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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.

[ONCOLOGY RESEARCH] OncoLand helps to quickly confirm functional gene fusion events from Cell Reports article

Vivian Zhang

Typical molecular and cell biology research takes years and significant amount of money from design, grant applications, experiments, and validation and reporting. A significant problem is that often times the results are not expected or not applicable for real world applications. The return on investment of research can be problematic and hard to justify (Science economics: What science is really worth). 

Luckily, at least in cancer research, there are increasing number of public datasets available each year. With the large amount of public data, researchers can potentially save time and money, with the discovery of a candidate gene target. If you are a biologist, a bioinformatican, a PI or a R&D project leader or decision maker in pharmaceutical, biotech companies or academic institutes doing cancer research, OncoLand can help. 

In five minutes, OncoLand can help you to identify recurrent fusion genes in gastric cancer, which recently too some effort to identify in a Cell Reports paper (1).

Figure 1. Characteristics of Somatic SVs Identified by DNA-PET in GC. (A) SV filtering procedure for GC patient 125 is shown. Yap et al. 2015

Figure 1. Characteristics of Somatic SVs Identified by DNA-PET in GC. (A) SV filtering procedure for GC patient 125 is shown. Yap et al. 2015

In the article, Yao et al. identified recurrent fusions between CLDN18, a tight junction gene, and ARHGAP26, a gene encoding a RHOA inhibitor. According to the article, "CLDN18-ARHGAP26 negatively affects cell-cell and cell-matrix interactions and epithelial barrier function, thereby potentially contributing to gastritis, a known risk factor for GC." To verify the discovery of CLDN18-ARHGAP26 fusion, the user can use TCGA (The Cancer Genome Atlas) Land data.

First, the user can search gene CLDN18 and ARHGAP26 through multiple gene search in TCGA Land. By clicking on RNA-Seq Fusion Details, the user could check the list of fusions for the two genes. Interestingly, all the fusions identified are from Stomach Adenocarcinoma (STAD) samples, consistent with the article where the authors identified the fusion gene in gastric cancer. 

The user can check out fusion site frequency and RPKM under RNA-Seq Fusion tab. 

Furthermore, the user can also check out our Genome Browser to visualize the reads of the fusion genes. The Land tab will link to the browser through Browse Selected Samples. Our browser will automatically show a multiple panels view splitting the browser into two panels for the two fusion genes:


REFERENCE:

(1) Yao, Fei, et al. "Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity." Cell Reports (2015).