Abstract 3105: PDCM Finder: An open global cancer research platform for patient-derived cancer models
| Autor: | Zinaida Perova, Csaba Halmagyi, Alex Follette, Mauricio Martinez, Federico Lopez-Gomez, Jeremy Mason, Abayomi Mosaku, Nathalie Conte, Ross Thorne, Steven Neuhauser, Dale Begley, Debra Krupke, Terrence Meehan, Carol Bult, Helen Parkinson |
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| Rok vydání: | 2022 |
| Předmět: | |
| Zdroj: | Cancer Research. 82:3105-3105 |
| ISSN: | 1538-7445 3053-5239 |
| Popis: | PDCM Finder (https://cancermodels.org) is a new portal that aggregates patient-derived models (xenografts, cell lines and organoids) from 27 academic and commercial providers, enables users to search and compare over 6000 models and associated molecular data, and connects users with model providers to facilitate collaboration among researchers. Users can search for models of interest by either (1) exploring molecular data summaries for models of specific cancer types, or (2) using the intuitive search and faceted filtering options of the web user interface or (3) access resource database via REST API to run their own analysis. The data includes gene expression, gene mutation, copy number alteration, cytogenetics, patient treatment and drug dosing studies. We link external resources like publication platforms and cancer specific annotation tools enabling exploration and prioritization of PDCM variation data (COSMIC, CIViC, OncoMX, OpenCRAVAT). In addition to exploring PDCM metadata and data, the portal enables users to validate their PDX models against PDX MI standard, get a FAIRness score of the model of interest, explore originating resource data processing protocols, training materials and contact the model supplier/provider. PDCM Finder builds on the success of the PDX Finder resource (PMID:30535239). Critical PDCM attributes, such as diagnosis, drug names and genes, are harmonized and integrated into a cohesive ontological model based on the PDX Minimal information standard (PDX MI, PMID: 29092942). PDX MI has become established in the community for data exchange, adopted by the PDX providers, consortia and informatics tools integrating PDX data. We are working with the community on the PDCM Minimal Information standard in an effort to make PDCM datasets adhere to the FAIR data principles. We are driving the development of and promoting the use of descriptive standards to facilitate data interoperability and promote global sharing of models. We provide expertise and software components to support several worldwide consortia including PDXNet, PDMR and EurOPDX. PDCM Finder is freely available under an Apache 2.0 license (https://github.com/PDCMFinder). This work is supported by NCI U24 CA204781 01, U24 CA253539, and R01 CA089713. We welcome feedback on the resource and are looking for participants for usability studies - please get in touch if interested. Citation Format: Zinaida Perova, Csaba Halmagyi, Alex Follette, Mauricio Martinez, Federico Lopez-Gomez, Jeremy Mason, Abayomi Mosaku, Nathalie Conte, Ross Thorne, Steven Neuhauser, Dale Begley, Debra Krupke, Terrence Meehan, Carol Bult, Helen Parkinson. PDCM Finder: An open global cancer research platform for patient-derived cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3105. |
| Databáze: | OpenAIRE |
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