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Reproducible Science: Cancer Researchers Embrace Containers in the Cloud

Tuesday, September 6, 2016

Posted by Dr. Kyle Ellrott, Oregon Health and Sciences University, Dr. Josh Stuart, University of California Santa Cruz, and Dr. Paul Boutros, Ontario Institute for Cancer ResearchToday we hear from the principal investigators of the ICGC-TCGA DREAM Somatic Mutation Calling Challenges about how they are encouraging cancer researchers to make use of Docker and Google Cloud Platform to gain a deeper understanding of the complex genetic mutations that occur in cancer, while doing so in a reproducible way.– Nicole Deflaux and Jonathan Bingham, Google GenomicsReproducibleCancer MoonshotBreak down silos and bring all the cancer fighters togethercontainersOntario Institute for Cancer ResearchUniversity of California Santa CruzSage BionetworksOregon Health and Sciences UniversityDockerCancer Cloud Pilots funded by the National Cancer InstituteICGC-TCGA DREAM Somatic Mutation Calling (SMC) ChallengesGoogle Cloud PlatformDNA somatic mutationsproviding key insightscontainerizationSMC-Het ChallengeSMC-RNA Challenge

SMC-Het Challenge: Tumour biopsies are composed of many different cell types in addition to tumour cells, including normal tissue and infiltrating immune cells. Furthermore, the tumours themselves are made of a mixture of different subpopulations, all related to one another through cell division and mutation. Critically, each sub-population can have distinct clinical outcomes, with some more resistant to treatment or more likely to metastasize than others. The goal of the SMC-Het Challenge is to identify the best methods for predicting tumor subpopulations and their “family tree” of relatedness from genome sequencing data.

SMC-RNA Challenge: The alteration of RNA production is a fundamental mechanism by which cancer cells rewire cellular circuitry. Genomic rearrangements in cancer cells can produce fused protein products that can bestow Frankenstein-like properties. Both RNA abundances and novel fusions can serve as the basis for clinically-important prognostic biomarkers. The SMC-RNA Challenge will identify the best methods to detect such rogue expressed RNAs in cancer cells.