ArticleResearch square2025
Replication and Functional Prediction of Two GWAS-Reported SNPs Located on RAD50 Gene Associated with Asthma in Pakistani Children.
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Abstract
Background: Genome-wide association studies (GWAS) have indicated that several single nucleotide variants (SNVs) of the Methods: The case-control study involved 355 participants: "176 asthma cases [mean age (sd) = 8.91 ±3.05] and 179 healthy controls [mean age (sd) = 11.10 ±8.86] from local Punjabi population of Pakistan. The SNPs were analyzed using a modified single base extension method. The allelic association with asthma and linkage disequilibrium (LD) between the two main SNPs were performed using the SHEsis tool. SNPStats was used to assess the association of SNPs under genotypic models and interaction with non-genetic factors. The LD calculator of ENSEMBL employed for the identification of proxy SNPs in high LD (r^2 > 0.97) to main SNPs. Additionally, HaploReg(v4.1) was utilized to gauge the impact of SNPs on genomic regulations. Results: In current study, both SNPs were found to have a significant association (p-value <0.05) with childhood-onset asthma development under allelic and genotypic models. The alternative "G" allele of rs2244012 is shown to modify two regulatory motifs: Nrf-2 and Zbtb12, while the alternative "C" allele of rs6871536 is predicted to alter the OSF-2 motif. Moreover, 10 SNVs proximal to rs2244012 and 21 SNVs near rs6871536 are in high LD in the Punjabi population of Lahore, Pakistan (PJL). These proxy/high-LD SNVs also displayed the potential to change DNA regulatory motifs. Conclusion: the rs2244012, and rs6871536 variants of
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