Exon-Wide Characterization Of Genetic Variation For Smad7 And Its Preliminary Analysis Of Genetic Association In Malay Patients With Ventricular Septal Defect (VSD)
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Date
2016-07
Authors
Mohamed Sa'dom, Siti Aisyah Faten
Journal Title
Journal ISSN
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Publisher
Universiti Sains Malaysia
Abstract
Congenital heart defects (CHD) occurs in approximately 8 out of 1000 live births worldwide. Ventricular septal defect (VSD) is the most common type and accounts for about 20% of all CHD. SMAD7 is an inhibitory protein that antagonizes the TGF-β signaling and was implicated to be involved in the embryogenesis of the mouse model, particularly in the formation of ventricular septum. It was hypothesized that SMAD7 could influence the risk of VSD. Therefore, this study was conducted to investigate SMAD7 in susceptibility to VSD in Malay patients. This case-control study involves 60 study subjects with 30 non-sydromic VSD patients and 30 healthy controls. Peripheral blood and saliva samples were collected from the study subjects. The genomic DNA was subjected to PCR amplification encompassing six exons of SMAD7 and subsequently, re-sequencing was conducted in the patients. Observed polymorphisms then were genotyped in the controls utilizing both re-sequencing and allele-specific PCR (AS-PCR) techniques. A total of 10 variants were identified from the sequencing analyses which were located in the 5’upstream promoter region (rs7236774), exonic regions (rs368427729, rs145686330, rs3764482, rs3809922, rs780863704 and rs3809923), intronic regions (rs3736242) and 3’UTR region (rs375444823 and rs16950113). Statistical analysis of all 10 variants did not show any significant differences between the cases and controls groups in terms of genotype and allele frequency as well as risk
association. Haplotype analysis of the major allele of rs36842779 (G) and minor allele of rs7236774 (C) significantly increase the association risk of VSD (p=0.0475). This study revealed two variants, rs3809922 and rs3809923 has a complete linkage disequilibrium (LD) with each other implicating that the allele from both SNPs is completely associated with identical allele frequency. Even though all of these variants did not affect amino acid changes and thus did not affect the SMAD7 protein, they might influence the transcriptional efficiency and stability at the mRNA level later on. Hence, this study concludes the identification of genetic polymorphisms in Malay VSD patients in Kelantan for the first time which provides a new perspective on the causation of VSD.
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Keywords
Genetic association in malay patients , with ventricular septal defect.