Identification Of Key Candidate SNPs Associated With Familial NSCL/P Risk

Objectives: Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common congenital birth defects that represents almost half of facial dysmorphology and accounts for 93% to 95% cases of Cleft of the Lip with or without Cleft Palate (CL/P). NSCL/P is a multifactorial disease caused by interactions between genetic and environmental factors. Current study aims to identify key candidate gene SNPs associated with Familial NSCL/P Risk.
Methods: We have previously reported a non-parametric linkage analysis study of a six-generation family with probable autosomal dominant, low penetrance inheritance of NSCL/P. Using Exome sequencing on 12 familial genomes (6 affected individuals, 2 obligate carriers, and 4 seemingly unaffected individuals), we identified a 5.7-Mb genomic region on 18q21.1 that may contain pathogenic, high-risk variant (s) for NSCL/P in this family. Further analysis found 200 variants within chr18q21.1 region that were called by both Broad's GATK and SAMtools and also survived genotype quality control (GATK QUAL > 50 and sample coverage rate > 50%). Subsequently, we performed Sequenom iPLEX genotpying on the NSCL/P family DNA samples for 40 single nucleotide polymorphisms (SNPs) selected based on the following SNP selection criteria: minor allele frequency (MAF) < 0.2 in 1000Genomes project and odds Ratio <= 0.5 or >= 3 in our Exome analysis data on 18q21.1 SNPs. Additionally, candidate SNPs found significant in relevant literatures on NSCL/P were also included in the genotyping panel. SNP vs NSCL/P association analysis was performed using Haploview and snpStats softwares using gender as a covariate.
Results: The following SNPs were found significantly associated with NSCL/P risk: rs1450425 (LOXHD1), rs6507992 (SKA1), rs78950893 (SMAD7), rs8097060, rs17713847 (SCARNA17), rs6507872 (CTIF), rs8091995 (CTIF), rs183559995 (MYO5B), rs17715416 (MYO5B).
Conclusions: Our results indicate mutations in several genes as key candidate SNPs associated with risk of familial NSCL/P.