Further Evidence of Association of ABCA4 with Cleft Lip/Palate

Objectives: Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common birth defect with complex etiology. Numerous genes and environmental factors and their interactions are thought to play a role in the susceptibility to CL/P. A recent genome-wide scan revealed markers in/near MAFB and ABCA4 genes as new susceptibility loci for CL/P, and such findings have been independently replicated in additional populations. To validate these findings in a population from Brazil, we evaluated if MAFB and ABCA4 genes were associated with CL/P in a case-control dataset.

Methods: The dataset was composed of 892 individuals (480 with nonsyndromic CL/P and 412 without CL/P or family history of CL/P) of Caucasian ancestry from the Southeast region of Brazil. Single nucleotide polymorphisms (SNPs) in ABCA4 [rs560426 and rs481931], and MAFB [rs13041247 and rs11696257] were genotyped in 5-uL volume reactions using Taqman chemistry, and detected in a 7900HT Sequence Detection System (Applied Biosystems Inc.). Allele frequencies and Hardy-Weinberg equilibrium (HWE) were calculated using PLINK (v1.06) for case-control comparisons, and for comparison of cleft subgroups with controls. Correction for multiple testing was performed using Bonferroni correction and a p-value £0.005 was considered significant.

Results: All SNPs were in HWE. Both SNPs in ABCA4 were associated with CL/P subgroups. SNP rs540426 showed strong association with several CL/P subgroups: cleft lip and palate (p=0.0002), unilateral and right cleft lip and palate (p=0.004 and p=0.003, respectively), and bilateral cleft lip and palate (p=0.0006). Meanwhile, SNP rs481931 showed borderline association with cleft lip and palate (p=0.02), and bilateral cleft lip and palate (p=0.01). No association was found for SNPs in MAFB with CL/P (P>0.05).

Conclusion: Our results further support previous findings of association of ABCA4 with CL/P and suggest that this gene may confer a risk for the development of CL/P in individuals from Brazil.