This report serves to describe the mutational landscape and

properties of a given cohort, as well as rank genes and genesets according to

was used to generate the results found in

The input for this pipeline is an annotated .maf file describing
             the mutations called for each individual in the given cancer
             cohort, and their properties.

Significantly mutated genes (q &le; 0.1):

A breakdown of mutation rates per category discovered for this cohort.

Breakdown of Mutation Rates by Category Type

The mutation spectrum is depicted in the lego plots below

in which the 96 possible mutation types are subdivided into six large blocks,

color-coded to reflect the base substitution type. Each large block is further

subdivided into the 16 possible pairs of 5' and 3' neighbors, as listed in the

4x4 trinucleotide context legend. The height of each block corresponds to

the mutation frequency for that kind of mutation (counts of mutations

normalized by the base coverage in a given bin). The shape of the spectrum is

a signature for dominant mutational mechanisms in different tumor types.

SNV Mutation rate lego plot for entire cohort. Each bin is normalized by base coverage for that bin. Colors represent the six SNV types on the upper right. The three-base context for each mutation is labeled in the 4x4 legend on the lower right. The fractional breakdown of SNV counts is shown in the pie chart on the upper left. If this figure is blank, not enough information was provided in the MAF to generate it.

SNV Mutation rate lego plots for 4 slices of mutation allele fraction (0<=AF<0.1, 0.1<=AF<0.25, 0.25<=AF<0.5, & 0.5<=AF) . The color code  and three-base context legends are the same as the previous figure. If this figure is blank, not enough information was provided in the MAF to generate it.

The matrix in the center of the figure represents individual mutations in

patient samples, color-coded by type of mutation, for the significantly mutated genes.

The rate of synonymous and non-synonymous mutations is displayed at the top of the matrix. The barplot on