‘Overcoming the Bottleneck’: Knowledge Architectures for Genomic Data Interpretation in Oncology

Cambrosio, Alberto; Campbell, Jonah; Vignola-Gagné, Étienne; Keating, Peter; Jordan, Bertrand; Bourret, Pascale

doi:10.1007/978-3-030-37177-7_16

Cited by 9 publications

(13 citation statements)

References 40 publications

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“…Subsequent studies have defined a consensus list of cancer driver genes 11 and patterns of cooccurrence and mutual exclusivity of these alterations across different cancer types. 12 Numerous groups maintain knowledge bases 13 of actionable alterations and their associated therapeutic implications. [14][15][16][17][18][19] These knowledge bases incorporate overlapping frameworks to describe genetic alterations by their current level of clinical actionability.…”

Section: Additional Resourcesmentioning

confidence: 99%

“…1 Memorial Sloan Kettering Cancer Center, New York City, NY 2 UT MD Anderson Cancer Center, Houston, TX 3 Yale School of Medicine, New Haven, CT 4 Brigham and Womens' Hospital, Harvard Medical School, Boston, MA 5 The Stephenson Cancer Center, Oklahoma City, OK 6 Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 7 Vanderbilt University Medical Center, Nashville, TN 8 Patient Representative, Gemini Group, Ann Arbor, MI 9 City of Hope, Duarte, CA 10 Levine Cancer Institute, Charlotte, NC 11 University of Colorado, Denver, CO 12 PRISM, Precision Medicine Center, Institut Gustave Roussy, Villejuif, France 13 Johns Hopkins, Baltimore, MD 14 Mayo Clinic, Phoenix, AZ 15 Dartmouth-Hitchcock Medical Center and The Geisel School of Medicine at Dartmouth, Darmouth, NH 16 American Society of Clinical Oncology, Alexandria, VA…”

Section: Affiliationsmentioning

confidence: 99%

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Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion

Chakravarty

Johnson

Sklar

et al. 2022

JCO

145

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PURPOSE An ASCO provisional clinical opinion offers timely clinical direction to ASCO's membership following publication or presentation of potentially practice-changing data from major studies. This provisional clinical opinion addresses the appropriate use of tumor genomic testing in patients with metastatic or advanced solid tumors. CLINICAL CONTEXT An increasing number of therapies are approved to treat cancers harboring specific genomic biomarkers. However, there is a lack of clarity as to when tumor genomic sequencing should be ordered, what type of assays should be performed, and how to interpret the results for treatment selection. PROVISIONAL CLINICAL OPINION Patients with metastatic or advanced cancer should undergo genomic sequencing in a certified laboratory if the presence of one or more specific genomic alterations has regulatory approval as biomarkers to guide the use of or exclusion from certain treatments for their disease. Multigene panel–based assays should be used if more than one biomarker-linked therapy is approved for the patient's disease. Site-agnostic approvals for any cancer with a high tumor mutation burden, mismatch repair deficiency, or neurotrophic tyrosine receptor kinase ( NTRK) fusions provide a rationale for genomic testing for all solid tumors. Multigene testing may also assist in treatment selection by identifying additional targets when there are few or no genotype-based therapy approvals for the patient's disease. For treatment planning, the clinician should consider the functional impact of the targeted alteration and expected efficacy of genomic biomarker–linked options relative to other approved or investigational treatments. Additional information is available at www.asco.org/assays-and-predictive-markers-guidelines .

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Section: Additional Resourcesmentioning

confidence: 99%

Section: Affiliationsmentioning

confidence: 99%

Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion

Chakravarty

Johnson

Sklar

et al. 2022

JCO

145

View full text Add to dashboard Cite

show abstract

“…in Ceci, 2018;Houtkoop et al, 2018). In line with previous studies (Bechtel, 2020;Boumans & Leonelli, 2020;Cambrosio et al, 2020), some interviewees did portray data management practices as driven by epistemic considerations and the desire to foster the development of a research field:…”

Section: Data Handovers and Academic Precaritymentioning

confidence: 57%

Mobile researchers, immobile data: Managing data (producers)

Reichmann

2023

Soc Stud Sci

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Scientific institutions have increasingly embraced formalized research data management strategies, which involve complex social practices of codifying the tacit dimensions of data practices. Several guidelines to facilitate these practices have been introduced in recent years, for example, the FAIR guiding principles. The aim of these practices is to foster transparency and reproducibility through ‘data sharing,’ the public release of data for unbounded reuse. However, a closer look suggests that many scientists’ practices of data release might be better described as what I call data handovers. These practices are not rooted in the lofty ideals of good scientific practice and global data reuse but in the more mundane necessities of research continuity, which have become more urgent in light of increasing academic mobility. The Austrian scientists interviewed for this study reinterpreted defining features of research data management – such as ensuring findability – as techniques for managing the effects of researcher mobility. This suggests that the adoption of Open Science practices might be dissociated from its stated epistemic goals, and explains why many Open Science initiatives at present are administratively strong but normatively weak.

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“…[8][9][10][11] MCG has distinguished itself through its inclusion of clinical trials and organization of content along cancer-relevant cell-signaling pathways. 9,[12][13][14] However, the site is also used by researchers, pathologists, and diagnostic labs developing interpretive reports, as well as patients and caregivers.…”

Section: Introductionmentioning

confidence: 99%

My Cancer Genome: Coevolution of Precision Oncology and a Molecular Oncology Knowledgebase

Holt

Mittendorf

Lenoue-Newton

et al. 2021

JCO Clinical Cancer Informatics

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PURPOSE The My Cancer Genome (MCG) knowledgebase and resulting website were launched in 2011 with the purpose of guiding clinicians in the application of genomic testing results for treatment of patients with cancer. Both knowledgebase and website were originally developed using a wiki-style approach that relied on manual evidence curation and synthesis of that evidence into cancer-related biomarker, disease, and pathway pages on the website that summarized the literature for a clinical audience. This approach required significant time investment for each page, which limited website scalability as the field advanced. To address this challenge, we designed and used an assertion-based data model that allows the knowledgebase and website to expand with the field of precision oncology. METHODS Assertions, or computationally accessible cause and effect statements, are both manually curated from primary sources and imported from external databases and stored in a knowledge management system. To generate pages for the MCG website, reusable templates transform assertions into reconfigurable text and visualizations that form the building blocks for automatically updating disease, biomarker, drug, and clinical trial pages. RESULTS Combining text and graph templates with assertions in our knowledgebase allows generation of web pages that automatically update with our knowledgebase. Automated page generation empowers rapid scaling of the website as assertions with new biomarkers and drugs are added to the knowledgebase. This process has generated more than 9,100 clinical trial pages, 18,100 gene and alteration pages, 900 disease pages, and 2,700 drug pages to date. CONCLUSION Leveraging both computational and manual curation processes in combination with reusable templates empowers automation and scalability for both the MCG knowledgebase and MCG website.

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‘Overcoming the Bottleneck’: Knowledge Architectures for Genomic Data Interpretation in Oncology

Cited by 9 publications

References 40 publications

Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion

Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion

Mobile researchers, immobile data: Managing data (producers)

My Cancer Genome: Coevolution of Precision Oncology and a Molecular Oncology Knowledgebase

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