Browsing ICGC data in IntOGen

//Browsing ICGC data in IntOGen

Browsing ICGC data in IntOGen

When we created IntOGen we had the motivation to convert it into a discovery tool for cancer researchers and a resource that integrates multidimensional OncoGenomics Data. We have now made a new important step in IntOGen project: we have included all somatic mutations detected by the International Cancer Genome Consortium (ICGC) projects.

For that we have prepared an automatic pipeline to import somatic variants from ICGC projects directly from theĀ ICGC Data Coordination Center. We use the genomic coordinates of the variants and their alternative alleles to assess their likely functional impact on genes. We also determine the recurrence of each variant within each project, for each tumor type (topography) and across all ICGC projects.

Finally, we have prepared a modified version of IntOGen browser to effectively navigate ICGC data, which provides an alternative way to navigate and visualize ICGC results. Browsing ICGC data in IntOGen provides some distinctive features such as:

  • Functional assessment of mutations
  • Browsing ICGC data together with IntOGen data
  • Visualizing ICGC mutations in a Genome Browser view

Related to the functional assessment of mutations, among other things, we compute the condel score of all non-synonymous variants detected by ICGC projects.

For more information about Condel look at this post and/or the Condel web page.

The IntOGen browser for ICGC data is still in a beta stage, as there are somethings that we plan to improve, but we are delighted to share it with you at this stage and we are open to suggestions by users.

To start navigating ICGC data in IntOGen go directly to http://icgc.intogen.org or click the ICGC link from the menu at IntOGen web page

We hope you like it.

By | 2011-07-18T07:50:30+00:00 July 18th, 2011|Categories: BG News|Tags: , , , , |0 Comments

About the Author:

Leave A Comment