We are proud to share with you the Beta version of IntOGen V.04 at http://beta.intogen.org. This new version includes many changes both in content and in layout. In this post I will summarize the main novelties and in following posts we will give more details of the new version.
IntOGen V.04 includes somatic mutations from cancer resequencing projects
In the last couple of years the genomes (or exomes) of a quite large number of tumors have been sequenced to identify catalogs of tumor somatic mutations. From this data it is possible to infer which are the candidate cancer driver genes and pathways (see more information on how to identify cancer drivers in this post). We have now created a complete pipeline to analyse tumor somatic mutations from cohorts of tumor samples and we have applied it to 19 tumor resequencing projects covering 10 anatomical sites (see table below). The plan is to keep adding new datasets as they are made available. In IntOGen you can now easily find which genes are mutated in different tumor types, which mutations have a predicted functional effect and which are the candidate driver genes and pathways in each tumor type or anatomical site.
IntOGen browser is created using Onexus, an open-source project developed in our lab to easily create web browsers for complex data. During the last months we have made substantial advancements in the development of Onexus leading to a more effective, fast and intuitive web browser for IntOGen. One important novel feature of the new browser is that it includes new types of visualizations for the data. In addition to table view, now some data types can also be visualized as interactive heatmaps and plots. Another interesting feature of the new browser is the search box at the main page, which makes it easier for users to start navigating according to their interests.
We make IntOGen SM pipeline available
The full pipeline that we have created to analyze catalogs of cancer somatic mutations for IntOGen is also now available. You can download the pipeline and run it on your own data. The input of the pipeline is a list of mutations found across a set of tumors of the same type. The pipeline will: 1) identify the consequence types of mutations, 2) assess the functional impact of non-synonymous cancer variants, 3) identify candidate driver genes, 4) identify candidate driver pathways and 5) find recurrently mutated genes and pathways. The results will be browsed the same way that you browse IntOGen (note that the browsing part is not ready, for now you download the datasets as text files).
As you can guess from the fact that V.04 is labelled as Beta, we are still working on it. The browser still needs some improvements and we are currently working to make the pipeline faster. We would be grateful to receive comments and suggestions from users that can help us improve IntOGen V.04.