The final session of the meeting, chaired by Nuria Lopez-Bigas, starts with the Bioinformatics Challenge results from Mike Schatz. Pan-cancer network analysis of combinations of somatic mutations Ben Raphael (Brown University) follows Mike with a slightly revised talk on mutational heterogeneity. Recap of driver mutations, intra-tumor heterogeneity, long tail discussion and inter-tumor heterogeneity. Announces a “whirlwind tour” of methods developed in his lab (uhoh). Can we infer tumor composition from single, mixed tumor sample? Number of SNV- and CNA based methods (shows dozen of reference ..read more

Visual Exploration of Genomic Data Helga Thorvaldsdottir from the Broad Institute resumes the session after the coffee break, tackling big data challenges in the context of visualization. Genomic data: anything specified as genomic coordinates and a reference genome. Exploration: interactively browsing through representation of the data with the purpose of finding ‘stuff’; re-inforces a number of key concepts from Cydney’s talk. Examples via IGV and how non-reference bases are highlighted in different colors, de-emphasis of low quality calls, highlight on interesting events in the summary plot ..read more

Chaired by Mike Schatz who also announces the now traditional computational challenge. Understanding intrinsic and extrinsic control of intra-tumor phenotype switching Talk by Rosalie Sears (Oregon) presenting on a collaboratie project with the Gray lab. Again an intro to tumor heterogeneity along different axes of differentiation (stem/differential, luminal/basal, mesenchymal/epithelial), but probably a combination of all three axes. The goal is to understand and manage heterogeneity. Useful public data on cell lines and patients. Problem that we are not getting full response to single drugs ..read more

Drugging the cancer interactome: rational target selection for drug discovery Presentation from Bissan Al-Lazikani (The Institute of Cancer Research, London, UK) starts with a quick intro of CRUK’s efforts in drug discovery and hurdles in drug discovery (target selection, biological validation, tracability for drugging, clinical efficacy). It’s an exciting time given the availability of large scale data for cancer gene identification (see previous talks), but every study identifies new/non-overlapping lists of cancer drivers resulting in a rather large target space. Try to assess targets throu ..read more

Chaired by Jan Korbel. I did skip the first (sponsored) talk from Bio-Rad laboratories but made it for the first regular talk of the session. Christopher Plass couldn’t make it, unfortunately, but the talk title remained similar. Epigenetic reprogramming in glioblastoma Mario Suva (MGH) stepped in for Christopher. Dissecting cellular state in glioblastoma: the most frequent brain tumor, peak incidence betwee 45 and 70 years, poor prognosis. Assumption of different cell populations, solid malignancy possibly following the cancer stem cell model with genetic and epigenetic changes (though disagr ..read more

The 2014 Beyond the Genome meeting has a simple tweet policy: talks are assumed to be sharable unless the speaker says otherwise, hashtag of the conference is #btgcg14. As always, all errors are mine. First talk by Gad Getz on Cancer genomics and evolution and completing the catalog of cancer genes who also multitasks as session chair. Quick summary of cancer mutations, driver events (which increase the fitness when it occurs), clonality, passenger events and Co. Cancer genes defined as genes that harbor driver events. Recap of the MutSig algorithm to assess mutation frequencies, adjusting for ..read more

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