PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery
Author:
Koc Soner1, Lloyd Michael W2ORCID, Grover Jeffrey W1ORCID, Xiao Nan1, Seepo Sara1, Subramanian Sai Lakshmi1, Ray Manisha1, Frech Christian1, DiGiovanna John1, Webster Phillip1, Neuhauser Steven2, Srivastava Anuj3, Woo Xing Yi3, Sanderson Brian J3, White Brian3, Lott Paul4, Dobrolecki Lacey E5, Dowst Heidi5, Bailey Matthew, Cortes-Sanchez Emilio, Scherer Sandra, Yang Chieh-Hsiang, Fujita Maihi, Chu Zhengtao, Zhao Ling, Butterfield Andrew, Akcakanat Argun, Boning Gao, Evans Kurt, Fang Bingliang, Gibbons Don, Jensen Vanessa, Keener Dara, Kim Michael, Kopetz Scott, Majidi Mourad, Menter David, Minna John, Park Hyunsil, Yang Fei, Timmons Brenda, Wang Jing, Westin Shannon, Yap Timothy, Zhang Jianhua, Zhang Ran, Ha Min Jin, Chen Huiqin, Xi Yuanxin, Girard Luc, Yucan Erkan, Kirby Bryce P, Dai Bingbing, Xu Yi, Sorokin Alexey, Gale Kelly, Augustine Jithesh, Scott Stephen, Meraz Ismail, Fingerman Dylan, Kossenkov Andrew, Liu Qin, Xiao Min, Wickramasinghe Jayamanna, Lin Haiyin, Ramirez-Salazar Eric, Nathanson Kate, Tetzlaff Mike, Xu George, Yennu-Nanda Vashisht G, Aft Rebecca, Andrews Jessica, Asaro Alicia, Cao Song, Chen Feng, Davies Sherri, DiPersio John, Fields Ryan, Foltz Steven, Fuh Katherine, Lim Kian, Held Jason, Hoog Jeremy, Jayasinghe Reyka G, Li Yize, Luo Jinqin, Ma Cynthia, Mashl Jay, Mo Chia-Kuei, Rodriguez Fernanda, Sun Hua, Terekhanova Nadezhda V, Tipton Rose, VanTine Brian, Wang-Gillam Andrea, Wendl Mike, Wu Yige, Wyczalkowski Matt, Yao Lijun, Zhou Daniel Cui, Ellis Matthew, Ittmann Michael, Hilsenbeck Susan, O’Malley Bert, Kirane Amanda, Cho May, Gandara David, Reiss Jonathan, Le Tiffany, White Ralph De Vere, Tepper Cliff, Cooke David, Godoy Luis, Brown Lisa, Dall’Era Marc, Evans Christopher, Verma Rashmi, Gholami Sepideh, Segal David J, Albeck John, Pugh Edward, Stewart Susan, Rocke David, Zhang Hongyong, Coggins Nicole, Estrada Ana, Toal Ted, Morales Alexa, Echeverry Guadalupe Polanco, Rocha Sienna, Ma Ai-Hong, Evrard Yvonne A6, Wallace Tiffany A7, Moscow Jeffrey A8, Doroshow James H9, Mitsiades Nicholas5, Kaochar Salma5, Pan Chong-xian410, Chen Moon S4, Carvajal-Carmona Luis4, Welm Alana L11, Welm Bryan E11, Lewis Michael T5, Govindan Ramaswamy12, Ding Li12, Li Shunqiang12, Herlyn Meenhard13, Davies Michael A14, Roth Jack14, Meric-Bernstam Funda14, Robinson Peter N3ORCID, Bult Carol J2ORCID, Davis-Dusenbery Brandi1, Dean Dennis A1, Chuang Jeffrey H3,
Affiliation:
1. Seven Bridges, Charlestown , MA 02129, USA 2. The Jackson Laboratory , Bar Harbor, ME 04609, USA 3. The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA 4. University of California - Davis , Davis, CA 95616, USA 5. Baylor College of Medicine , Houston, TX 77030, USA 6. Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research , Frederick, MD 21701, USA 7. Center to Reduce Health Disparities, National Cancer Institute , Bethesda, MD 20814, USA 8. Investigational Drug Branch, National Cancer Institute , Bethesda, MD 20814, USA 9. Division of Cancer Treatment and Diagnosis, National Cancer Institute , Bethesda, MD 20814, USA 10. Harvard Medical School , West Roxbury, MA 02115, USA 11. Huntsman Cancer Institute , Salt Lake City, UT 84112, USA 12. Washington University School of Medicine , St. Louis, MO 63110, USA 13. The Wistar Institute , Philadelphia, PA 19104, USA 14. The University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA
Abstract
Abstract
We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources, to facilitate collaboration among researchers and to make these data 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. Currently, the portal contains PDXNet model information and data resources from 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 2134 associated sequencing files from 873 samples across 308 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 includes results from freely available, robust, validated and standardized analysis workflows on PDXNet sequencing files and PDMR data (3857 samples from 629 patients across 85 disease types). The PDXNet portal is continuously updated with new data and is of significant utility to the cancer research community as it provides a centralized location for PDXNet resources, which support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials.
Funder
National Institutes of Health National Cancer Institute
Publisher
Oxford University Press (OUP)
Cited by
7 articles.
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