ArticleBioinformatics (Oxford, England)2025
Oncopacket: integration of cancer research data using GA4GH phenopackets.
Michael Sierk, Daniel Danis, Sujay Patil, Nobal Kishor, Rajdeep Mondal, Abhishek Jha, Qingrong Chen, Chunhua Yan, Monica Munoz-Torres, Daoud Meerzaman and 2 more
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In one paragraphArticle in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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5 · Who and what moneyAuthors and funding
12 authors.
Michael SierkCenter for Biomedical Informatics & Information Technology, National Cancer Institute (NCI) Bethesda, MD 20850, United States.ORCID 0000-0002-0657-0288 Daniel DanisBerlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin 10117, Germany.
Sujay PatilDivision of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, 94720, United States.ORCID 0000-0001-6142-1106 Nobal KishorElucidata, San Francisco, CA 94114, United States.
Rajdeep MondalElucidata, San Francisco, CA 94114, United States.
Abhishek JhaElucidata, San Francisco, CA 94114, United States.
Qingrong ChenCenter for Biomedical Informatics & Information Technology, National Cancer Institute (NCI) Bethesda, MD 20850, United States.
Chunhua YanCenter for Biomedical Informatics & Information Technology, National Cancer Institute (NCI) Bethesda, MD 20850, United States.
Monica Munoz-TorresDepartment of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.
Daoud MeerzamanCenter for Biomedical Informatics & Information Technology, National Cancer Institute (NCI) Bethesda, MD 20850, United States.
Peter N RobinsonBerlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin 10117, Germany.ORCID 0000-0002-0736-9199 Justin T ReeseDivision of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, 94720, United States.ORCID 0000-0002-2170-2250 Funding
The Monarch Initiative: Linking Diseases to Model Organism ResourcesR24OD011883 · OD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAENDEL, MELISSA A, MUNGALL, CHRISTOPHER J · 2012 to 2024
$16.0MImprovements to the LinkML framework to support the Phenomics First open science resourceRM1HG010860 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAENDEL, MELISSA A, MUNGALL, CHRISTOPHER J · 2020 to 2024
$10.3MThe Human Phenotype Ontology: Accelerating Computational Integration of Clinical Data for GenomicsU24HG011449 · NHGRI · JACKSON LABORATORY · PI Peter Nicholas Robinson · 2021 to 2026
$6.7MIncreasing the Yield and Utility of Pediatric Genomic Medicine with ExomiserR01HD103805 · NICHD · JACKSON LABORATORY · PI Valentina Cipriani, CHRISTOPHER J MUNGALL · 2021 to 2026
$4.3MAlexander von Humboldt foundationNHGRI NIH HHS RM1 HG010860NHGRI NIH HHS U24 HG011449NICHD NIH HHS R01 HD103805NIH HHS 5R01HD103805-04NIH HHS 5R24OD011883-12NIH HHS 5RM1HG010860-03NIH HHS 5U24HG011449-04NIH HHS R24 OD011883Office of Basic Energy Sciences of the U.S. Department of Energy DE-AC02-05CH11231
6 · The paper itselfAbstract
summaryLack of data integration remains a significant impediment to cancer research, and many analyses still require customized software to transform and prepare cancer data. We describe a software package to harmonize genetic and clinical cancer data into the GA4GH Phenopacket schema, an ISO standard for representing clinical case data. We integrated demographic, mutation, morphology, diagnosis, intervention, and survival data using case data from the National Cancer Institute for 12 cancer types. The Phenopacket standard provides a foundation for downstream use, including sophisticated statistical and AI/ML analyses. We demonstrate fitness for purpose by using the integrated data to recapitulate a known association between mutations in the gene encoding isocitrate dehydrogenase 1 and survival time in brain cancer patients. AVAILABILITY AND IMPLEMENTATION: Source code is freely available at: https://github.com/monarch-initiative/oncopacket (archived at 10.5281/zenodo.15353125).
Indexed as
Computational BiologyNeoplasmsSoftwareDatabases, GeneticHumansIsocitrate DehydrogenaseMutationIsocitrate Dehydrogenase
Identifiers
PMID41017641
PMCPMC12516310
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