The Cancer Genome Atlas Pan-Cancer Project

Yesterday the paper describing TCGA Pan-Cancer Project was published in Nature Genetics. We’ve had the opportunity to participate in this exciting project and here I would like to explain our experience and contribution to it.


We have been interested for quite a while in the study of patterns of genomics alterations in cancer across tumor types. Thus a project like the TCGA Pan-Cancer provided a unique opportunity to apply our tools and expertise to a unique collection of data.


In the past few years we have developed computational methodologies to identify cancer drivers by analyzing the patterns of somatic mutations across tumors (i.e OncodriveFM and OncodriveCLUST) as well as tools to facilitate the visual exploration of multidimensional cancer genomics datasets (i.e. GitoolsIntOGen, see our review on this topic if you are interested in this), we now had the opportunity to apply those tools to TCGA Pan-Cancer data.

Read the rest of this entry »

Chromatin maintenance and cancer

It is now well established that cancer is a collection of mostly genetic diseases. They progress through the accumulation of alterations, such as point mutations in genes that affect mechanisms, often known as the hallmarks of cancer which ultimately confer the altered cell some advantageous properties with respect to neighboring ‘normal’ cells. Decades of intense research on the molecular biology of cancer have delineated many of such hallmarks. Nevertheless, some others have only begun to appear with the advent of large Cancer Genomics initiatives, such as The Cancer Genome Atlas and the International Cancer Genome Consortium.

One of these novel hallmarks has to do with the alteration of general mechanisms of chromatin regulation and maintenance. It is now clear that these mechanisms become altered in one way or another across many tumor types, and that their alteration in principle could lead to the de-regulation of several cellular functions that promote tumorigenesis. With this in mind, we have examined the mutations that occur in chromatin regulatory factors (CRFs) across 4623 tumor samples representing 31 cancer genome re-sequencing projects from 13 anatomical sites. The results of this study have just been published in Genome Biology.


I want to highlight here the main findings of our study.

Read the rest of this entry »

Oncogenomics workshop: my slides on the analysis of Somatic Mutations in IntOGen

Last week I attended the Oncogenomics Workshop in Hinxton. This was a really interesting Workshop organized by the Industry program of the EBI. It addressed the issues of which data are becoming available and how to access them, how to best analyze the oncogenomics data and interpret them, and which are the challenges ahead in terms of translating these data and knowledge into therapeutic opportunities. I was invited to present IntOGen and I thought it would be of interest to some followers of our blog if I shared the slides of the talk.

  Read the rest of this entry »

New IntOGen Somatic Mutations Analysis version available

We are proud to announce the brand new version of the IntOGen Somatic Mutations Analysis (IntOGen SM) pipeline. We call it version 2.0.0 as it has been completely rewritten from scratch with a strong focus on quality, efficiency and scalability.

The IntOGen SM pipeline addresses the challenge of identifying which somatic mutations are important for the development of tumors. The input for the analysis is a list of somatic mutations detected in a cohort of tumors. Read the rest of this entry »