Non-syndromic oral clefts comprising cleft lip with and without cleft palate (CL/P) and cleft palate only (CPO) are common birth defects worldwide. Their aetiology involves both environmental and genetic factors. FOXE1 has previously been reported to be associated with oral clefts in some populations. Here, we investigate whether mutations in FOXE1 play a part in the formation of oral cleft in a Thai population. We first performed PCR–RFLP to genotype a previously reported associated polymorphism, c.-1204C > G (rs111846096), in our cohort. No association was found. In addition, two unrelated unaffected controls were found to be homozygous GG, indicating that homozygous GG at this c.-1204 position was not sufficient for the development of oral clefts. We then sequenced the entire coding region of FOXE1 in 458 unrelated individuals (146 CPOs, 108 CL/Ps and 204 Thai controls). Five different non-synonymous variants, c.274G > T (p.D92Y), c.569C > G (p.P190R), c.569C > T (p.P190L), c.664C > T (p.R222C) and c.1090G > A (p.G364S), were identified in CPOs and one, c.572C > G (p.P191R), in CL/P. All these six variants were in heterozygous state, each identified in one patient, and absent in 204 controls. Except the p.P190R, which was previously reported, the other five variants were novel. Our study identifies probable susceptibility variants of FOXE1 for oral clefts in the Thai population.

The 9p21 chromosomal region has been associated with coronary artery disease (CAD) in many genome wide association studies (GWAS). To date no information exists regarding the rs1333039 SNP which showed the strongest association in the WTCCC GWAS with CAD risk in the Indian population. The present study attempts to replicate the findings in the Indian population.

Genotyping for rs1333049 was done in 229 cases and 151 controls by allele-specific real-time assay.

A higher frequency of the risk allele rs1333049C was seen in cases (0·60) as compared with controls (0·49), which associated with CAD risk both in univariate (OR = 1·564, 95%CI = 1·154–2·119, P = 0·003) and multivariate analysis (OR = 2·460, 95%CI = 1·139–5·314, P = 0·022). Increased frequency of the risk allele was seen in younger individuals with CAD where 40% individuals in the age group 30–55 years had the CC genotype as compared with 29 and 24·5% in the age group 56–65 years and > 65 years, respectively (CC versus GG, P = 0·045). Higher incidence of the CC genotype was seen in MI patients, but missed significance when compared with controls (OR = 1·361, 95%CI = 0·954–1·942, P = 0·084).

In conclusion, the rs1333049 variant is significantly associated with CAD risk and also with age of onset in the Western Indian population. However there are differences in the haplotype structure of this SNP with the neighbouring rs10757278 SNP, these differences emphasize the importance of genotyping all risk variants at this locus which could underlie the differences in risk susceptibility to CAD across populations.

Calpain 10 (CAPN10) variants have been associated with the genetic susceptibility to type 2 diabetes (T2D). In the present case-control study, we analysed the distribution of SNP-19 insertion/deletion (I/D) polymorphism in a total of 607 samples (103 T2D cases and 102 healthy controls) from Brahmin; (100 T2D cases and 100 healthy controls) from Bania and (100 T2D cases and 102 healthy controls) from Jat Sikh ethnic groups of the North-West Indian population. Increased frequency of I allele and II genotype was found in T2D in Brahmin ethnic group [P = 0·003, OR = 2·83 (1·43–5·61 at 95% CI)]. Significant correlation between II genotype and body mass index (BMI) was also observed [P = 0·003, OR = 3·31 (1·52–7·20 at 95% CI)]. No association for the genotypes and alleles was seen in Banias and Jat Sikhs. Our data suggests that SNP-19 I/D variation in the CAPN10 gene is modulated by ethnicity and influences the susceptibility to T2D in the North-West Indian population. We also performed a meta-analysis of relevant studies to assess the validity of this association. Data from 13 case-control studies with 15 760 samples comprising of 8395 T2D cases and 7365 controls were finally analysed. Significant heterogeneity between individual studies was evident in dominant and codominant models. The results of present meta-analysis indicate an association of T2D with carriers of DD genotype of CAPN10 I/D polymorphism. However, further analyses on a larger sample size are required to establish a conclusive association in meta-analysis.