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Genomics and clinical data at your fingertips with open-source software: tranSMART & cBioPortal

The CORBEL webinar series continues with a presentation by Jan-Willem Boiten, programme manager at Lygature and Menno de Vries, data manager at the Netherlands Cancer Institute.

The propelling importance of genomics data in present-day health research is not yet supported with user-friendly software solutions that expose these data in a manner easily appreciated by clinical researchers. Clearly, there is a need for tools that integrate genomics and other molecular biology results with the phenotypic and clinical outcome data. This webinar presents an overview of such data tools that are used in the Dutch context and how they have been implemented in practice, including projects that are supported by CORBEL WP3. Two widely used open-source solutions specifically, tranSMART and cBioPortal, will be demonstrated:

  1. tranSMART (http://transmartfoundation.org/) is a data integration, sharing, and analysis platform for clinical and translational research. It allows users to search, view, and analyze data through a web interface, thereby allowing easy access to explore such data from multiple domains at study level. As a knowledge management platform, it enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data and assessing their analytical results in the context of other data sets. tranSMART was initially developed by Johnson&Johnson, and released as an open-source project in 2012.
  2. The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-source resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 20,000 tumor samples from almost 100 cancer studies. It now also serves oncologists in their use and interpretation of clinical sequencing data from cancer patients and enables precision oncology. The cBioPortal software was originally developed by the Memorial Sloan Kettering Cancer Center and released as open-source in 2015.

This webinar intends to give a flavor of the potential of these solutions in practical translational research. For those scientists interested in a functional and/or technical deep-dive, a CORBEL training will be scheduled for later this year.

The CORBEL webinar series aims to address challenges and share best practice between biological and medical research infrastructures. The series is aimed at technical operators of RIs and is aligned with the CORBEL competency framework.

CORBEL webinars include an audience Q&A session during which attendees can ask questions and make suggestions.

This webinar took place on 4 June 2019 and is part of the CORBEL webinar series. It is best viewed in full screen mode using Google Chrome. The slides from this webinar will be made available via SlideShare soon.

About the speakers...

Jan-Willem Boiten is programme manager at Lygature (Utrecht, Netherlands). He has more than 20 years’ experience supporting biomedical researchers in pharmaceutical industry and academia with data and IT solutions that have attracted large user communities. In his current role, he leads several of the Dutch national data infrastructure programmes and the IT work packages of those programmes. These include: Translational Research IT (‘TraIT’), the national data infrastructure for biomarker research; BBMRI-NL, the national biobanking infrastructure; and Data4lifesciences, the national data infrastructure collaboration between the Dutch university medical centres (UMCs). In addition, he is a project member in several European projects and infrastructures (e.g. CORBEL, EATRIS). Jan-Willem Boiten received a PhD in chemistry from Radboud University Nijmegen. He completed his thesis on the topic of ‘Computer Methods in Organic Synthesis Design’.

Menno de Vries is data steward at the Netherlands Cancer Institute (Amsterdam, the Netherlands). He is experienced with aiding researchers in working towards FAIR data by assisting them in preparation and curation of their generated data. He is especially involved with readying their data for import of ‘processed’ or ‘final’ data to the data-integration platforms tranSMART and cBioPortal. In the past he has been involved in the complex documentation logistics and data registry of numerous clinical trials. Menno de Vries received a MSc in biomedical sciences from the University Utrecht.