IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-28348-y.html
   My bibliography  Save this article

A platform for oncogenomic reporting and interpretation

Author

Listed:
  • Caralyn Reisle

    (Canada’s Michael Smith Genome Sciences Centre
    University of British Columbia)

  • 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
    University of British Columbia)

  • Stephen Yip

    (University of British Columbia)

  • Janessa Laskin

    (BC Cancer)

  • Marco A. Marra

    (Canada’s Michael Smith Genome Sciences Centre
    University of British Columbia)

  • Steven J. M. Jones

    (Canada’s Michael Smith Genome Sciences Centre
    University of British Columbia
    Simon Fraser University)

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.

Suggested Citation

  • 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 Beck, 2022. "A platform for oncogenomic reporting and interpretation," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28348-y
    DOI: 10.1038/s41467-022-28348-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-28348-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-28348-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Ludmil B. Alexandrov & Serena Nik-Zainal & David C. Wedge & Samuel A. J. R. Aparicio & Sam Behjati & Andrew V. Biankin & Graham R. Bignell & Niccolò Bolli & Ake Borg & Anne-Lise Børresen-Dale & Sandri, 2013. "Correction: Corrigendum: Signatures of mutational processes in human cancer," Nature, Nature, vol. 502(7470), pages 258-258, October.
    2. Ludmil B. Alexandrov & Serena Nik-Zainal & David C. Wedge & Samuel A. J. R. Aparicio & Sam Behjati & Andrew V. Biankin & Graham R. Bignell & Niccolò Bolli & Ake Borg & Anne-Lise Børresen-Dale & Sandri, 2013. "Signatures of mutational processes in human cancer," Nature, Nature, vol. 500(7463), pages 415-421, August.
    3. Ludmil B. Alexandrov & Jaegil Kim & Nicholas J. Haradhvala & Mi Ni Huang & Alvin Wei Tian Ng & Yang Wu & Arnoud Boot & Kyle R. Covington & Dmitry A. Gordenin & Erik N. Bergstrom & S. M. Ashiqul Islam , 2020. "The repertoire of mutational signatures in human cancer," Nature, Nature, vol. 578(7793), pages 94-101, February.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Rebecca J. Deyell & Yaoqing Shen & Emma Titmuss & Katherine Dixon & Laura M. Williamson & Erin Pleasance & Jessica M. T. Nelson & Sanna Abbasi & Martin Krzywinski & Linlea Armstrong & Melika Bonakdar , 2024. "Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Papadopoulos, Nicolas & Cleveland, Mark, 2023. "An international and cross-cultural perspective on ‘the wired consumer’: The digital divide and device difference dilemmas," Journal of Business Research, Elsevier, vol. 156(C).

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ambrocio Sanchez & Pedro Ortega & Ramin Sakhtemani & Lavanya Manjunath & Sunwoo Oh & Elodie Bournique & Alexandrea Becker & Kyumin Kim & Cameron Durfee & Nuri Alpay Temiz & Xiaojiang S. Chen & Reuben , 2024. "Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Teresa Maria Rosaria Noviello & Anna Maria Giacomo & Francesca Pia Caruso & Alessia Covre & Roberta Mortarini & Giovanni Scala & Maria Claudia Costa & Sandra Coral & Wolf H. Fridman & Catherine Sautès, 2023. "Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Sujath Abbas & Oriol Pich & Ginny Devonshire & Shahriar A. Zamani & Annalise Katz-Summercorn & Sarah Killcoyne & Calvin Cheah & Barbara Nutzinger & Nicola Grehan & Nuria Lopez-Bigas & Rebecca C. Fitzg, 2023. "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Sriram Vijayraghavan & Thomas Blouin & James McCollum & Latarsha Porcher & François Virard & Jiri Zavadil & Carol Feghali-Bostwick & Natalie Saini, 2024. "Widespread mutagenesis and chromosomal instability shape somatic genomes in systemic sclerosis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. Josefine Radke & Naveed Ishaque & Randi Koll & Zuguang Gu & Elisa Schumann & Lina Sieverling & Sebastian Uhrig & Daniel Hübschmann & Umut H. Toprak & Cristina López & Xavier Pastor Hostench & Simone B, 2022. "The genomic and transcriptional landscape of primary central nervous system lymphoma," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    6. Yasha Butt & Ramin Sakhtemani & Rukshana Mohamad-Ramshan & Michael S. Lawrence & Ashok S. Bhagwat, 2024. "Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Peter Georgeson & Tabitha A. Harrison & Bernard J. Pope & Syed H. Zaidi & Conghui Qu & Robert S. Steinfelder & Yi Lin & Jihoon E. Joo & Khalid Mahmood & Mark Clendenning & Romy Walker & Efrat L. Amita, 2022. "Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    8. Bernard C. H. Lee & Philip S. Robinson & Tim H. H. Coorens & Helen H. N. Yan & Sigurgeir Olafsson & Henry Lee-Six & Mathijs A. Sanders & Hoi Cheong Siu & James Hewinson & Sarah S. K. Yue & Wai Yin Tsu, 2022. "Mutational landscape of normal epithelial cells in Lynch Syndrome patients," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    9. Amanda Fitzpatrick & Marjan Iravani & Adam Mills & David Vicente & Thanussuyah Alaguthurai & Ioannis Roxanis & Nicholas C. Turner & Syed Haider & Andrew N. J. Tutt & Clare M. Isacke, 2023. "Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    10. Daan M. K. Soest & Paulien E. Polderman & Wytze T. F. Toom & Janneke P. Keijer & Markus J. Roosmalen & Tim M. F. Leyten & Johannes Lehmann & Susan Zwakenberg & Sasha Henau & Ruben Boxtel & Boudewijn M, 2024. "Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    11. Jurica Levatić & Marina Salvadores & Francisco Fuster-Tormo & Fran Supek, 2022. "Mutational signatures are markers of drug sensitivity of cancer cells," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    12. Qingli Guo & Eszter Lakatos & Ibrahim Al Bakir & Kit Curtius & Trevor A. Graham & Ville Mustonen, 2022. "The mutational signatures of formalin fixation on the human genome," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    13. Maria Zhivagui & Areebah Hoda & Noelia Valenzuela & Yi-Yu Yeh & Jason Dai & Yudou He & Shuvro P. Nandi & Burcak Otlu & Bennett Houten & Ludmil B. Alexandrov, 2023. "DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    14. Sebastian Carrasco Pro & Heather Hook & David Bray & Daniel Berenzy & Devlin Moyer & Meimei Yin & Adam Thomas Labadorf & Ryan Tewhey & Trevor Siggers & Juan Ignacio Fuxman Bass, 2023. "Widespread perturbation of ETS factor binding sites in cancer," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    15. Jessica S. Williams & Scott. A. Lujan & Mercedes E. Arana & Adam B. Burkholder & Percy P. Tumbale & R. Scott Williams & Thomas A. Kunkel, 2024. "High fidelity DNA ligation prevents single base insertions in the yeast genome," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    16. Antonio Rodriguez-Calero & John Gallon & Dilara Akhoundova & Sina Maletti & Alison Ferguson & Joanna Cyrta & Ursula Amstutz & Andrea Garofoli & Viola Paradiso & Scott A. Tomlins & Ekkehard Hewer & Ver, 2022. "Alterations in homologous recombination repair genes in prostate cancer brain metastases," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    17. Christopher Ruis & Aaron Weimann & Gerry Tonkin-Hill & Arun Prasad Pandurangan & Marta Matuszewska & Gemma G. R. Murray & Roger C. Lévesque & Tom L. Blundell & R. Andres Floto & Julian Parkhill, 2023. "Mutational spectra are associated with bacterial niche," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    18. Thomas G. Paulson & Patricia C. Galipeau & Kenji M. Oman & Carissa A. Sanchez & Mary K. Kuhner & Lucian P. Smith & Kevin Hadi & Minita Shah & Kanika Arora & Jennifer Shelton & Molly Johnson & Andre Co, 2022. "Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    19. Heather E. Machado & Nina F. Øbro & Nicholas Williams & Shengjiang Tan & Ahmed Z. Boukerrou & Megan Davies & Miriam Belmonte & Emily Mitchell & E. Joanna Baxter & Nicole Mende & Anna Clay & Philip Anc, 2023. "Convergent somatic evolution commences in utero in a germline ribosomopathy," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    20. Mei Lin & Xiao-Long Zhang & Rui You & You-Ping Liu & Hong-Min Cai & Li-Zhi Liu & Xue-Fei Liu & Xiong Zou & Yu-Long Xie & Ru-Hai Zou & Yi-Nuan Zhang & Rui Sun & Wei-Yi Feng & Hai-Yan Wang & Gui-Hua Tao, 2023. "Evolutionary route of nasopharyngeal carcinoma metastasis and its clinical significance," Nature Communications, Nature, vol. 14(1), pages 1-21, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28348-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.