Abstract 4682: PDCM Finder: an open global research platform for patient-derived cancer models

Autor: Zinaida Perova, Mauricio Martinez, Tushar Mandloi, Federico Lopez Gomez, Csaba Halmagyi, Alex Follette, Jeremy Mason, Steven Neuhauser, Dale A. Begley, Debra M. Krupke, Carol Bult, Helen Parkinson, Tudor Groza, Marcelo P. Rios Almanza
Rok vydání: 2023
Předmět:
Zdroj: Cancer Research. 83:4682-4682
ISSN: 1538-7445
3053-5239
Popis: PDCM Finder (www.cancermodels.org) is a cancer research platform that aggregates clinical, genomic and functional data from patient-derived xenografts, organoids and cell lines. Currently, the portal has over 6300 models across 13 cancer types, including rare pediatric models (17%) and models from minority ethnic backgrounds (33%), making it the largest free to consumer and open access resource of this kind. The PDCM Finder standardizes, harmonizes and integrates the complex and diverse data associated with PDCMs for the cancer community and displays over 90 million data points across a variety of data types (clinical metadata, molecular and treatment-based). PDCM Finder was launched in April 2022 and has been recently enhanced with new functionality and an updated user interface. 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) accessing 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). 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 driving the development of and promoting the use of descriptive standards to facilitate data interoperability and promote global sharing of models. PDCM Finder data is FAIR and underpins the generation and testing of new hypotheses in cancer mechanisms and personalized medicine development. 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, Mauricio Martinez, Tushar Mandloi, Federico Lopez Gomez, Csaba Halmagyi, Alex Follette, Jeremy Mason, Steven Neuhauser, Dale A. Begley, Debra M. Krupke, Carol Bult, Helen Parkinson, Tudor Groza, Marcelo P. Rios Almanza. PDCM Finder: an open global research platform for patient-derived cancer models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4682.
Databáze: OpenAIRE
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