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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] Summarize per-sample and per-tumor mutations across multiple genes

Vivian Zhang

Summarizing mutation frequencies within a protein complex, members of a pathway, or even across the genome, can give insights into differences between tumors. Combining the power of OncoLand and Array Studio functions, you can explore mutation frequencies. For example, let's take a research example using the Swi/Snf complex, which can regulate chromatin remodeling. 

Swi/Snf complex is multi-subunit ATP-dependent chromatin-remodeling complex. Early studies have suggested that the Swi/Snf complex plays a role in cancer development, likely to be tumor suppressors. ( Nature Reviews Cancer article: The SWI/SNF complex — chromatin and cancer). Mutations in the members of this complex have been linked to various cancers. You can leverage OncoLand to query samples containing those mutations. Please check out the detailed OncoLand case study video tutorials.

 

Identify samples with mutations in the Swi/Snf complex

To find out how often the genes from the Swi/Snf complex are mutated in tumors, you can use Summarize Sample Mutation Count to generate a SampleSet through Analytics tab and use this SampleSet for downstream analysis:

SampleSet results from Summarize Sample Mutation Count analysis by inputing all gene names from Swi/Snf complex as GeneSet and group by Tumor Type. The mutation count is sorted by the number of mutations in each sample.

SampleSet results from Summarize Sample Mutation Count analysis by inputing all gene names from Swi/Snf complex as GeneSet and group by Tumor Type. The mutation count is sorted by the number of mutations in each sample.

 

Visualize differences in Swi/Snf complex mutations using TCGALand Views

There are multiple ways to visualize mutation (frequency) differences in Swi/Snf. Without using land views, we can still achieve this goal in Array Studio. Array Studio empowers users to perform hundreds of different types of analysis with flexibility, and can potentially save biologists the hassle of waiting for a bioinformatician to get back the results for weeks. However, with OncoLand, we can visualize the mutation frequency in minutes. The following analysis pipeline clearly demonstrates the difference of using Array Studio and OncoLand.

OncoLand makes cancer genomics research easy. Again, please check out our case study video tutorials for more details.