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In addition, the rows of the sample mutation dataset to be analyzed must be appended to the modified reference dataset.

In accordance with (Gonzalez-Perez et al., 2012), and to enable a fair comparison to be made between our algorithm and the Mutation Assessor TransFIC, we adjusted our prediction thresholds across the nine mutation datasets to maximize the Matthews correlation coefficient (MCC) of our algorithm.

The frequency-based approaches reviewed above are contingent upon either an assumption of a background mutation rate or the availability of a large number of mutations in the dataset to calculate an empirical background mutation rate for the sample of interest.

The selection pressure can be calculated on different levels, from a single gene to the whole mutation dataset, from which candidate driver genes can be predicted and the number of driver mutations can be estimated.

Figure 3 represents the relative weight of each mutation in the dataset to calculate the first PLS component.

The correlation of the mutations amongst them and to the principal components allowed identifying some clusters as for example mutations 10, 46 and 90 or mutations 32 and 47 already known to be associated together (figure 1). Figure 2 represents the relative weight of each mutation in the dataset to calculate the first principal component.

We find that the use of a B-SIFT cutoff allows for enriching a mutation dataset for activating mutations, but there continues to be a high rate of false negatives and false positives (Fig. 2B).

Next, we applied it to a practical cancer mutation dataset and explored the availability of our method.

Bioinformatics analysis of The Cancer Genome Atlas (TCGA) melanoma mutation dataset also revealed a frequency of mutations in the 41 epigenetic genes comparable to that found within our cohort of patient melanoma samples.

This provided a uniquely high-resolution mutation dataset for mapping LD.

For the sample mutation dataset (TCGA UCEC), the same steps used for the modified COSMIC reference dataset must be performed.