Sequencing of the interferon regulatory factor 6 (IRF6) gene and correlation to its phenotypes in familial non-syndromic cleft lip and palate in North Indian population

Abstract

The incidence of orofacial clefting varies depending upon geographical location, ethnicity, sex and even socioeconomic status. The study aimed to test the contribution of interferon regulatory factor 6 (IRF6) gene allelic variation to the incidence of non-syndromic cleft lip and/or cleft palate (CL/P) from the population of North India. Patients from 12 North Indian families with non-syndromic cleft lip with or without cleft palate (NSCL/P) with at least two members affected were clinically evaluated and tested. DNA was extracted from the blood, and three exonic part of the IRF6 gene (exons 2, 5 and 7) were amplified by PCR. Direct sequencing was performed by PCR product, and sequencing results were compared with the reference DNA sequence of the IRF6 gene. Three SNPs (rs861019, rs2013162 and rs2235372) in 4 out of 12 families were observed. SNP rs861019 was detected in family no. 4 (F4) around exon 2, SNP 2013162 was detected in family no. 10 (F10) and SNP 2235372 was detected in family nos. 5 and 9 (F5 and F9). This study demonstrates that the three SNPs within the IRF6 gene are associated with NSCL/P, suggesting IRF6 gene sequence variability and variation in this gene, providing first genetic clue to the NSCL/P phenotype in North Indian families. This is our initial step to demonstrate the involvement of the IRF6 gene in NSCL/P patients in North India. Further extensive study and statistical analysis are needed to validate our result. Level of Evidence: Level IV, diagnostic study.