[OncoLand Case Study] Empower OncoLand with Array Studio Analysis: Visualize "mutation burden" in each tumor in TCGALand
One of the common goals in cancer research is identification of genes or samples with mutations that occur during tumor development. The number of identified mutations in cancer samples can vary wildly, but some tumors tend to aggregate widespread alterations. This Nature paper about the mutation landscape and significance across 12 major cancer types (as part of the TCGA Pan-Cancer effort) is a good example. In the very first figure, the authors investigated the mutation frequencies of six transition (Ti) and transversion (Tv) categories for each cancer type:
In another recent Nature paper, Whole-genome mutational burden analysis of three pluripotency induction methods, the authors researched mutational subtypes in each sample:
Using OncoLand, you can easily calculate and visualize total mutation burden of every sample or tumor type. Check out this OncoLand case study: Visualize "mutation burden" of each tumor in TCGALand
1. Calculate total mutation burden of every sample in TCGALand.
To calculate the number of total mutations per tumor sample (mutation burden), you can simply use Summarize Sample Mutation Count under Analytics tab in Land. By specifying the individual nucleotide changes, for example "A->C", the result will calculate the total number of mutations (from a selected GeneSet) mutated in each sample (from selected SampleSet).
You can further summarize the data by downloading this TotalMutationBurdenByNTchange table to Array Studio's local analysis. For example, adding a variable view to better visualize mutation burden across samples:
2. Calculate average mutation burden in each tumor in TCGALand
Using local analysis functions, you can further research mutation burden in each tumor in Land data. The Summarize function allows user to calculate the mean mutation number grouped by tumor type, or other preferred grouping options.
After Stacking the table, you can plot another variable view to visualize the distribution of each type of nucleotide change in each tumor type
In this way, we can easily tell which tumor type has the highest mutation burden.
To learn how to exactly perform the above analysis, please watch our OncoLand case study: Visualize "mutation burden" of each tumor in TCGALand.