Evaluating eight newly identified susceptibility loci for nonsyndromic cleft lip with or without cleft palate in a Mesoamerican population

<jats:p><jats:bold>Background:</jats:bold> Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is among the most frequently occurring congenital malformations worldwide. The number of genetic loci identified as being involved in NSCL/P etiology was recently increased by a large genome‐wide meta‐analysis of European and Asian samples. This meta‐analysis confirmed all six previously recognized genetic susceptibility loci and identified six novel ones. <jats:bold>Methods:</jats:bold> To investigate which of these 12 loci contribute to NSCL/P risk in an independent sample of distinct ethnicity, we performed a case–control association analysis in a sample of the Mesoamerican population. A total of 153 individuals with NSCL/P (cases) and 337 unaffected controls were included. Top single‐nucleotide polymorphisms (SNPs) at 8 of the 12 loci (1p22.1, 1p36, 2p21, 3p11.1, 8q21.3, 13q31.1, 15q22, and 20q12) were analyzed using mass spectroscopy and restriction‐length‐fragment polymorphism analyses. In a previous study, we had analyzed the remaining four NSCL/P susceptibility regions (<jats:italic>IRF6</jats:italic>, 8q24, 10q25, and 17q22) in the same sample. <jats:bold>Results:</jats:bold> Single‐marker association analyses applying allelic, dominant, and recessive models revealed nominal significant associations for four of the eight loci, with two additional loci showing at least a trend of association in the hypothesized direction. <jats:bold>Conclusion:</jats:bold> In combination with results from our previous study using the same sample, our data suggest that the majority of the known NSCL/P susceptibility regions identified to date also confer risk for this malformation in the Mesoamerican population. <jats:italic>Birth Defects Research (Part A) 100:43–47, 2014</jats:italic>. © 2013 Wiley Periodicals, Inc.</jats:p>