6  and  ADH1C  in both populations, but only HAPLIN found an association with  FGF12 . For isolated cleft palate (I-CP), TRIMM found associations with  ALX3 ,  MKX , and  PDGFC  in both populations, but only the association with  PDGFC  was identified by HAPLIN. In addition, HAPLIN identified an association with  ETV5  that was not detected by TRIMM.    Conclusion/Significance  Strong associations with seven genes were replicated in the Scandinavian samples and our approach effectively replicated the strongest previously known association in clefting—with  IRF6 . Based on two national cleft cohorts of similar ancestry, two robust statistical methods and a large panel of SNPs in the most promising cleft candidate genes to date, this study identified a previously unknown association with clefting for  ADH1C  and provides additional candidates and analytic approaches to advance the field.

Genetic Determinants of Facial Clefting: Analysis of 357 Candidate Genes Using Two National Cleft Studies from Scandinavia