Finally, generate equal-sized random samples of mutations from each set of sites, and analyze the number of "hotspots" as in the NSMC method.
Our sample of mutation carriers had power of approximately 75% for TP53 and 40% for MDM2 to detect significant associations (P<0.05) for a per-allele HR of 1.1 and power of 100 and 90% respectively for a HR of 1.2, suggesting that we can reliably dismiss previously suggested associations (Martin et al, 2003; Osorio et al, 2006; Yarden et al, 2008).
However, this analysis does not take into account the non-random sampling of mutation carriers with respect to disease phenotype, or possible family relations within the individuals studied, so inference based on this analysis is not directly comparable with the single SNP analysis which was based on modelling the retrospective likelihood.
Given that these tests aim to infer a complex genome-wide relationship between average mutational effects and the form of epistasis from a small sample of mutations, it is encouraging to find such a strong trend.
Efficient sampling of mutations likely to affect enzyme function has been conducted both experimentally and, on a much greater scale, computationally, with remarkable improvements in substrate selectivity and specificity and in the de novo design of enzyme activities within scaffolds of known structure.
Conversely, positive selection will tend to increase the frequency in a sample of mutations segregating at high frequencies.
However, this comparison is problematic because it fails to account for the contingent and limited sampling of mutations by natural evolution.
In this context, we can examine related sets of these single-double equations to ask whether one mutation is a better mixer than another in the context of the sample of mutations with which they were each tested.
Therefore, the sampling of mutations is sufficiently complete to provide information on the effects of most amino-acid mutations when the data from the three experimental replicates are combined.
Our study shares the same ancestral phage sequence and similar propagation methods with a conventional sequencing study of ΦX174 that tracked changes occurring throughout its 180-day duration possibly caused by selection under within-host competition (Wichman et al. 2005), but we maintained a larger population in our study (see Methods) to increase population sampling of mutations.
