title: Polymorphic variants near 1p22 and 20q11.2 loci and the risk of non-syndromic cleft lip and palate in South Indian population.
abstract: BACKGROUND
  Recent genome-wide association studies (GWAS) have reported multiple genetic risk loci for non-syndromic orofacial clefts (NSOFCs) in many populations. However, the contribution of these loci to NSOFC in India, which comprises one-fifth of the global population, is completely lacking. Our aim was to replicate the association of the SNPs located on 1p22 chromosomal loci (rs540026, rs481931) and 20q11.2 (rs13041247, rs11696257) in the aetiology of NSOFCs, in South Indian populations.
  
  
  METHODS
  The SNPs were genotyped by using KBiosciences KASPar SNP genotyping chemistry in 173 cases and 176 controls for NSOFCs in South India. To estimate the association between these SNPs and NSOFCs, chi-square test was adopted. Odds ratios (OR) with 95% confidence intervals (CI) were also calculated in order to assess the risk.
  
  
  RESULTS
  Single nucleotide polymorphisms located at chromosomal region 1p22 are not found to be associated with cleft lip with or without non-syndromic cleft palate (NSCL/P) and non-syndromic cleft palate only (NSCPO) at either the genotype or allele levels. Further, there is no LD observed between these variants. The polymorphic variants near 20q11.2 (rs13041247, rs11696257) are in complete linkage disequilibrium (LD) and are significantly associated with only NSCL/P in genotypic (p=0.013) and allelic models (p=0.029). In the genotypic model significance persisted even after Bonferroni correction (p<0.016).
  
  
  CONCLUSIONS
  These results suggest that 20q11.2 SNPs could play a contributory role in the pathophysiology and risk of NSCL/P, while the variations in 1p22 do not underlie the pathophysiology of NSOFCs in South Indian populations.
authors.affiliation: Department of Biomedical Sciences, Sri Ramachandra University, Chennai, India.
authors.forename: Venkatesh
authors.initials: V
authors.lastname: Babu Gurramkonda
authors.affiliation: Department of Plastic Surgery, Sri Ramachandra University, Chennai, India.
authors.forename: Altaf
authors.initials: A
authors.lastname: Hussain Syed
authors.affiliation: Department of Plastic Surgery, Sri Ramachandra University, Chennai, India.
authors.forename: Jyotsna
authors.initials: J
authors.lastname: Murthy
authors.affiliation: Estonian Biocentre, Riia23b, Tartu, Estonia.
authors.forename: Gyaneshwer
authors.initials: G
authors.lastname: Chaubey
authors.affiliation: Department of Biomedical Sciences, Sri Ramachandra University, Chennai, India. Electronic address: lvksbhaskar@gmail.com.
authors.forename: V K S
authors.initials: VK
authors.lastname: Bhaskar Lakkakula
mesh_terms: D000483:Alleles; D044466:Asian People / Q000235:genetics; D016022:Case-Control Studies; D002971:Cleft Lip / Q000453:epidemiology / Q000235:genetics*; D002972:Cleft Palate / Q000453:epidemiology / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D007194:India; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012306:Risk
keywords: 1p22 and 20q11.2 chromosomal loci; India; NSCL/P; NSCPO; NSOFCs; SNP