PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery
Authors: Koc Soner , Lloyd Michael W , Grover Jeffrey W , Xiao Nan , Seepo Sara , Subramanian Sai Lakshmi , Ray Manisha , Frech Christian , DiGiovanna John , Webster Phillip , Neuhauser Steven , Srivastava Anuj , Woo Xing Yi , Sanderson Brian J , White Brian , Lott Paul , Dobrolecki Lacey E , Dowst Heidi ,   PDXNet Consortium, 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 A , Wallace Tiffany A , Moscow Jeffrey A , Doroshow James H , Mitsiades Nicholas , Kaochar Salma , Pan Chong-xian , Chen Moon S , Carvajal-Carmona Luis , Welm Alana L , Welm Bryan E , Lewis Michael T , Govindan Ramaswamy , Ding Li , Li Shunqiang , Herlyn Meenhard , Davies Michael A , Roth Jack , Meric-Bernstam Funda , Robinson Peter N , Bult Carol J , Davis-Dusenbery Brandi , Dean Dennis A , Chuang Jeffrey H 
Published: April 2022

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.