A set-based analysis of all SNPs was performed using the most inclusive settings, and single-marker P-values were summarized by the overall mean of all SNPs to estimate the average association of the entire SNP-set with longevity. Significance was determined by permuting the phenotype labels 10000 times. A gene-set analysis using the competitive gene-set enrichment method published by Wang et al was also performed in four steps.

The set-based test resulted in an overall P-value supporting that variation in DNA-damage response and repair genes appears to be important for human longevity. The competitive gene-set analysis showed that the sub-processes BER, HRR, and RECQ had P-values below 0.05, whereas the remaining sub-processes were non-significant. However, only HRR showed a q-value below 0.05 and only in setup II.

In conclusion, this study suggests that genetic variation in sub-processes of DNA-damage response and repair genes may play a role in human longevity. Further studies are needed to confirm these findings and explore the underlying mechanisms.Response and DNA repair processes have a greater influence on human longevity than other processes. It is important to understand how each sub-process contributes to genetic stability, as they have different biological roles that affect longevity in various ways. Table 3 shows the ranking of genes in the BER, HRR, and RECQ sub-processes. The gene statistics for all genes in these sub-processes were inspected to determine which genes contributed to the nominal significance of BER, HRR, and RECQ. We found several low-ranking genes for BER, while HRR was mostly associated with RAD52 and to a lesser extent NBN, MRE11A, and RAD54L. Similarly, the P-value for RECQ was mainly due to WRN and BLM. A post-hoc analysis was conducted by repeating the gene-set analysis of BER, RECQ, and HRR without the respective lowest ranking gene from the dataset. Only BER remained nominally significant, while RECQ and HRR lost significance, confirming that each sub-process's importance was induced by only one gene.

The single-SNP data from the German replication population can be found in the GWAS Central database (www.gwascentral.org). Repeating the self-contained set-based analysis of all SNPs as well as the competitive gene-set analysis of BER, HRR, and RECQ in males and females yielded consistent significance of BER. However, HRR and RECQ did not show significance, possibly due to reduced power from an inadequate sample size. Gender-specific differences were not overly relevant in this study.

Our findings suggest that repairing certain types of DNA damage induced by ROS or ionizing radiation is particularly important for human longevity. Damage induced by ROS is repaired by BER, while damage induced by ionizing radiation is repaired by HRR. Moreover, ROS-induced damage can give rise to DNA DSBs during DNA replication, inducing replication stress and fork collapse where HRR is crucial. The RECQ helicases' roles in ensuring proper DNA structure during repair could also be central, especially considering the existence of premature aging syndromes like Werner syndrome, caused by RECQ gene mutations.

The lack of replication in the German study population may be due to differences in genotyping procedures, coverage of variation in gene regions, and potentially not tagging all discovery SNPs. Additionally, the Germans were older than the Danes, and if associations are not constant throughout old age, they may not replicate well. Population-specific effects may also be a factor.

The gene-set analysis indicated that the nominal significance of BER, HRR, and RECQ was primarily driven by one gene rather than a combined effect of several genes. For RECQ and HRR, the associations were mainly driven by WRN and RAD52, respectively. This may indicate that variation in one sub-unit of the Rad51/Rad52/Rad54 protein complex could modify the entire HRR's function. Additional studies in other populations are needed to draw final conclusions.Also, indicate that RAD52 and WRN have roles beyond HRR and RECQ. WRN is a clear example of this, as it takes part in three of the nine sub-processes. Similarly, one study indicates that Rad52 may affect BER via an interaction with OGG1. Finally, our definition of the sub-processes is based on existing knowledge of DNA damage response and repair mechanisms. Therefore, we cannot exclude the possibility that additional cross-talks between the sub-processes are yet to be discovered. Contrary to this, the association of BER appears scattered over the entire gene-set, suggesting that variation in different parts of the sub-process may have consequences for longevity. Considering the central role of oxidative damage to several proposed biological theories of aging, the fact that we observe this for BER, the DNA repair process primarily responsible for repair of oxidative DNA lesions is indeed interesting. The details and widths of the sub-processes are identified through a complicated task since there is no gold standard and available databases may lack sufficient detail. Consequently, some relevant genetic variation may not be covered in the present study.

CONCLUSION