A platform for oncogenomic reporting and interpretation

Caralyn Reisle, Laura M. Williamson, Erin Pleasance, Anna Davies, Brayden Pellegrini, Dustin W. Bleile, Karen L. Mungall, Eric Chuah, Martin R. Jones, Yussanne Ma, Eleanor Lewis, Isaac Beckie, David Pham, Raphael Matiello Pletz, Amir Muhammadzadeh, Brandon M. Pierce, Jacky Li, Ross Stevenson, Hansen Wong, Lance Bailey, Abbey Reisle, Matthew Douglas, Melika Bonakdar, Jessica M. T. Nelson, Cameron J. Grisdale, Martin Krzywinski, Ana Fisic, Teresa Mitchell, Daniel J. Renouf, Stephen Yip, Janessa Laskin, Marco A. Marra and Steven J. M. Jones ()
Additional contact information
Caralyn Reisle: Canada’s Michael Smith Genome Sciences Centre
Laura M. Williamson: Canada’s Michael Smith Genome Sciences Centre
Erin Pleasance: Canada’s Michael Smith Genome Sciences Centre
Anna Davies: Canada’s Michael Smith Genome Sciences Centre
Brayden Pellegrini: Canada’s Michael Smith Genome Sciences Centre
Dustin W. Bleile: Canada’s Michael Smith Genome Sciences Centre
Karen L. Mungall: Canada’s Michael Smith Genome Sciences Centre
Eric Chuah: Canada’s Michael Smith Genome Sciences Centre
Martin R. Jones: Canada’s Michael Smith Genome Sciences Centre
Yussanne Ma: Canada’s Michael Smith Genome Sciences Centre
Eleanor Lewis: Canada’s Michael Smith Genome Sciences Centre
Isaac Beckie: Canada’s Michael Smith Genome Sciences Centre
David Pham: Canada’s Michael Smith Genome Sciences Centre
Raphael Matiello Pletz: Canada’s Michael Smith Genome Sciences Centre
Amir Muhammadzadeh: Canada’s Michael Smith Genome Sciences Centre
Brandon M. Pierce: Canada’s Michael Smith Genome Sciences Centre
Jacky Li: Canada’s Michael Smith Genome Sciences Centre
Ross Stevenson: Canada’s Michael Smith Genome Sciences Centre
Hansen Wong: Canada’s Michael Smith Genome Sciences Centre
Lance Bailey: Canada’s Michael Smith Genome Sciences Centre
Abbey Reisle: Canada’s Michael Smith Genome Sciences Centre
Matthew Douglas: Canada’s Michael Smith Genome Sciences Centre
Melika Bonakdar: Canada’s Michael Smith Genome Sciences Centre
Jessica M. T. Nelson: Canada’s Michael Smith Genome Sciences Centre
Cameron J. Grisdale: Canada’s Michael Smith Genome Sciences Centre
Martin Krzywinski: Canada’s Michael Smith Genome Sciences Centre
Ana Fisic: BC Cancer
Teresa Mitchell: BC Cancer
Daniel J. Renouf: Pancreas Centre BC
Stephen Yip: University of British Columbia
Janessa Laskin: BC Cancer
Marco A. Marra: Canada’s Michael Smith Genome Sciences Centre
Steven J. M. Jones: Canada’s Michael Smith Genome Sciences Centre

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract Manual interpretation of variants remains rate limiting in precision oncology. The increasing scale and complexity of molecular data generated from comprehensive sequencing of cancer samples requires advanced interpretative platforms as precision oncology expands beyond individual patients to entire populations. To address this unmet need, we introduce a Platform for Oncogenomic Reporting and Interpretation (PORI), comprising an analytic framework that facilitates the interpretation and reporting of somatic variants in cancer. PORI integrates reporting and graph knowledge base tools combined with support for manual curation at the reporting stage. PORI represents an open-source platform alternative to commercial reporting solutions suitable for comprehensive genomic data sets in precision oncology. We demonstrate the utility of PORI by matching 9,961 pan-cancer genome atlas tumours to the graph knowledge base, calculating therapeutically informative alterations, and making available reports describing select individual samples.

Date: 2022
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Citations: View citations in EconPapers (3)

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DOI: 10.1038/s41467-022-28348-y

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