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

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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] Find genes that are frequently co-mutated with your gene-of-interest: Co-mutation of TP53 and ATRX when IDH1-R132 is mutated

Vivian Zhang

The IDH1 gene encodes isocitrate dehydrogenase, which is  involved in NADPH production, especially in the brain. Mutations in IDH1 are frequently found in low grade and high grade gliomas (Low grade (grade II), anaplastic (grade III), and glioblastoma (GBM, grade IV).). (Research Article: IDH1 and IDH2 Mutations in Gliomas) These mutations play an important role in gliomagenesis and thus have clinical interest. We can query OncoLand to learn about IDH1 mutations, and other genes frequently co-mutated. For details, please refer to our OncoLand case study wiki:

Identify mutation hotspots in a gene of interest

In several cancers, IDH1 is frequently mutated at arginine 132, which alters the enzyme's active site. We can visualize the frequencies of mutations at different sites in each tumor. As we can see, our data confirms that IDH1 arginine 132 is frequently mutated in low grade gliomas (LGG) and glioblastoma (GBM):

TCGALand DNA-Seq Somatic Mutation Site Distribution View. 

TCGALand DNA-Seq Somatic Mutation Site Distribution View. 

The user can create a SampleSet, for example the one shown below, IDH1_mutaion, from the Analytics | Generate Sample Set | Generate Site Mutation Status SampleSet. 

SampleSet: IDH1_mutation

SampleSet: IDH1_mutation

Identify other genes that are co-mutated with your gene of interest

With the SampleSet, we can identify the gene mutations that are correlated through Analytics | Integration Analysis | Sample Grouping to Mutation. The test may take a few minutes if all genes are queried, and the results will be available from the Analytics | Open Result Set menu. From the results table, we can rank genes with the PValue from the Fisher Exact Test to identify the correlated genes, for instance ARRX and TP53 in LGG and GBM:

Analytics | Integration Analysis | Sample Grouping to Mutation Test results. Rank by PValue, filter by only co-occurring gene in LGG and GBM.

Analytics | Integration Analysis | Sample Grouping to Mutation Test results. Rank by PValue, filter by only co-occurring gene in LGG and GBM.

Visualize Co-mutation patterns with the Alteration Omicprint

There are several ways to visualize co-mutation frequencies of multiple genes. While the "Alteration Distribution" displays the number of samples mutated in any gene of the GeneSet, "Somatic Co-mutation Frequencies" will display the distribution of samples with different mutation loads. The "Alteration Omicprint" efficiently displays per-sample mutation status of one, ten, or even hundreds of genes. You can also generate custom Omicprinst based on custom queries if you want to query mutation status. Please check out our case study tutorial videos to learn how to perform the analysis. 

Alteration Omicprint displays gene alteration status for multiple genes for corresponding samples. Custom quires for IDH1 and TP53 somatic mutation status, and BMP2 RNA-Seq FPKM are created. Next, check out Custom Query Omicprint view. For each custom query, sample status is displayed. As we can see, samples with mutated IDH1 and TP53 frequently over-express BMP2 in GBM. 

Alteration Omicprint displays gene alteration status for multiple genes for corresponding samples. Custom quires for IDH1 and TP53 somatic mutation status, and BMP2 RNA-Seq FPKM are created. Next, check out Custom Query Omicprint view. For each custom query, sample status is displayed. As we can see, samples with mutated IDH1 and TP53 frequently over-express BMP2 in GBM.