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We expand earlier mathematical forms to include epistasis, or interactions between mutations at all pairs of loci.
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It would be interesting to investigate possible association between mutations at E2-60 and the rare neurological complications and fatalities that were reported for the first time during the recent chikungunya epidemics [42].
We then conducted a meta-analysis from published data on the association between mutations at MUTYH and colorectal cancer risk.
Of course, fitness advantages will also differ between mutations at different loci, even within the same cancer type.
In this work we present a method to infer selection in an evolving population characterized by multiple genetic linkages between mutations at different loci.
Other intriguing observations include a mutual exclusion in lower grade glioma between ATRX and CIC, a transcriptional repressor that may play a role in development of the central nervous system [ 38], and mutual exclusion in uterine corpus endometrial carcinoma between mutations at TP53 and SWI/SNF remodeling complex protein ARID1A (Additional file 5: Table S2).
Lopez et al. [ 13] describe another test for comparing not just the invariant sites, but the distribution of mutations at all variable sites between two subtrees.
Competition between mutations occurring at different points on a genetically linked region of the genome may correspond to reduced effective population sizes, but these mutations would occur sporadically.
A comparative study of birds revealed a positive correlation between mutation rate at minisatellite loci and extra-pair paternity, but not between mutation rate and relative testes mass which is a measure of relative sperm production.
Based on the SNP profiles investigated in this report, the absolute risk difference between mutation carriers at the top 5% of the risk distribution compared to the bottom 5% is much greater for ER-positive breast cancer than for ER-negative breast cancer for both BRCA1 and BRCA2.
In order to illustrate functional significance of structural effects and concomitant protein stability changes for kinase cancer mutations, we compared protein stability differences between oncogenic KIT mutations at the D816 position and a spectrum of disease-causing KIT variants (Figure 11).
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