Thread by @nlbigas

Very happy to announce a major IntOGen update. This new version contains a comprehensive and reliable compendium of cancer genes and their mutational features across 61 tumour types, obtained by analysing 26,955 cancer genomes intogen.org. Thread 👇

How does intOGen identify cancer genes?

Briefly, intOGen runs six complementary driver discovery methods that analyze the pattern of mutations per gene and cohort and combines their output to produce a compendium of driver genes and a repository of their mutational features

How did you collect genomic data from >26,000 tumors?

We manually downloaded, processed and annotated tumor genomic data from different sources, such as @cbioportal #PedcBioPortal @icgc_dcc #TCGA #PCAWG @HartwigMedical #TARGET @StJude and others. 190 cohorts in total👇

What can I do at IntOGen.org?

You can search for a gene and see if it has driver mutations in any of the 61 cancer types analyzed. Or you can search for a cancer type and see all genes with driver mutations.

Can I download and use intOGen data?

Yes, all the data generated by intOGen can be downloaded and is available for use free of restrictions under the @creativecommons Zero Public Domain Dedication (creativecommons.org/publicdomain/z…).

Can I run the pipeline myself?

Yes, we have implemented a @nextflowio pipeline that can be run locally. The source code of the intOGen pipeline is provided under The GNU General Public Licen v3.0

👉Pipeline code: bitbucket.org/intogen/intoge…
👉Documentation: intogen.readthedocs.io/en/latest/data…

What did it take to develop this new intOGen release?

Who has contributed to develop this version of intOGen?

IntOGen is a team effort from @bbglab.

See intogen.org/beta/about

IntOGen is possible thanks to the generosity of patients who share samples for research, and the clinicians/researchers who obtain the data and make it available for other researchers.

We hope to make a convincing case of the benefit of accessible data to progress in science