How to identify cancer drivers from tumor somatic mutations?

Cartoon representing genomic alterations in a tumor cell. Image from NCI.

I have recently seen several presentations by groups that systematically explore alterations in cancer genomes that deliver the same message. One of the main challenges faced by their projects is to identify genes and pathways involved in tumor development (drivers). Very good methods based on the recurrence of somatic mutations have been developed to identify cancer drivers (see, for example MutSig and the Significantly Mutated Gene (SMG) test from MuSiC). They rely on the assumption that genes that exhibit more mutations than expected by chance are putative drivers. Even though these methods are successful in identifying clear cancer drivers, they also face some known challenges. For instance, the background mutation rate is hard to estimate accurately and important genes that are mutated only in a small number of tumors may be overlooked. Besides, these methods treat all mutations that may affect protein sequence equally, when their impact on protein function clearly differ.

 

Some time ago we thought that a good way to address these challenges would be to use the Functional Impact Bias (FM bias) observed in genes across a cohort of tumor samples. In other words, we wanted to estimate how the accumulation of mutations with high functional impact on each gene deviates from the average observed in all tumor samples.

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Barcelona Summer School in Genomics and Bioinformatics

The course will take place at the Barcelona Biomedical Research Park

I am happy to announce the Barcelona Summer School in Genomics and Bioinformatics, which will take place from September 17th to 21st 2012. The course is organized by Ferran Casals from the IBE and UPF. He has  put together a very interesting program with a great list of speakers and topics. We will participate teaching Cancer Genomics and Functional Annotation of Variants.

If you are interested you can register at http://biologiaevolutiva.org/BSSGB/

I give you further details of the course, list of speakers and program in this post.

 

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