Replication and Functional Prediction of Two GWAS-Reported SNPs Located on RAD50 Gene Associated with Asthma in Pakistani Children

Background: Genome-wide association studies (GWAS) have indicated that several single nucleotide variants (SNVs) of the RAD50 gene are significantly associated with childhood-onset asthma. However, the biological role of RAD50 , and its genomic variants that predispose individuals to asthma, remains unclear. This case-control study aimed to investigate the association of two Single nucleotide polymorphisms (SNPs) rs2244012, and rs6871536 of RAD50 with asthma susceptibility using experimental and computational tools . 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 RAD50 gene are significantly association with childhood asthma in Pakistan. Despite being intronic variants, it is our inference that these two SNPs have the potential to either independently or synergistically regulate inflammatory responses via nearby SNVs.