PRICING & INQUIRIES

For pricing and inquiries, send an email to sales@omicsoft.com.

5001 Weston Parkway, Suite 201
Cary, NC 27513
US

888-259-6642

Overview

Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis.

Exciting Updates and Latest News

Keeping you up-to-date with the latest in NGS, Bioinformatics Analysis, and cancer genomics with blogs on Array Suite, OncoLand (TCGA and more), ImmunoLand, and more.

[OncoLand Case Study] Empower OncoLand with Array Studio Analysis: Visualize "mutation burden" in each tumor in TCGALand

Vivian Zhang

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:

Figure 1: Mutation frequencies, spectra and contexts across 12 cancer types. Kandoth, Cyriac, et al. "Mutational landscape and significance across 12 major cancer types." Nature 502.7471 (2013): 333-339.

Figure 1: Mutation frequencies, spectra and contexts across 12 cancer types. Kandoth, Cyriac, et al. "Mutational landscape and significance across 12 major cancer types." Nature 502.7471 (2013): 333-339.

In another recent Nature paper, Whole-genome mutational burden analysis of three pluripotency induction methods, the authors researched mutational subtypes in each sample:

Figure 2: Characterization of variants caused by reprogramming method. Bhutani, Kunal, et al. "Whole-genome mutational burden analysis of three pluripotency induction methods." Nature communications 7 (2016). 

Figure 2: Characterization of variants caused by reprogramming method. Bhutani, Kunal, et al. "Whole-genome mutational burden analysis of three pluripotency induction methods." Nature communications 7 (2016). 

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:

Mutation burden variable view. Y-axis represents mutation number. X-axis represents different samples.

Mutation burden variable view. Y-axis represents mutation number. X-axis represents different 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

                                                                               Stack table by row to generate variable view 

                                                                               Stack table by row to generate variable view 

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.