When I’m looking for upcoming Tips of the Week, frequently one tool or paper will lead me to looking at other related tools in that sphere. Last week’s tip on COSMIC got me looking through cancer genomics resources, and one of the others that I came across is IntOGen, “Integrative Onco Genomics”.
Their Nature Methods paper has a nice summary of their goals:
The IntOGen-mutations platform (http://www.intogen.org/mutations/) summarizes somatic mutations, genes and pathways involved in tumorigenesis. It identifies and visualizes cancer drivers, analyzing 4,623 exomes from 13 cancer sites. It provides support to cancer researchers, aids the identification of drivers across tumor cohorts and helps rank mutations for better clinical decision-making.
The paper has a nice description of the features that they have incorporated into their interface. They have different mutation-calling workflows that are run, and then scores are derived from them. There is a searchable component–where data from projects like TCGA and ICGC have been assessed with these tools and you can explore the outcomes with their browser function. In this video from their team you can get a sense of how to search and examine the data [no audio, annotated with text for guidance]:
You can also upload samples that you have to examine and compare in their Mutation Analysis component. There are separate additional videos that they offer to help you to perform this type of analysis at their site. Here’s one of them:
I had actually been at their site recently looking at a blog post about mutation diagrams: How to generate mutation distribution and frequency plots? People who read our blog seem to really gravitate towards tools that help them to visualize various features of the research they are doing. Domain drawing, motif representation, and sets are popular. Recently one of the posts I did highlighting a domain and mutation mapper at the cBio Portal got some traction. According to the blog post, the team from IntOGen decided to create a helpful similar tool that they can incorporate in an upcoming release of IntOGen. So it’s great to see new ideas and new tools coming along as well.
The tools they offer look very nice, check them out. And I’m trying not to be jealous of their location and photos as I continue to shovel snow….
Gonzalez-Perez A., Christian Perez-Llamas, Jordi Deu-Pons, David Tamborero, Michael P Schroeder, Alba Jene-Sanz, Alberto Santos & Nuria Lopez-Bigas (2013). IntOGen-mutations identifies cancer drivers across tumor types, Nature Methods, 10 (11) 1081-1082. DOI: http://dx.doi.org/10.1038/nmeth.2642