Abstract
We created the PDX Network (PDXNet) Portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources (i.e., PDX models, sequencing data, treatment response data, and bioinformatics workflows), to facilitate collaboration among researchers, and to make resources easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet activities, data processing protocols, and training materials for processing PDX data.
The initial portal release highlights PDXNet model and data resources, including 334 new models across 33 cancer types. Tissue samples of these models were deposited in the NCI’s Patient-Derived Model Repository (PDMR) for public access. These models have 2,822 associated sequencing files from 873 samples across 307 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal also includes results from standardized analysis workflows on PDXNet sequencing files and PDMR data (2,594 samples from 463 patients across 78 disease types). These 15 analysis workflows for whole-exome and RNA-Seq data are freely available, robust, validated, and standardized.
The model and data lists will grow substantially over the next two years and will be continuously updated as new data are available. PDXNet models support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials. The PDXNet portal is a centralized location for these data and resources, which we expect to be of significant utility for the cancer research community.
Competing Interest Statement
The University of Utah may choose to license PDX models developed in the Welm labs, which may result in tangible property royalties to Drs. Welm and members of their lab who developed the models. MTL is a founder and limited partner in StemMed Ltd. and a manager in StemMed Holdings, it's general partner. He is a founder and equity stake holder in Tvardi Theraeutics Inc. Some PDX are exclusively licensed to StemMed Ltd. resulting in royalty income to MTL. Lacey Dobrolecki is a compensated employee of StemMed Ltd. The other authors declare no competing interest.
Footnotes
↵# Drs. Dean and Chuang are co-senior authors providing equivalent oversight to work presented in this manuscript
Financial Support: This work was supported by NIH funding to the PDXNet Data Commons and Coordination Center (NCI U24-CA224067) to the PDX Development and Trial Centers (NCI U54-CA224083, NCI U54-CA224070, NCI U54-CA224065, NCI U54-CA224076, NCI U54-CA233223, and NCI U54-CA233306). The Cancer Genomics Cloud powered by Seven Bridges is a Cancer Research Data Commons Cloud Resource, funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, Contract No. HHSN261201400008C and ID/IQ Agreement No. 17X146 under Contract No. HHSN261201500003I and 75N91019D00024.
Conflict of Interest: The University of Utah may choose to license PDX models developed in the Welm labs, which may result in tangible property royalties to Drs. Welm and members of their lab who developed the models. MTL is a founder and limited partner in StemMed Ltd. and a manager in StemMed Holdings, it’s general partner. He is a founder and equity stake holder in Tvardi Theraeutics Inc. Some PDX are exclusively licensed to StemMed Ltd. resulting in royalty income to MTL. Lacey Dobrolecki is a compensated employee of StemMed Ltd. The other authors declare no competing interest.
Contact information: Prof. Jeffrey H. Chuang, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive Farmington, CT 06032, Phone: 837-856-2473, Email: jeff.chuang{at}jax.org
Update to author list affiliations and spelling correct.