Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems.
Bottom Line: Individuals in the derived groups show an A&T-increase/G&C-decrease pattern compared with the basal groups.For three DNA repair genes (BRIP1, PMS2P3 and TTDN), ENCODE data provided evidence for interaction between genomic regions containing these genes and regions containing the significant SNPs.Our findings provide insights into the mechanisms of genome evolution.
Affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA.Show MeSH
Related in: MedlinePlus
Mentions: Although complex evolutionary history is challenging to study and multiple factors are likely to be involved, it should not deter us from making attempts to identify potential genomic regions that drive the divergence in base composition in humans. With this in mind, we first conducted a genome-wide scan with a mixed model controlling for both population structure (fixed effect) and relatedness (random effect) following established methods (27,28) (Figure 3). In this analysis, individual SNPs were tested for association with the genome-wide [A] values while controlling the population structure and relatedness. Given the strong divergence of base composition and the control for population structure, this set of identified genomic regions is more likely to underlie within-population variation in base composition.
Affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA.