This research project started with a GWAS as an exploratory expedition to the nature of genetic variations that increase SCD in HF patients. We used an appropriate ICD shock phenotype as a surrogate for SCD phenotype that is difficult to study directly. Although no SNP in the GWAS reached the genome-wide significance (5E-8), rs10251943 in the DPP6 gene was chosen for further analysis and investigation because the literature review revealed that the (T) allele of a different SNP (rs606231226) in DPP6 is associated with overexpression of the gene, gain-of-function effect i.e. increase in the transient outward current (Ito) in Purkinje fibers, and IVF/SCD events in several members of a big family in the Netherland. We conducted a Kaplan-Meier survival analysis to estimate the association of different genotypes of rs10251943 with the Freedom from shock phenotype i.e. survival from shock in HF patients of European and African descents. The (TT) genotype was associated with more shocks than other genotypes in both descents. In other words, the minor allele (T) is a potential pathological SNP or a tag SNP associated with a pathological SNP. We thought of many hypotheses to answer the question of why rs10251943 increases shock events. We hypothesized that this SNP might be associated with increasing the frequency of shocks through the same mechanism as rs606231226. We also hypothesized that the rs606231226 (not included in the GWAS) might be in linkage disequilibrium with rs10251943 and that the subjects of our cohort may be genealogically linked to the family in the Netherlands (founder effect). To investigate these hypotheses, we sequenced the whole genome of 9 subjects in GRADE including 4 GG individuals that suffered no shocks versus 5 TT individuals that suffered multiple shocks during the 5 year follow-up period of the study. The sequencing results disproved the founder effect hypothesis because none of the sequenced subjects had a CT substitution in rs606231226. It also unveiled a haplotype of 10 SNPs that are in LD with rs10251943. One of the SNPs in this haplotype overlaps with the enhancer (GH07J154195). This finding increased our desire to investigate the shock mechanism hypothesis mentioned above. We examined the differential expression of the DPP6 mRNA in healthy subjects comprising the 3 genotypes for rs10251943. We measured the mRNA using TaqMan Probe-based qPCR in 10 GG, 10 GT, and 4 TT samples. The differential expression analysis showed that there is no significant difference among the 3 groups. We conclude that the SNP rs10251943 has no or very low effect on regulating DPP6 mRNA expression. In the future, we will test the difference in protein expression among the 3 genotypic groups.
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