Lack of association between IRF6 polymorphisms and nonsyndromic oral clefts in South Indian population

Objec ve: This present study is aimed to inves gate the associa on between interferon regulatory factor 6 (IRF6), single nucleo de polymorphisms (SNPs), and nonsyndromic cle lip without without cle palate (NSCLP) in the South Indian popula on. Subject and Methods: For this study, 190 unrelated NSCLP pa ents and 189 controls with‐ out cle s were genotyped with rs2235371 (V2741) and rs642961 SNPs using PCR‐RFLP. The associa ons between NSCLP groups and IRF6 gene polymorphisms, as well as haplotypes, were analyzed using chi‐squared test and 95% confidence interval (95%CI) of the odds ra ‐ os were calculated with the control groups as reference. Results: For controls, the minor allele frequencies of both variants, V2741 and rs642961, were 7.1% and 21.1%, respec vely. Genotype data for both variants in control and cle groups follow the Hardy Weinberg Equilibrium. Between cases with NSCLP and controls, the two SNPs showed no differences in frequencies of the genotypes or alleles. The pairwise linkage disequilibrium (LD) values (D’=1 and r=0.027) between V2741 and rs642961 re‐ vealed that these two SNPs are not in strong LD. Haplotype G‐T showed a significantly re‐ duced risk for oral cle s (p<0.001) and haplotype A‐T increased the risk for oral cle s (p=0.043). Gene‐gene interac on showed that the higher risk group contains more GG‐CC combina on of cases that the controls, but this model was not significantly associated with cle status (p=0.136) Conclusion: In conclusion, while IRF6 is strongly associated in other popula ons, this study demonstrated that variants in IRF6 may play a role in NSCLP in a South Indian popula on, but other genes are expected to play a role in this popula on as well. Cita on: Gurramkonda VB, Murthy J, Syed AH, and Lakkakula BVKS (2013) Evidence of associa on between IRF6 polymorphisms and nonsyndromic oral cle s in South Indian popula on. Den stry 3000 1:a001 doi:10.5195/d3000.2013.9 Received: March 25, 2013 Accepted: June 20, 2013 Published: August 1, 2013 Copyright: ©2013 Gurramkonda et al. This is an open‐ access ar cle licensed under a Crea ve Commons A ribu on 3.0 United States License. Email: [email protected] Introduc on Cleft lip with or without cleft palate is an extremely complex orofacial birth defect and is found to be more common in Asian and Asian‐American populations and less common in Africans and African‐Americans. Roughly 70% of CLP cases are nonsyndrom‐ ic, occurring as an isolated condition, while the remaining 30% of CLP cases are present in association with syndromes [1]. Converg‐ ing lines of evidence suggest that the non‐ syndromic cleft lip with or without cleft palate (NSCLP) involves interplay of both genetic and environmental factors. NSCLP most often occurs as an isolated de‐ fect in families with no history of clefts. NSCLP gene identification is difficult be‐ cause of varying levels of penetrance, sex differences, and environmental overlays that increase etiological heterogeneity [2]. Despite having a substantial genet‐ ic component, only a fraction of all predis‐ posing genes have been convincingly con‐ firmed as playing role in NSCLP. Many genes associated with syndromic cases of CLP have been identified to contribute to the incidence of NSCLP [3]. This approach led to the identification of several genes that con‐ tribute to the isolated clefting [4‐9]. Van Der Woude syndrome (VWS; OMIM 119300) is the most common autosomal dominant clefting syndrome and is distinguished by the presence of highly characteristic pitting of lower lip mucosa and CLP [10]. The VWS locus was initially mapped to hu‐ man chromosome 1q32–q41 region that harbors interferon regulatory factor 6 (IRF6) gene [11]. Numerous mutations in the IRF6 were reported to cause VWS [11‐ 14]. The IRF6 gene encodes a transcription fac‐ tor characterized by a highly conserved DNA‐binding domain in addition to a less well‐conserved protein interaction domain [15]. Several polymorphisms in the IRF6 gene have been studied to check their asso‐ ciation with cleft lip and palate, but the re‐ sults are inconclusive. Genome‐wide and candidate gene studies and a subse‐ quent meta‐analysis have identified IRF6 as a plausible gene contributing to cleft lip and palate in different ethnicities [16‐18]. The present study is aimed to investigate the association between IRF6 single nucleotide polymorphisms and NSCLP in a South Indi‐ an population. We chose two markers: Lack of associa on between IRF6 polymorphisms and nonsyndromic oral cle s in South Indian popula on Vol 1, No 1 (2013) DOI 10.5195/d3000.2013.9 http://dentistry3000.pitt.edu 2 rs2235371 (V274I), a non‐synonymous SNP, and rs642961, located in the newly identified IRF6 enhancer region. In addition to this, HapMap data on these polymor‐ phisms in GIH samples (Gujarati ‐ a West Indian population) showed that these SNPs are polymorphic and located in two differ‐ ent linkage disequilibrium (LD) blocks. Since the present study population is near‐ est to GIH, it is likely that these two poly‐ morphisms are the best fit for the study undertaken. Materials and Methods