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248 results on '"Davies, Sherri R."'

1. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

Author

Sun, Hua, Cao, Song, Mashl, R Jay, Mo, Chia-Kuei, Zaccaria, Simone, Wendl, Michael C, Davies, Sherri R, Bailey, Matthew H, Primeau, Tina M, Hoog, Jeremy, Mudd, Jacqueline L, Dean, Dennis A, Patidar, Rajesh, Chen, Li, Wyczalkowski, Matthew A, Jayasinghe, Reyka G, Rodrigues, Fernanda Martins, Terekhanova, Nadezhda V, Li, Yize, Lim, Kian-Huat, Wang-Gillam, Andrea, Van Tine, Brian A, Ma, Cynthia X, Aft, Rebecca, Fuh, Katherine C, Schwarz, Julie K, Zevallos, Jose P, Puram, Sidharth V, Dipersio, John F, Davis-Dusenbery, Brandi, Ellis, Matthew J, Lewis, Michael T, Davies, Michael A, Herlyn, Meenhard, Fang, Bingliang, Roth, Jack A, Welm, Alana L, Welm, Bryan E, Meric-Bernstam, Funda, Chen, Feng, Fields, Ryan C, Li, Shunqiang, Govindan, Ramaswamy, Doroshow, James H, Moscow, Jeffrey A, Evrard, Yvonne A, Chuang, Jeffrey H, Raphael, Benjamin J, and Ding, Li

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Cancer, Human Genome, Biotechnology, Good Health and Well Being, Animals, Disease Models, Animal, Female, Gene Expression Regulation, Neoplastic, Genome, Genomics, Heterografts, Humans, Male, Mice, Models, Biological, Mutation, Neoplasms, Transcriptome, Xenograft Model Antitumor Assays, NCI PDXNet Consortium
Abstract

Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors.

Published
2021

2. Research-based PAM50 signature and long-term breast cancer survival

Author

Pu, Minya, Messer, Karen, Davies, Sherri R, Vickery, Tammi L, Pittman, Emily, Parker, Barbara A, Ellis, Matthew J, Flatt, Shirley W, Marinac, Catherine R, Nelson, Sandahl H, Mardis, Elaine R, Pierce, John P, and Natarajan, Loki

Subjects
Cancer, Aging, Breast Cancer, Genetics, Genetic Testing, 4.1 Discovery and preclinical testing of markers and technologies, 4.2 Evaluation of markers and technologies, Detection, screening and diagnosis, Adult, Aged, Biomarkers, Tumor, Breast Neoplasms, Cancer Survivors, Cell Hypoxia, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, Middle Aged, Neoplasm Staging, Prognosis, Survival Analysis, Breast cancer, Long-term survival, Gene signatures, Hypoxia, PAM50 subtypes, Prognostic modeling, Clinical Sciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

PurposeMulti-gene signatures provide biological insight and risk stratification in breast cancer. Intrinsic molecular subtypes defined by mRNA expression of 50 genes (PAM50) are prognostic in hormone-receptor positive postmenopausal breast cancer. Yet, for 25-40% in the PAM50 intermediate risk group, long-term risk remains uncertain. Our study aimed to (i) test the long-term prognostic value of the PAM50 signature in pre- and post-menopausal breast cancer; (ii) investigate if the PAM50 model could be improved by addition of other mRNAs implicated in oncogenesis.MethodsWe used archived FFPE samples from 1723 breast cancer survivors; high quality reads were obtained on 1253 samples. Transcript expression was quantified using a custom codeset with probes for > 100 targets. Cox models assessed gene signatures for breast cancer relapse and survival.ResultsOver 15 + years of follow-up, PAM50 subtypes were (P  60% higher hazard. Addition of a 13-gene hypoxia signature improved prognostication with > 40% higher hazard in the highest vs lowest hypoxia tertiles.ConclusionsPAM50 intrinsic subtypes were independently prognostic for long-term breast cancer survival, irrespective of menopausal status. Addition of hypoxia signatures improved risk prediction. If replicated, incorporating the 13-gene hypoxia signature into the existing PAM50 risk assessment tool, may refine risk stratification and further clarify treatment for breast cancer.

Published
2020

3. Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer

Author

Cui Zhou, Daniel, Jayasinghe, Reyka G., Chen, Siqi, Herndon, John M., Iglesia, Michael D., Navale, Pooja, Wendl, Michael C., Caravan, Wagma, Sato, Kazuhito, Storrs, Erik, Mo, Chia-Kuei, Liu, Jingxian, Southard-Smith, Austin N., Wu, Yige, Naser Al Deen, Nataly, Baer, John M., Fulton, Robert S., Wyczalkowski, Matthew A., Liu, Ruiyang, Fronick, Catrina C., Fulton, Lucinda A., Shinkle, Andrew, Thammavong, Lisa, Zhu, Houxiang, Sun, Hua, Wang, Liang-Bo, Li, Yize, Zuo, Chong, McMichael, Joshua F., Davies, Sherri R., Appelbaum, Elizabeth L., Robbins, Keenan J., Chasnoff, Sara E., Yang, Xiaolu, Reeb, Ashley N., Oh, Clara, Serasanambati, Mamatha, Lal, Preet, Varghese, Rajees, Mashl, Jay R., Ponce, Jennifer, Terekhanova, Nadezhda V., Yao, Lijun, Wang, Fang, Chen, Lijun, Schnaubelt, Michael, Lu, Rita Jui-Hsien, Schwarz, Julie K., Puram, Sidharth V., Kim, Albert H., Song, Sheng-Kwei, Shoghi, Kooresh I., Lau, Ken S., Ju, Tao, Chen, Ken, Chatterjee, Deyali, Hawkins, William G., Zhang, Hui, Achilefu, Samuel, Chheda, Milan G., Oh, Stephen T., Gillanders, William E., Chen, Feng, DeNardo, David G., Fields, Ryan C., and Ding, Li

Published
2022
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4. Supplementary Table S1 from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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5. FIGURE 5 from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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6. FIGURE 4 from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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7. Supplementary Figure S4 from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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8. FIGURE 6 from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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9. FIGURE 1 from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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10. FIGURE 2 from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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11. FIGURE 3 from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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12. Data from Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

Author

Guo, Zhanfang, primary, Luo, Jingqin, primary, Mashl, R. Jay, primary, Hoog, Jeremy, primary, Maiti, Piyush, primary, Fettig, Nikki, primary, Davies, Sherri R., primary, Aft, Rebecca, primary, Held, Jason M., primary, Govindan, Ramaswamy, primary, Ding, Li, primary, Li, Shunqiang, primary, von Morze, Cornelius, primary, Wulf, Gerburg M., primary, Shoghi, Kooresh I., primary, and Ma, Cynthia X., primary

Published
2024
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13. Evaluation of copanlisib in combination with eribulin in triple negative breast cancer patient-derived xenograft models

Author

Guo, Zhanfang, primary, Luo, Jingqin, additional, Mashl, R. Jay, additional, Hoog, Jeremy, additional, Maiti, Piyush, additional, Fettig, Nikki, additional, Davies, Sherri R., additional, Aft, Rebecca, additional, Held, Jason M., additional, Govindan, Ramaswamy, additional, Ding, Li, additional, Li, Shunqiang, additional, von Morze, Cornelius, additional, Wulf, Gerburg M., additional, Shoghi, Kooresh I., additional, and Ma, Cynthia X., additional

Published
2024
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14. miRNAs and Long-term Breast Cancer Survival: Evidence from the WHEL Study

Author

Natarajan, Loki, Pu, Minya, Davies, Sherri R, Vickery, Tammi L, Nelson, Sandahl H, Pittman, Emily, Parker, Barbara A, Ellis, Matthew J, Flatt, Shirley W, Mardis, Elaine R, Marinac, Catherine R, Pierce, John P, and Messer, Karen

Subjects
Health Services and Systems, Biomedical and Clinical Sciences, Health Sciences, Oncology and Carcinogenesis, Biotechnology, Breast Cancer, Genetics, Human Genome, Prevention, Genetic Testing, Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Good Health and Well Being, Adolescent, Adult, Aged, Breast Neoplasms, Female, Humans, Middle Aged, Survival Analysis, Young Adult, Medical and Health Sciences, Epidemiology, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundThere is substantial variation in breast cancer survival rates, even among patients with similar clinical and genomic profiles. New biomarkers are needed to improve risk stratification and inform treatment options. Our aim was to identify novel miRNAs associated with breast cancer survival and quantify their prognostic value after adjusting for established clinical factors and genomic markers.MethodsUsing the Women's Healthy Eating and Living (WHEL) breast cancer cohort with >15 years of follow-up and archived tumor specimens, we assayed PAM50 mRNAs and 25 miRNAs using the Nanostring nCounter platform.ResultsWe obtained high-quality reads on 1,253 samples (75% of available specimens) and used an existing research-use algorithm to ascertain PAM50 subtypes and risk scores (ROR-PT). We identified miRNAs significantly associated with breast cancer outcomes and then tested these in independent TCGA samples. miRNAs that were also prognostic in TCGA samples were further evaluated in multiple regression Cox models. We also used penalized regression for unbiased discovery.ConclusionsTwo miRNAs, 210 and 29c, were associated with breast cancer outcomes in the WHEL and TCGA studies and further improved risk stratification within PAM50 risk groups: 10-year survival was 62% in the node-negative high miR-210-high ROR-PT group versus 75% in the low miR-210- high ROR-PT group. Similar results were obtained for miR-29c. We identified three additional miRNAs, 187-3p, 143-3p, and 205-5p, via penalized regression.ImpactOur findings suggest that miRNAs might be prognostic for long-term breast cancer survival and might improve risk stratification. Further research to incorporate miRNAs into existing clinicogenomic signatures is needed.

Published
2019

15. Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

Author

Sun, Hua, Cao, Song, Mashl, R. Jay, Mo, Chia-Kuei, Zaccaria, Simone, Wendl, Michael C., Davies, Sherri R., Bailey, Matthew H., Primeau, Tina M., Hoog, Jeremy, Mudd, Jacqueline L., Dean, II, Dennis A., Patidar, Rajesh, Chen, Li, Wyczalkowski, Matthew A., Jayasinghe, Reyka G., Rodrigues, Fernanda Martins, Terekhanova, Nadezhda V., Li, Yize, Lim, Kian-Huat, Wang-Gillam, Andrea, Van Tine, Brian A., Ma, Cynthia X., Aft, Rebecca, Fuh, Katherine C., Schwarz, Julie K., Zevallos, Jose P., Puram, Sidharth V., Dipersio, John F., Davis-Dusenbery, Brandi, Ellis, Matthew J., Lewis, Michael T., Davies, Michael A., Herlyn, Meenhard, Fang, Bingliang, Roth, Jack A., Welm, Alana L., Welm, Bryan E., Meric-Bernstam, Funda, Chen, Feng, Fields, Ryan C., Li, Shunqiang, Govindan, Ramaswamy, Doroshow, James H., Moscow, Jeffrey A., Evrard, Yvonne A., Chuang, Jeffrey H., Raphael, Benjamin J., and Ding, Li

Published
2022
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16. A randomized phase 2 study of neoadjuvant carboplatin and paclitaxel with or without atezolizumab in triple negative breast cancer (TNBC) - NCI 10013

Author

Ademuyiwa, Foluso O., Gao, Feng, Street, Cherease R., Chen, Ina, Northfelt, Donald W., Wesolowski, Robert, Arora, Mili, Brufsky, Adam, Dees, E. Claire, Santa-Maria, Cesar A., Connolly, Roisin M., Force, Jeremy, Moreno-Aspitia, Alvaro, Herndon, John M., Carmody, Madelyn, Davies, Sherri R., Larson, Sarah, Pfaff, Kathleen L., Jones, Stephanie M., Weirather, Jason L., Giobbie-Hurder, Anita, Rodig, Scott J., Liu, Zheng, Hagemann, Ian S., Sharon, Elad, and Gillanders, William E.

Published
2022
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17. Table S5 from Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Author

Wu, Yige, primary, Chen, Siqi, primary, Yang, Xiaolu, primary, Sato, Kazuhito, primary, Lal, Preet, primary, Wang, Yuefan, primary, Shinkle, Andrew T., primary, Wendl, Michael C., primary, Primeau, Tina M., primary, Zhao, Yanyan, primary, Gould, Alanna, primary, Sun, Hua, primary, Mudd, Jacqueline L., primary, Hoog, Jeremy, primary, Mashl, R. Jay, primary, Wyczalkowski, Matthew A., primary, Mo, Chia-Kuei, primary, Liu, Ruiyang, primary, Herndon, John M., primary, Davies, Sherri R., primary, Liu, Di, primary, Ding, Xi, primary, Evrard, Yvonne A., primary, Welm, Bryan E., primary, Lum, David, primary, Koh, Mei Yee, primary, Welm, Alana L., primary, Chuang, Jeffrey H., primary, Moscow, Jeffrey A., primary, Meric-Bernstam, Funda, primary, Govindan, Ramaswamy, primary, Li, Shunqiang, primary, Hsieh, James, primary, Fields, Ryan C., primary, Lim, Kian-Huat, primary, Ma, Cynthia X., primary, Zhang, Hui, primary, Ding, Li, primary, and Chen, Feng, primary

Published
2023
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18. Supplementary Data 1 from Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Author

Wu, Yige, primary, Chen, Siqi, primary, Yang, Xiaolu, primary, Sato, Kazuhito, primary, Lal, Preet, primary, Wang, Yuefan, primary, Shinkle, Andrew T., primary, Wendl, Michael C., primary, Primeau, Tina M., primary, Zhao, Yanyan, primary, Gould, Alanna, primary, Sun, Hua, primary, Mudd, Jacqueline L., primary, Hoog, Jeremy, primary, Mashl, R. Jay, primary, Wyczalkowski, Matthew A., primary, Mo, Chia-Kuei, primary, Liu, Ruiyang, primary, Herndon, John M., primary, Davies, Sherri R., primary, Liu, Di, primary, Ding, Xi, primary, Evrard, Yvonne A., primary, Welm, Bryan E., primary, Lum, David, primary, Koh, Mei Yee, primary, Welm, Alana L., primary, Chuang, Jeffrey H., primary, Moscow, Jeffrey A., primary, Meric-Bernstam, Funda, primary, Govindan, Ramaswamy, primary, Li, Shunqiang, primary, Hsieh, James, primary, Fields, Ryan C., primary, Lim, Kian-Huat, primary, Ma, Cynthia X., primary, Zhang, Hui, primary, Ding, Li, primary, and Chen, Feng, primary

Published
2023
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19. Supplementary Figures from Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Author

Wu, Yige, primary, Chen, Siqi, primary, Yang, Xiaolu, primary, Sato, Kazuhito, primary, Lal, Preet, primary, Wang, Yuefan, primary, Shinkle, Andrew T., primary, Wendl, Michael C., primary, Primeau, Tina M., primary, Zhao, Yanyan, primary, Gould, Alanna, primary, Sun, Hua, primary, Mudd, Jacqueline L., primary, Hoog, Jeremy, primary, Mashl, R. Jay, primary, Wyczalkowski, Matthew A., primary, Mo, Chia-Kuei, primary, Liu, Ruiyang, primary, Herndon, John M., primary, Davies, Sherri R., primary, Liu, Di, primary, Ding, Xi, primary, Evrard, Yvonne A., primary, Welm, Bryan E., primary, Lum, David, primary, Koh, Mei Yee, primary, Welm, Alana L., primary, Chuang, Jeffrey H., primary, Moscow, Jeffrey A., primary, Meric-Bernstam, Funda, primary, Govindan, Ramaswamy, primary, Li, Shunqiang, primary, Hsieh, James, primary, Fields, Ryan C., primary, Lim, Kian-Huat, primary, Ma, Cynthia X., primary, Zhang, Hui, primary, Ding, Li, primary, and Chen, Feng, primary

Published
2023
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20. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages

Author

Iglesia, Michael D., primary, Jayasinghe, Reyka G., additional, Chen, Siqi, additional, Terekhanova, Nadezhda V., additional, Herndon, John M., additional, Storrs, Erik, additional, Karpova, Alla, additional, Zhou, Daniel Cui, additional, Al Deen, Nataly Naser, additional, Shinkle, Andrew T., additional, Lu, Rita Jui-Hsien, additional, Caravan, Wagma, additional, Houston, Andrew, additional, Zhao, Yanyan, additional, Sato, Kazuhito, additional, Lal, Preet, additional, Street, Cherease, additional, Rodrigues, Fernanda Martins, additional, Southard-Smith, Austin N., additional, Targino da Costa, André Luiz N., additional, Zhu, Houxiang, additional, Mo, Chia-Kuei, additional, Crowson, Lisa, additional, Fulton, Robert S., additional, Wyczalkowski, Matthew A., additional, Fronick, Catrina C., additional, Fulton, Lucinda A., additional, Sun, Hua, additional, Davies, Sherri R., additional, Appelbaum, Elizabeth L., additional, Chasnoff, Sara E., additional, Carmody, Madelyn, additional, Brooks, Candace, additional, Liu, Ruiyang, additional, Wendl, Michael C., additional, Oh, Clara, additional, Bender, Diane, additional, Cruchaga, Carlos, additional, Harari, Oscar, additional, Bredemeyer, Andrea, additional, Lavine, Kory, additional, Bose, Ron, additional, Margenthaler, Julie, additional, Held, Jason M., additional, Achilefu, Samuel, additional, Ademuyiwa, Foluso, additional, Aft, Rebecca, additional, Ma, Cynthia, additional, Colditz, Graham A., additional, Ju, Tao, additional, Oh, Stephen T., additional, Fitzpatrick, James, additional, Hwang, E. Shelley, additional, Shoghi, Kooresh I., additional, Chheda, Milan G., additional, Veis, Deborah J., additional, Chen, Feng, additional, Fields, Ryan C., additional, Gillanders, William E., additional, and Ding, Li, additional

Published
2023
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21. Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Author

Wu, Yige, primary, Chen, Siqi, additional, Yang, Xiaolu, additional, Sato, Kazuhito, additional, Lal, Preet, additional, Wang, Yuefan, additional, Shinkle, Andrew T., additional, Wendl, Michael C., additional, Primeau, Tina M., additional, Zhao, Yanyan, additional, Gould, Alanna, additional, Sun, Hua, additional, Mudd, Jacqueline L., additional, Hoog, Jeremy, additional, Mashl, R. Jay, additional, Wyczalkowski, Matthew A., additional, Mo, Chia-Kuei, additional, Liu, Ruiyang, additional, Herndon, John M., additional, Davies, Sherri R., additional, Liu, Di, additional, Ding, Xi, additional, Evrard, Yvonne A., additional, Welm, Bryan E., additional, Lum, David, additional, Koh, Mei Yee, additional, Welm, Alana L., additional, Chuang, Jeffrey H., additional, Moscow, Jeffrey A., additional, Meric-Bernstam, Funda, additional, Govindan, Ramaswamy, additional, Li, Shunqiang, additional, Hsieh, James, additional, Fields, Ryan C., additional, Lim, Kian-Huat, additional, Ma, Cynthia X., additional, Zhang, Hui, additional, Ding, Li, additional, and Chen, Feng, additional

Published
2023
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22. Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

Author

Mertins, Philipp, Tang, Lauren C., Krug, Karsten, Clark, David J., Gritsenko, Marina A., Chen, Lijun, Clauser, Karl R., Clauss, Therese R., Shah, Punit, Gillette, Michael A., Petyuk, Vladislav A., Thomas, Stefani N., Mani, D. R., Mundt, Filip, Moore, Ronald J., Hu, Yingwei, Zhao, Rui, Schnaubelt, Michael, Keshishian, Hasmik, Monroe, Matthew E., Zhang, Zhen, Udeshi, Namrata D., Mani, Deepak, Davies, Sherri R., Townsend, R. Reid, Chan, Daniel W., Smith, Richard D., Zhang, Hui, Liu, Tao, and Carr, Steven A.

Published
2018
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23. Abstract 5407: A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis

Author

White, Brian S., primary, Woo, Xing Yi, additional, Koc, Soner, additional, Sheridan, Todd, additional, Neuhauser, Steven B., additional, Wang, Shidan, additional, Evrard, Yvonne A., additional, Landua, John David, additional, Mashl, R Jay, additional, Davies, Sherri R., additional, Fang, Bingliang, additional, Raso, Maria Gabriela, additional, Evans, Kurt W., additional, Bailey, Matthew H., additional, Chen, Yeqing, additional, Xiao, Min, additional, Rubinstein, Jill, additional, Foroughi pour, Ali, additional, Dobrolecki, Lacey Elizabeth, additional, Fujita, Maihi, additional, Fujimoto, Junya, additional, Xiao, Guanghua, additional, Fields, Ryan C., additional, Mudd, Jacqueline L., additional, Xu, Xiaowei, additional, Hollingshead, Melinda G., additional, Jiwani, Shahanawaz, additional, consortium, PDXNet, additional, Wallace, Tiffany A., additional, Moscow, Jeffrey A., additional, Doroshow, James H., additional, Mitsiades, Nicholas, additional, Kaochar, Salma, additional, Pan, Chong-xian, additional, Chen, Moon S., additional, Carvajal-Carmona, Luis G., additional, Welm, Alana L., additional, Welm, Bryan E., additional, Govindan, Ramaswamy, additional, Li, Shunqiang, additional, Davies, Michael A., additional, Roth, Jack A., additional, Meric-Bernstam, Funda, additional, Xie, Yang, additional, Herlyn, Meenhard, additional, Ding, Li, additional, Lewis, Michael T., additional, Bolt, Carol J., additional, Dean, Dennis A., additional, and Chuang, Jeffrey H., additional

Published
2023
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24. Supplementary File 5 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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25. Supplementary File 1 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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26. Supplementary File 2 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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27. Extended Methods from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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28. Supplementary File 3 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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29. Supplementary Figures from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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30. Data from A Comparison of PAM50 Intrinsic Subtyping with Immunohistochemistry and Clinical Prognostic Factors in Tamoxifen-Treated Estrogen Receptor–Positive Breast Cancer

Author

Nielsen, Torsten O., primary, Parker, Joel S., primary, Leung, Samuel, primary, Voduc, David, primary, Ebbert, Mark, primary, Vickery, Tammi, primary, Davies, Sherri R., primary, Snider, Jacqueline, primary, Stijleman, Inge J., primary, Reed, Jerry, primary, Cheang, Maggie C.U., primary, Mardis, Elaine R., primary, Perou, Charles M., primary, Bernard, Philip S., primary, and Ellis, Matthew J., primary

Published
2023
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31. Supplementary tables 1 and 2 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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32. Data from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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33. Supplementary File 4 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers

Author

Mundt, Filip, primary, Rajput, Sandeep, primary, Li, Shunqiang, primary, Ruggles, Kelly V., primary, Mooradian, Arshag D., primary, Mertins, Philipp, primary, Gillette, Michael A., primary, Krug, Karsten, primary, Guo, Zhanfang, primary, Hoog, Jeremy, primary, Erdmann-Gilmore, Petra, primary, Primeau, Tina, primary, Huang, Shixia, primary, Edwards, Dean P., primary, Wang, Xiaowei, primary, Wang, Xuya, primary, Kawaler, Emily, primary, Mani, D.R., primary, Clauser, Karl R., primary, Gao, Feng, primary, Luo, Jingqin, primary, Davies, Sherri R., primary, Johnson, Gary L., primary, Huang, Kuan-lin, primary, Yoon, Christopher J., primary, Ding, Li, primary, Fenyö, David, primary, Ellis, Matthew J., primary, Townsend, R. Reid, primary, Held, Jason M., primary, Carr, Steven A., primary, and Ma, Cynthia X., primary

Published
2023
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34. Supplementary Data from A Comparison of PAM50 Intrinsic Subtyping with Immunohistochemistry and Clinical Prognostic Factors in Tamoxifen-Treated Estrogen Receptor–Positive Breast Cancer

Author

Nielsen, Torsten O., primary, Parker, Joel S., primary, Leung, Samuel, primary, Voduc, David, primary, Ebbert, Mark, primary, Vickery, Tammi, primary, Davies, Sherri R., primary, Snider, Jacqueline, primary, Stijleman, Inge J., primary, Reed, Jerry, primary, Cheang, Maggie C.U., primary, Mardis, Elaine R., primary, Perou, Charles M., primary, Bernard, Philip S., primary, and Ellis, Matthew J., primary

Published
2023
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35. Data from PIK3CA and PIK3CB Inhibition Produce Synthetic Lethality when Combined with Estrogen Deprivation in Estrogen Receptor–Positive Breast Cancer

Author

Crowder, Robert J., primary, Phommaly, Chanpheng, primary, Tao, Yu, primary, Hoog, Jeremy, primary, Luo, Jingqin, primary, Perou, Charles M., primary, Parker, Joel S., primary, Miller, Melinda A., primary, Huntsman, David G., primary, Lin, Li, primary, Snider, Jacqueline, primary, Davies, Sherri R., primary, Olson, John A., primary, Watson, Mark A., primary, Saporita, Anthony, primary, Weber, Jason D., primary, and Ellis, Matthew J., primary

Published
2023
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36. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays

Author

Whiteaker, Jeffrey R., primary, Halusa, Goran N., additional, Hoofnagle, Andrew N., additional, Sharma, Vagisha, additional, MacLean, Brendan, additional, Yan, Ping, additional, Wrobel, John A., additional, Kennedy, Jacob, additional, Mani, D. R., additional, Zimmerman, Lisa J., additional, Meyer, Matthew R., additional, Mesri, Mehdi, additional, Boja, Emily, additional, Carr, Steven A., additional, Chan, Daniel W., additional, Chen, Xian, additional, Chen, Jing, additional, Davies, Sherri R., additional, Ellis, Matthew J. C., additional, Fenyö, David, additional, Hiltke, Tara, additional, Ketchum, Karen A., additional, Kinsinger, Chris, additional, Kuhn, Eric, additional, Liebler, Daniel C., additional, Liu, Tao, additional, Loss, Michael, additional, MacCoss, Michael J., additional, Qian, Wei-Jun, additional, Rivers, Robert, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Scott, Mitchell G., additional, Smith, Richard D., additional, Thomas, Stefani, additional, Townsend, R. Reid, additional, Whiteley, Gordon, additional, Wu, Chaochao, additional, Zhang, Hui, additional, Zhang, Zhen, additional, Rodriguez, Henry, additional, and Paulovich, Amanda G., additional

Published
2016
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37. Correction: Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

Author

Huang, Kuan-lin, Li, Shunqiang, Mertins, Philipp, Cao, Song, Gunawardena, Harsha P., Ruggles, Kelly V., Mani, D. R., Clauser, Karl R., Tanioka, Maki, Usary, Jerry, Kavuri, Shyam M., Xie, Ling, Yoon, Christopher, Qiao, Jana W., Wrobel, John, Wyczalkowski, Matthew A., Erdmann-Gilmore, Petra, Snider, Jacqueline E., Hoog, Jeremy, Singh, Purba, Niu, Beifang, Guo, Zhanfang, Sun, Sam Qiancheng, Sanati, Souzan, Kawaler, Emily, Wang, Xuya, Scott, Adam, Ye, Kai, McLellan, Michael D., Wendl, Michael C., Malovannaya, Anna, Held, Jason M., Gillette, Michael A., Fenyö, David, Kinsinger, Christopher R., Mesri, Mehdi, Rodriguez, Henry, Davies, Sherri R., Perou, Charles M., Ma, Cynthia, Townsend, R. Reid, Chen, Xian, Carr, Steven A., Ellis, Matthew J., and Ding, Li

Published
2017
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39. Proteogenomic characterization of human colon and rectal cancer

Author

Zhang, Bing, Wang, Jing, Wang, Xiaojing, Zhu, Jing, Liu, Qi, Shi, Zhiao, Chambers, Matthew C., Zimmerman, Lisa J., Shaddox, Kent F., Kim, Sangtae, Davies, Sherri R., Wang, Sean, Wang, Pei, Kinsinger, Christopher R., Rivers, Robert C., Rodriguez, Henry, Townsend, R. Reid, Ellis, Matthew J.C., Carr, Steven A., Tabb, David L., Coffey, Robert J., Slebos, Robbert J.C., and Liebler, Daniel C.

Subjects
United States. National Cancer Institute, Methylation -- Analysis, Colon cancer -- Genetic aspects -- Care and treatment, Colorectal cancer -- Chemical properties -- Comparative analysis -- Genetic aspects -- Care and treatment, RNA -- Analysis, Environmental issues, Science and technology, Zoology and wildlife conservation, Vanderbilt University. School of Medicine
Abstract

Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem, we analysed proteomes of colon and rectal tumours characterized previously by The Cancer Genome Atlas (TCGA) and perform integrated proteogenomic analyses. Somatic variants displayed reduced protein abundance compared to germline variants. Messenger RNA transcript abundance did not reliably predict protein abundance differences between tumours. Proteomics identified five proteomic subtypes in the TCGA cohort, two of which overlapped with the TCGA 'microsatellite instability/CpG island methylation phenotype' transcriptomic subtype, but had distinct mutation, methylation and protein expression patterns associated with different clinical outcomes. Although copy number alterations showed strong cis- and trans-effects on mRNA abundance, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. The chromosome 20q amplicon was associated with the largest global changes at both mRNA and protein levels; proteomics data highlighted potential 20q candidates, including HNF4A (hepatocyte nuclear factor 4, alpha), TOMM34 (translocase of outer mitochondrial membrane 34) and SRC (SRC proto-oncogene, non-receptor tyrosine kinase). Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords a new paradigm for understanding cancer biology., TCGA has characterized the genomic features of human cancers (1-6) and this has presented a new challenge of explaining how genomic alterations drive cancers (7). As proteins link genotypes to [...]

Published
2014
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40. Proteogenomics connects somatic mutations to signalling in breast cancer

Author

Mertins, Philipp, Mani, D. R., Ruggles, Kelly V., Gillette, Michael A., Clauser, Karl R., Wang, Pei, Wang, Xianlong, Qiao, Jana W., Cao, Song, Petralia, Francesca, Kawaler, Emily, Mundt, Filip, Krug, Karsten, Tu, Zhidong, Lei, Jonathan T., Gatza, Michael L., Wilkerson, Matthew, Perou, Charles M., Yellapantula, Venkata, Huang, Kuan-lin, Lin, Chenwei, McLellan, Michael D., Yan, Ping, Davies, Sherri R., Townsend, Reid R., Skates, Steven J., Wang, Jing, Zhang, Bing, Kinsinger, Christopher R., Mesri, Mehdi, Rodriguez, Henry, Ding, Li, Paulovich, Amanda G., Fenyö, David, Ellis, Matthew J., and Carr, Steven A.

Published
2016
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41. Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer

Author

Zhou, Daniel Cui, primary, Jayasinghe, Reyka G., additional, Herndon, John M., additional, Storrs, Erik, additional, Mo, Chia-Kuei, additional, Wu, Yige, additional, Fulton, Robert S., additional, Wyczalkowski, Matthew A., additional, Fronick, Catrina C., additional, Fulton, Lucinda A., additional, Thammavong, Lisa, additional, Sato, Kazuhito, additional, Zhu, Houxiang, additional, Sun, Hua, additional, Wang, Liang-Bo, additional, Li, Yize, additional, Zuo, Chong, additional, McMichael, Joshua F., additional, Davies, Sherri R., additional, Appelbaum, Elizabeth L., additional, Robbins, Keenan J., additional, Chasnoff, Sara E., additional, Yang, Xiaolu, additional, Liu, Ruiyang, additional, Reeb, Ashley N., additional, Wendl, Michael C., additional, Oh, Clara, additional, Serasanambati, Mamatha, additional, Lal, Preet, additional, Varghese, Rajees, additional, Mashl, R. Jay, additional, Ponce, Jennifer, additional, Terekhanova, Nadezhda V., additional, Al Deen, Nataly Naser, additional, Yao, Lijun, additional, Wang, Fang, additional, Chen, Lijun, additional, Schnaubelt, Michael, additional, Puram, Sidharth V., additional, Kim, Albert H., additional, Song, Sheng-Kwei, additional, Shoghi, Kooresh I., additional, Ju, Tao, additional, Hawkins, William G., additional, Chen, Ken, additional, Chatterjee, Deyali, additional, Zhang, Hui, additional, Chheda, Milan G., additional, Achilefu, Samuel, additional, DeNardo, David G., additional, Oh, Stephen T., additional, Chen, Feng, additional, Gillanders, William E., additional, Fields, Ryan C., additional, and Ding, Li, additional

Published
2021
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42. Proteomic Resistance Biomarkers for PI3K Inhibitor in Triple Negative Breast Cancer Patient-Derived Xenograft Models

Author

Guo, Zhanfang, primary, Primeau, Tina, additional, Luo, Jingqin, additional, Zhang, Cynthia, additional, Sun, Hua, additional, Hoog, Jeremy, additional, Gao, Feng, additional, Huang, Shixia, additional, Edwards, Dean P., additional, Davies, Sherri R., additional, Aft, Rebecca, additional, Ding, Li, additional, Ellis, Matthew J., additional, Li, Shunqiang, additional, and Ma, Cynthia X., additional

Published
2020
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43. Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma

Author

Hu, Yingwei, primary, Pan, Jianbo, additional, Shah, Punit, additional, Ao, Minghui, additional, Thomas, Stefani N., additional, Liu, Yang, additional, Chen, Lijun, additional, Schnaubelt, Michael, additional, Clark, David J., additional, Rodriguez, Henry, additional, Boja, Emily S., additional, Hiltke, Tara, additional, Kinsinger, Christopher R., additional, Rodland, Karin D., additional, Li, Qing Kay, additional, Qian, Jiang, additional, Zhang, Zhen, additional, Chan, Daniel W., additional, Zhang, Hui, additional, Pandey, Akhilesh, additional, Paulovich, Amanda, additional, Hoofnagle, Andrew, additional, Zhang, Bing, additional, Mani, D.R., additional, Liebler, Daniel C., additional, Ransohoff, David F., additional, Fenyo, David, additional, Tabb, David L., additional, Levine, Douglas A., additional, Kuhn, Eric, additional, White, Forest M., additional, Whiteley, Gordon A., additional, Zhu, Heng, additional, Shih, Ie-Ming, additional, Bavarva, Jasmin, additional, McDermott, Jason E., additional, Whiteaker, Jeffrey, additional, Ketchum, Karen A., additional, Clauser, Karl R., additional, Ruggles, Kelly, additional, Elburn, Kimberly, additional, Ding, Li, additional, Hannick, Linda, additional, Zimmerman, Lisa J., additional, Watson, Mark, additional, Thiagarajan, Mathangi, additional, Ellis, Matthew J.C., additional, Oberti, Mauricio, additional, Mesri, Mehdi, additional, Sanders, Melinda E., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Snyder, Michael, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Rudnick, Paul A., additional, McGarvey, Peter B., additional, Mertins, Philip, additional, Townsend, R. Reid, additional, Thangudu, Ratna R., additional, Smith, Richard D., additional, Rivers, Robert C., additional, Slebos, Robert J.C., additional, Payne, Samuel H., additional, Davies, Sherri R., additional, Cai, Shuang, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Skates, Steven J., additional, Madhavan, Subha, additional, Liu, Tao, additional, Chen, Xian, additional, Zhao, Yingming, additional, Wang, Yue, additional, and Shi, Zhiao, additional

Published
2020
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44. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Author

Rozenblatt-Rosen, Orit, primary, Regev, Aviv, additional, Oberdoerffer, Philipp, additional, Nawy, Tal, additional, Hupalowska, Anna, additional, Rood, Jennifer E., additional, Ashenberg, Orr, additional, Cerami, Ethan, additional, Coffey, Robert J., additional, Demir, Emek, additional, Ding, Li, additional, Esplin, Edward D., additional, Ford, James M., additional, Goecks, Jeremy, additional, Ghosh, Sharmistha, additional, Gray, Joe W., additional, Guinney, Justin, additional, Hanlon, Sean E., additional, Hughes, Shannon K., additional, Hwang, E. Shelley, additional, Iacobuzio-Donahue, Christine A., additional, Jané-Valbuena, Judit, additional, Johnson, Bruce E., additional, Lau, Ken S., additional, Lively, Tracy, additional, Mazzilli, Sarah A., additional, Pe’er, Dana, additional, Santagata, Sandro, additional, Shalek, Alex K., additional, Schapiro, Denis, additional, Snyder, Michael P., additional, Sorger, Peter K., additional, Spira, Avrum E., additional, Srivastava, Sudhir, additional, Tan, Kai, additional, West, Robert B., additional, Williams, Elizabeth H., additional, Aberle, Denise, additional, Achilefu, Samuel I., additional, Ademuyiwa, Foluso O., additional, Adey, Andrew C., additional, Aft, Rebecca L., additional, Agarwal, Rachana, additional, Aguilar, Ruben A., additional, Alikarami, Fatemeh, additional, Allaj, Viola, additional, Amos, Christopher, additional, Anders, Robert A., additional, Angelo, Michael R., additional, Anton, Kristen, additional, Aster, Jon C., additional, Babur, Ozgun, additional, Bahmani, Amir, additional, Balsubramani, Akshay, additional, Barrett, David, additional, Beane, Jennifer, additional, Bender, Diane E., additional, Bernt, Kathrin, additional, Berry, Lynne, additional, Betts, Courtney B., additional, Bletz, Julie, additional, Blise, Katie, additional, Boire, Adrienne, additional, Boland, Genevieve, additional, Borowsky, Alexander, additional, Bosse, Kristopher, additional, Bott, Matthew, additional, Boyden, Ed, additional, Brooks, James, additional, Bueno, Raphael, additional, Burlingame, Erik A., additional, Cai, Qiuyin, additional, Campbell, Joshua, additional, Caravan, Wagma, additional, Chaib, Hassan, additional, Chan, Joseph M., additional, Chang, Young Hwan, additional, Chatterjee, Deyali, additional, Chaudhary, Ojasvi, additional, Chen, Alyce A., additional, Chen, Bob, additional, Chen, Changya, additional, Chen, Chia-hui, additional, Chen, Feng, additional, Chen, Yu-An, additional, Chheda, Milan G., additional, Chin, Koei, additional, Chiu, Roxanne, additional, Chu, Shih-Kai, additional, Chuaqui, Rodrigo, additional, Chun, Jaeyoung, additional, Cisneros, Luis, additional, Colditz, Graham A., additional, Cole, Kristina, additional, Collins, Natalie, additional, Contrepois, Kevin, additional, Coussens, Lisa M., additional, Creason, Allison L., additional, Crichton, Daniel, additional, Curtis, Christina, additional, Davidsen, Tanja, additional, Davies, Sherri R., additional, de Bruijn, Ino, additional, Dellostritto, Laura, additional, De Marzo, Angelo, additional, DeNardo, David G., additional, Diep, Dinh, additional, Diskin, Sharon, additional, Doan, Xengie, additional, Drewes, Julia, additional, Dubinett, Stephen, additional, Dyer, Michael, additional, Egger, Jacklynn, additional, Eng, Jennifer, additional, Engelhardt, Barbara, additional, Erwin, Graham, additional, Esserman, Laura, additional, Felmeister, Alex, additional, Feiler, Heidi S., additional, Fields, Ryan C., additional, Fisher, Stephen, additional, Flaherty, Keith, additional, Flournoy, Jennifer, additional, Fortunato, Angelo, additional, Frangieh, Allison, additional, Frye, Jennifer L., additional, Fulton, Robert S., additional, Galipeau, Danielle, additional, Gan, Siting, additional, Gao, Jianjiong, additional, Gao, Long, additional, Gao, Peng, additional, Gao, Vianne R., additional, Geiger, Tim, additional, George, Ajit, additional, Getz, Gad, additional, Giannakis, Marios, additional, Gibbs, David L., additional, Gillanders, William E., additional, Goedegebuure, Simon P., additional, Gould, Alanna, additional, Gowers, Kate, additional, Greenleaf, William, additional, Gresham, Jeremy, additional, Guerriero, Jennifer L., additional, Guha, Tuhin K., additional, Guimaraes, Alexander R., additional, Gutman, David, additional, Hacohen, Nir, additional, Hanlon, Sean, additional, Hansen, Casey R., additional, Harismendy, Olivier, additional, Harris, Kathleen A., additional, Hata, Aaron, additional, Hayashi, Akimasa, additional, Heiser, Cody, additional, Helvie, Karla, additional, Herndon, John M., additional, Hirst, Gilliam, additional, Hodi, Frank, additional, Hollmann, Travis, additional, Horning, Aaron, additional, Hsieh, James J., additional, Hughes, Shannon, additional, Huh, Won Jae, additional, Hunger, Stephen, additional, Hwang, Shelley E., additional, Ijaz, Heba, additional, Izar, Benjamin, additional, Jacobson, Connor A., additional, Janes, Samuel, additional, Jayasinghe, Reyka G., additional, Jiang, Lihua, additional, Johnson, Brett E., additional, Johnson, Bruce, additional, Ju, Tao, additional, Kadara, Humam, additional, Kaestner, Klaus, additional, Kagan, Jacob, additional, Kalinke, Lukas, additional, Keith, Robert, additional, Khan, Aziz, additional, Kibbe, Warren, additional, Kim, Albert H., additional, Kim, Erika, additional, Kim, Junhyong, additional, Kolodzie, Annette, additional, Kopytra, Mateusz, additional, Kotler, Eran, additional, Krueger, Robert, additional, Krysan, Kostyantyn, additional, Kundaje, Anshul, additional, Ladabaum, Uri, additional, Lake, Blue B., additional, Lam, Huy, additional, Laquindanum, Rozelle, additional, Laughney, Ashley M., additional, Lee, Hayan, additional, Lenburg, Marc, additional, Leonard, Carina, additional, Leshchiner, Ignaty, additional, Levy, Rochelle, additional, Li, Jerry, additional, Lian, Christine G., additional, Lim, Kian-Huat, additional, Lin, Jia-Ren, additional, Lin, Yiyun, additional, Liu, Qi, additional, Liu, Ruiyang, additional, Longabaugh, William J.R., additional, Longacre, Teri, additional, Ma, Cynthia X., additional, Macedonia, Mary Catherine, additional, Madison, Tyler, additional, Maher, Christopher A., additional, Maitra, Anirban, additional, Makinen, Netta, additional, Makowski, Danika, additional, Maley, Carlo, additional, Maliga, Zoltan, additional, Mallo, Diego, additional, Maris, John, additional, Markham, Nick, additional, Marks, Jeffrey, additional, Martinez, Daniel, additional, Mashl, Robert J., additional, Masilionais, Ignas, additional, Mason, Jennifer, additional, Massagué, Joan, additional, Massion, Pierre, additional, Mattar, Marissa, additional, Mazurchuk, Richard, additional, Mazutis, Linas, additional, McKinley, Eliot T., additional, McMichael, Joshua F., additional, Merrick, Daniel, additional, Meyerson, Matthew, additional, Miessner, Julia R., additional, Mills, Gordon B., additional, Mills, Meredith, additional, Mondal, Suman B., additional, Mori, Motomi, additional, Mori, Yuriko, additional, Moses, Elizabeth, additional, Mosse, Yael, additional, Muhlich, Jeremy L., additional, Murphy, George F., additional, Navin, Nicholas E., additional, Nederlof, Michel, additional, Ness, Reid, additional, Nevins, Stephanie, additional, Nikolov, Milen, additional, Nirmal, Ajit Johnson, additional, Nolan, Garry, additional, Novikov, Edward, additional, O’Connell, Brendan, additional, Offin, Michael, additional, Oh, Stephen T., additional, Olson, Anastasiya, additional, Ooms, Alex, additional, Ossandon, Miguel, additional, Owzar, Kouros, additional, Parmar, Swapnil, additional, Patel, Tasleema, additional, Patti, Gary J., additional, Pe'er, Itsik, additional, Peng, Tao, additional, Persson, Daniel, additional, Petty, Marvin, additional, Pfister, Hanspeter, additional, Polyak, Kornelia, additional, Pourfarhangi, Kamyar, additional, Puram, Sidharth V., additional, Qiu, Qi, additional, Quintanal-Villalonga, Álvaro, additional, Raj, Arjun, additional, Ramirez-Solano, Marisol, additional, Rashid, Rumana, additional, Reeb, Ashley N., additional, Reid, Mary, additional, Resnick, Adam, additional, Reynolds, Sheila M., additional, Riesterer, Jessica L., additional, Rodig, Scott, additional, Roland, Joseph T., additional, Rosenfield, Sonia, additional, Rotem, Asaf, additional, Roy, Sudipta, additional, Rozenblatt-Rosen, Orit, additional, Rudin, Charles M., additional, Ryser, Marc D., additional, Santi-Vicini, Maria, additional, Sato, Kazuhito, additional, Schrag, Deborah, additional, Schultz, Nikolaus, additional, Sears, Cynthia L., additional, Sears, Rosalie C., additional, Sen, Subrata, additional, Sen, Triparna, additional, Shalek, Alex, additional, Sheng, Jeff, additional, Sheng, Quanhu, additional, Shoghi, Kooresh I., additional, Shrubsole, Martha J., additional, Shyr, Yu, additional, Sibley, Alexander B., additional, Siex, Kiara, additional, Simmons, Alan J., additional, Singer, Dinah S., additional, Sivagnanam, Shamilene, additional, Slyper, Michal, additional, Sokolov, Artem, additional, Song, Sheng-Kwei, additional, Southard-Smith, Austin, additional, Spira, Avrum, additional, Stein, Janet, additional, Storm, Phillip, additional, Stover, Elizabeth, additional, Strand, Siri H., additional, Su, Timothy, additional, Sudar, Damir, additional, Sullivan, Ryan, additional, Surrey, Lea, additional, Suvà, Mario, additional, Terekhanova, Nadezhda V., additional, Ternes, Luke, additional, Thammavong, Lisa, additional, Thibault, Guillaume, additional, Thomas, George V., additional, Thorsson, Vésteinn, additional, Todres, Ellen, additional, Tran, Linh, additional, Tyler, Madison, additional, Uzun, Yasin, additional, Vachani, Anil, additional, Van Allen, Eliezer, additional, Vandekar, Simon, additional, Veis, Deborah J., additional, Vigneau, Sébastien, additional, Vossough, Arastoo, additional, Waanders, Angela, additional, Wagle, Nikhil, additional, Wang, Liang-Bo, additional, Wendl, Michael C., additional, West, Robert, additional, Wu, Chi-yun, additional, Wu, Hao, additional, Wu, Hung-Yi, additional, Wyczalkowski, Matthew A., additional, Xie, Yubin, additional, Yang, Xiaolu, additional, Yapp, Clarence, additional, Yu, Wenbao, additional, Yuan, Yinyin, additional, Zhang, Dadong, additional, Zhang, Kun, additional, Zhang, Mianlei, additional, Zhang, Nancy, additional, Zhang, Yantian, additional, Zhao, Yanyan, additional, Zhou, Daniel Cui, additional, Zhou, Zilu, additional, Zhu, Houxiang, additional, Zhu, Qin, additional, Zhu, Xiangzhu, additional, Zhu, Yuankun, additional, and Zhuang, Xiaowei, additional

Published
2020
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45. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Author

Clark, David J., primary, Dhanasekaran, Saravana M., additional, Petralia, Francesca, additional, Pan, Jianbo, additional, Song, Xiaoyu, additional, Hu, Yingwei, additional, da Veiga Leprevost, Felipe, additional, Reva, Boris, additional, Lih, Tung-Shing M., additional, Chang, Hui-Yin, additional, Ma, Weiping, additional, Huang, Chen, additional, Ricketts, Christopher J., additional, Chen, Lijun, additional, Krek, Azra, additional, Li, Yize, additional, Rykunov, Dmitry, additional, Li, Qing Kay, additional, Chen, Lin S., additional, Ozbek, Umut, additional, Vasaikar, Suhas, additional, Wu, Yige, additional, Yoo, Seungyeul, additional, Chowdhury, Shrabanti, additional, Wyczalkowski, Matthew A., additional, Ji, Jiayi, additional, Schnaubelt, Michael, additional, Kong, Andy, additional, Sethuraman, Sunantha, additional, Avtonomov, Dmitry M., additional, Ao, Minghui, additional, Colaprico, Antonio, additional, Cao, Song, additional, Cho, Kyung-Cho, additional, Kalayci, Selim, additional, Ma, Shiyong, additional, Liu, Wenke, additional, Ruggles, Kelly, additional, Calinawan, Anna, additional, Gümüş, Zeynep H., additional, Geiszler, Daniel, additional, Kawaler, Emily, additional, Teo, Guo Ci, additional, Wen, Bo, additional, Zhang, Yuping, additional, Keegan, Sarah, additional, Li, Kai, additional, Chen, Feng, additional, Edwards, Nathan, additional, Pierorazio, Phillip M., additional, Chen, Xi Steven, additional, Pavlovich, Christian P., additional, Hakimi, A. Ari, additional, Brominski, Gabriel, additional, Hsieh, James J., additional, Antczak, Andrzej, additional, Omelchenko, Tatiana, additional, Lubinski, Jan, additional, Wiznerowicz, Maciej, additional, Linehan, W. Marston, additional, Kinsinger, Christopher R., additional, Thiagarajan, Mathangi, additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Hiltke, Tara, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Qian, Jiang, additional, Fenyö, David, additional, Zhang, Bing, additional, Ding, Li, additional, Schadt, Eric, additional, Chinnaiyan, Arul M., additional, Zhang, Zhen, additional, Omenn, Gilbert S., additional, Cieslik, Marcin, additional, Chan, Daniel W., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Zhang, Hui, additional, Hashimi, Abdul Samad, additional, Pico, Alexander R., additional, Karpova, Alla, additional, Charamut, Alyssa, additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Malovannaya, Anna, additional, Marrero-Oliveras, Annette, additional, Agarwal, Anupriya, additional, Hindenach, Barbara, additional, Pruetz, Barbara, additional, Kim, Beom-Jun, additional, Druker, Brian J., additional, Newton, Chelsea J., additional, Birger, Chet, additional, Jones, Corbin D., additional, Tognon, Cristina, additional, Mani, D.R., additional, Valley, Dana R., additional, Rohrer, Daniel C., additional, Zhou, Daniel C., additional, Tansil, Darlene, additional, Chesla, David, additional, Heiman, David, additional, Wheeler, David, additional, Tan, Donghui, additional, Chan, Doug, additional, Demir, Emek, additional, Malc, Ewa, additional, Modugno, Francesmary, additional, Getz, Gaddy, additional, Hostetter, Galen, additional, Wilson, George D., additional, Hart, Gerald W., additional, Zhu, Heng, additional, Liu, Hongwei, additional, Culpepper, Houston, additional, Sun, Hua, additional, Zhou, Hua, additional, Day, Jacob, additional, Suh, James, additional, Huang, Jasmine, additional, McDermott, Jason, additional, Whiteaker, Jeffrey R., additional, Tyner, Jeffrey W., additional, Eschbacher, Jennifer, additional, Chen, Jin, additional, McGee, John, additional, Zhu, Jun, additional, Ketchum, Karen A., additional, Rodland, Karin D., additional, Clauser, Karl, additional, Robinson, Karna, additional, Krug, Karsten, additional, Hoadley, Katherine A., additional, Um, Ki Sung, additional, Elburn, Kim, additional, Holloway, Kimberly, additional, Wang, Liang-Bo, additional, Blumenberg, Lili, additional, Hannick, Linda, additional, Qi, Liqun, additional, Sokoll, Lori J., additional, Cornwell, MacIntosh, additional, Loriaux, Marc, additional, Domagalski, Marcin J., additional, Gritsenko, Marina A., additional, Anderson, Matthew, additional, Monroe, Matthew E., additional, Ellis, Matthew J., additional, Dyer, Maureen, additional, Anurag, Meenakshi, additional, Burke, Meghan C., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Lewis, Michael, additional, Ittmann, Michael M., additional, Smith, Michael, additional, Vernon, Michael, additional, Chaikin, Michelle, additional, Chheda, Milan G., additional, Khan, Munziba, additional, Roche, Nancy, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Tignor, Nicole, additional, Beckmann, Noam, additional, Grady, Pamela, additional, Castro, Patricia, additional, Piehowski, Paul, additional, McGarvey, Peter B., additional, Mieczkowski, Piotr, additional, Hariharan, Pushpa, additional, Gao, Qingsong, additional, Dhir, Rajiv, additional, Kothadia, Ramani Bhupendra, additional, Thangudu, Ratna R., additional, Montgomery, Rebecca, additional, Jayasinghe, Reyka G., additional, Smith, Richard D., additional, Edwards, Robert, additional, Zelt, Robert, additional, Bremner, Ross, additional, Liu, Ruiyang, additional, Hong, Runyu, additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cottingham, Sandra, additional, Markey, Sanford P., additional, Jewell, Scott D., additional, Patel, Shalin, additional, Satpathy, Shankha, additional, Richey, Shannon, additional, Davies, Sherri R., additional, Cai, Shuang, additional, Boca, Simina M., additional, Patil, Snehal, additional, Sengupta, Sohini, additional, Carter, Sonya, additional, Gabriel, Stacey, additional, Thomas, Stefani N., additional, De Young, Stephanie, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Foltz, Steven M., additional, Hilsenbeck, Sue, additional, Krubit, Tanya, additional, Liu, Tao, additional, Skelly, Tara, additional, Westbrook, Thomas, additional, Borate, Uma, additional, Velvulou, Uma, additional, Petyuk, Vladislav A., additional, Bocik, William E., additional, Chen, Xi, additional, Shi, Yan, additional, Geffen, Yifat, additional, Lu, Yihao, additional, Wang, Ying, additional, Maruvka, Yosef, additional, Li, Zhi, additional, Shi, Zhiao, additional, and Tu, Zhidong, additional

Published
2020
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47. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.

Author

Sun, Hua, Cao, Song, Mashl, R. Jay, Mo, Chia-Kuei, Zaccaria, Simone, Wendl, Michael C., Davies, Sherri R., Bailey, Matthew H., Primeau, Tina M., Hoog, Jeremy, Mudd, Jacqueline L., Dean II, Dennis A., Patidar, Rajesh, Chen, Li, Wyczalkowski, Matthew A., Jayasinghe, Reyka G., Rodrigues, Fernanda Martins, Terekhanova, Nadezhda V., Li, Yize, and Lim, Kian-Huat

Subjects
WEB portals, PHARMACOGENOMICS, TRANSCRIPTOMES, SOURCE code, SCIENTIFIC community, TUMOR markers, CANCER treatment
Abstract

Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors. Patient-derived xenograft models (PDX) have been extensively used to study the molecular and clinical features of cancers. Here the authors present a cohort of 536 PDX models from 25 cancers, as well as their genomic and evolutionary profiles and their suitability for clinical trials. [ABSTRACT FROM AUTHOR]

Published
2021
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48. Estrogen Receptor Expression Is High but Is of Lower Intensity in Tubular Carcinoma Than in Well-Differentiated Invasive Ductal Carcinoma

Author

Jorns, Julie M., Thomas, Dafydd G., Healy, Patrick N., Daignault, Stephanie, Vickery, Tammi L., Snider, Jacqueline E., Mardis, Elaine R., Davies, Sherri R., Ellis, Matthew J., and Visscher, Daniel W.

Subjects
Immunohistochemistry -- Comparative analysis, Gene expression -- Comparative analysis, Cancer -- Adjuvant treatment, Genes -- Comparative analysis, Phenols -- Comparative analysis, Progesterone -- Comparative analysis, Estrogen -- Comparative analysis, Health
Abstract

Context.--Tubular carcinoma (TC) is a rare, luminal A subtype of breast carcinoma with excellent prognosis, for which adjuvant chemotherapy is usually contraindicated. Objective.--To examine the levels of estrogen receptor (ER) and progesterone receptor expression in cases of TC and well-differentiated invasive ductal carcinoma as compared to normal breast glands and to determine if any significant differences could be detected via molecular testing. Design.--We examined ER and progesterone receptor via immunohistochemistry in tubular (N = 27), mixed ductal/tubular (N = 16), and well-differentiated ductal (N = 27) carcinomas with comparison to surrounding normal breast tissue. We additionally performed molecular sub-typing of 10 TCs and 10 ductal carcinomas via the PAM50 assay. Results.--Although ER expression was high for all groups, TC had statistically significantly lower ER staining percentage (ER%) (P = .003) and difference in ER expression between tumor and accompanying normal tissue (P = .02) than well-differentiated ductal carcinomas, with mixed ductal/tubular carcinomas falling between these 2 groups. Mean ER% was 79%, 87%, and 94%, and mean tumor-normal ER% differences were 13.6%, 25.9%, and 32.6% in tubular, mixed, and ductal carcinomas, respectively. Most tumors that had molecular subtyping were luminal A (9 of 10 tubular and 8 of 10 ductal), and no significant differences in specific gene expression between the 2 groups were identified. Conclusions.--Tubular carcinoma exhibited decreased intensity in ER expression, closer to that of normal breast parenchyma, likely as a consequence of a high degree of differentiation. Lower ER% expression by TC may represent a potential pitfall when performing commercially available breast carcinoma prognostic assays that rely heavily on ER-related gene expression. (Arch Pathol Lab Med. 2014;138:1507-1513; doi: 10.5858/arpa.2013-0621-OA), Tubular carcinoma (TC) of the breast is uncommon, comprising fewer than 2% of invasive breast carcinoma cases. Histologically, TC is infiltrative but well differentiated, forming evenly spaced, small, often angulated [...]

Published
2014
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49. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Author

Clark, David J., primary, Dhanasekaran, Saravana M., additional, Petralia, Francesca, additional, Pan, Jianbo, additional, Song, Xiaoyu, additional, Hu, Yingwei, additional, da Veiga Leprevost, Felipe, additional, Reva, Boris, additional, Lih, Tung-Shing M., additional, Chang, Hui-Yin, additional, Ma, Weiping, additional, Huang, Chen, additional, Ricketts, Christopher J., additional, Chen, Lijun, additional, Krek, Azra, additional, Li, Yize, additional, Rykunov, Dmitry, additional, Li, Qing Kay, additional, Chen, Lin S., additional, Ozbek, Umut, additional, Vasaikar, Suhas, additional, Wu, Yige, additional, Yoo, Seungyeul, additional, Chowdhury, Shrabanti, additional, Wyczalkowski, Matthew A., additional, Ji, Jiayi, additional, Schnaubelt, Michael, additional, Kong, Andy, additional, Sethuraman, Sunantha, additional, Avtonomov, Dmitry M., additional, Ao, Minghui, additional, Colaprico, Antonio, additional, Cao, Song, additional, Cho, Kyung-Cho, additional, Kalayci, Selim, additional, Ma, Shiyong, additional, Liu, Wenke, additional, Ruggles, Kelly, additional, Calinawan, Anna, additional, Gümüş, Zeynep H., additional, Geiszler, Daniel, additional, Kawaler, Emily, additional, Teo, Guo Ci, additional, Wen, Bo, additional, Zhang, Yuping, additional, Keegan, Sarah, additional, Li, Kai, additional, Chen, Feng, additional, Edwards, Nathan, additional, Pierorazio, Phillip M., additional, Chen, Xi Steven, additional, Pavlovich, Christian P., additional, Hakimi, A. Ari, additional, Brominski, Gabriel, additional, Hsieh, James J., additional, Antczak, Andrzej, additional, Omelchenko, Tatiana, additional, Lubinski, Jan, additional, Wiznerowicz, Maciej, additional, Linehan, W. Marston, additional, Kinsinger, Christopher R., additional, Thiagarajan, Mathangi, additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Hiltke, Tara, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Qian, Jiang, additional, Fenyö, David, additional, Zhang, Bing, additional, Ding, Li, additional, Schadt, Eric, additional, Chinnaiyan, Arul M., additional, Zhang, Zhen, additional, Omenn, Gilbert S., additional, Cieslik, Marcin, additional, Chan, Daniel W., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Zhang, Hui, additional, Hashimi, Abdul Samad, additional, Pico, Alexander R., additional, Karpova, Alla, additional, Charamut, Alyssa, additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Malovannaya, Anna, additional, Marrero-Oliveras, Annette, additional, Agarwal, Anupriya, additional, Hindenach, Barbara, additional, Pruetz, Barbara, additional, Kim, Beom-Jun, additional, Druker, Brian J., additional, Newton, Chelsea J., additional, Birger, Chet, additional, Jones, Corbin D., additional, Tognon, Cristina, additional, Mani, D.R., additional, Valley, Dana R., additional, Rohrer, Daniel C., additional, Zhou, Daniel C., additional, Tansil, Darlene, additional, Chesla, David, additional, Heiman, David, additional, Wheeler, David, additional, Tan, Donghui, additional, Chan, Doug, additional, Demir, Emek, additional, Malc, Ewa, additional, Modugno, Francesmary, additional, Getz, Gaddy, additional, Hostetter, Galen, additional, Wilson, George D., additional, Hart, Gerald W., additional, Zhu, Heng, additional, Liu, Hongwei, additional, Culpepper, Houston, additional, Sun, Hua, additional, Zhou, Hua, additional, Day, Jacob, additional, Suh, James, additional, Huang, Jasmine, additional, McDermott, Jason, additional, Whiteaker, Jeffrey R., additional, Tyner, Jeffrey W., additional, Eschbacher, Jennifer, additional, Chen, Jin, additional, McGee, John, additional, Zhu, Jun, additional, Ketchum, Karen A., additional, Rodland, Karin D., additional, Clauser, Karl, additional, Robinson, Karna, additional, Krug, Karsten, additional, Hoadley, Katherine A., additional, Um, Ki Sung, additional, Elburn, Kim, additional, Holloway, Kimberly, additional, Wang, Liang-Bo, additional, Blumenberg, Lili, additional, Hannick, Linda, additional, Qi, Liqun, additional, Sokoll, Lori J., additional, Cornwell, MacIntosh, additional, Loriaux, Marc, additional, Domagalski, Marcin J., additional, Gritsenko, Marina A., additional, Anderson, Matthew, additional, Monroe, Matthew E., additional, Ellis, Matthew J., additional, Dyer, Maureen, additional, Anurag, Meenakshi, additional, Burke, Meghan C., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Lewis, Michael, additional, Ittmann, Michael M., additional, Smith, Michael, additional, Vernon, Michael, additional, Chaikin, Michelle, additional, Chheda, Milan G., additional, Khan, Munziba, additional, Roche, Nancy, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Tignor, Nicole, additional, Beckmann, Noam, additional, Grady, Pamela, additional, Castro, Patricia, additional, Piehowski, Paul, additional, McGarvey, Peter B., additional, Mieczkowski, Piotr, additional, Hariharan, Pushpa, additional, Gao, Qingsong, additional, Dhir, Rajiv, additional, Kothadia, Ramani Bhupendra, additional, Thangudu, Ratna R., additional, Montgomery, Rebecca, additional, Jayasinghe, Reyka G., additional, Smith, Richard D., additional, Edwards, Robert, additional, Zelt, Robert, additional, Bremner, Ross, additional, Liu, Ruiyang, additional, Hong, Runyu, additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cottingham, Sandra, additional, Markey, Sanford P., additional, Jewell, Scott D., additional, Patel, Shalin, additional, Satpathy, Shankha, additional, Richey, Shannon, additional, Davies, Sherri R., additional, Cai, Shuang, additional, Boca, Simina M., additional, Patil, Snehal, additional, Sengupta, Sohini, additional, Carter, Sonya, additional, Gabriel, Stacey, additional, Thomas, Stefani N., additional, De Young, Stephanie, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Foltz, Steven M., additional, Hilsenbeck, Sue, additional, Krubit, Tanya, additional, Liu, Tao, additional, Skelly, Tara, additional, Westbrook, Thomas, additional, Borate, Uma, additional, Velvulou, Uma, additional, Petyuk, Vladislav A., additional, Bocik, William E., additional, Chen, Xi, additional, Shi, Yan, additional, Geffen, Yifat, additional, Lu, Yihao, additional, Wang, Ying, additional, Maruvka, Yosef, additional, Li, Zhi, additional, Shi, Zhiao, additional, and Tu, Zhidong, additional

Published
2019
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50. Research-based PAM50 signature and long-term breast cancer survival

Author

Pu, Minya, primary, Messer, Karen, additional, Davies, Sherri R., additional, Vickery, Tammi L., additional, Pittman, Emily, additional, Parker, Barbara A., additional, Ellis, Matthew J., additional, Flatt, Shirley W., additional, Marinac, Catherine R., additional, Nelson, Sandahl H., additional, Mardis, Elaine R., additional, Pierce, John P., additional, and Natarajan, Loki, additional

Published
2019
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