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202. Evolution of androgen receptor variant (ARV) profiles in serial metastatic solid and liquid biopsies in metastatic castrate resistant prostate cancer (mCRPC) treated with abiraterone acetate/ prednisone (AA/P).

Author

Giridhar, Karthik, primary, Sosa, Carlos, additional, Sicotte, Hugues, additional, Wang, Liewei, additional, Wang, Liguo, additional, Sinnwell, Jason P., additional, Tan, Winston, additional, Costello, Brian Addis, additional, Quevedo, Fernando, additional, Pitot, Henry C., additional, Bryce, Alan Haruo, additional, Jimenez, Rafael E., additional, Weinshilboum, Richard M., additional, Dehm, Scott, additional, Kalari, Krishna R., additional, and Kohli, Manish, additional

Published
2019
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203. Plasma cell free DNA (cfDNA) based somatic aberrations detected in treatment naïve metastatic hormone sensitive prostate cancer (mHSPC), hormonally ablated mHSPC and metastatic castration resistant prostate cancer (mCRPC) states and their impact on survival.

Author

Kohli, Manish, primary, Tan, Winston, additional, Zheng, Tiantian, additional, Wang, Amy, additional, Wong, Calvin, additional, Tan, Meng-Yao, additional, Jia, Shidong, additional, and Yu, Jianjun, additional

Published
2019
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204. Progastrin, a novel ubiquitous cancer blood biomarker for early detection and monitoring.

Author

You, Benoit, primary, Assenat, Eric, additional, Glehen, Olivier, additional, Maucort-Boulch, Delphine, additional, Payen, Lea Francoise, additional, Kepenekian, Vahan, additional, Dupuy, Marie, additional, Liaud, Pierre, additional, Mazard, Thibault, additional, Ferron, Gwenael, additional, Flaceliere, Maud, additional, Soulé, Julien, additional, Saywell, Veronique, additional, Tan, Winston, additional, Villeneuve, Laurent, additional, Ychou, Marc, additional, Beloin, Fanny, additional, Kohli, Manish, additional, Joubert, Dominique, additional, and Prieur, Alexandre, additional

Published
2019
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205. HSR19-108: A Meta-Analysis of Randomized Controlled Trials (RCTs) for Efficacy and Safety of Vascular Endothelial Growth Factor Tyrosine Kinase Inhibitors (VEGF-TKIs) Adjuvant Therapy in High-Risk Renal Cell Cancer (RCC)

Author

Riaz, Irbaz Bin, primary, Malik, Saad Ullah, additional, Husnain, Muhammad, additional, Ain Riaz Sipra, Qurat Ul, additional, Faridi, Warda, additional, Gondal, Farva R., additional, Ho, Thanh, additional, Yadav, Siddhartha, additional, Wang, Zhen, additional, and Kohli, Manish, additional

Published
2019
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206. Apalutamide (APA) or enzalutamide (ENZA) in men with nonmetastatic castration-resistant prostate cancer (CRPC): A systematic review and network meta-analysis of randomized clinical trials (RCTs).

Author

Riaz, Irbaz Bin, primary, Bhattacharjee, Sandipan, additional, Malik, Saad, additional, Ho, Thanh P., additional, Sipra, Qurat Ul Ain Riaz, additional, Farooq, Muhammad Zain, additional, Khan, Safi U., additional, Murad, M. Hassan, additional, and Kohli, Manish, additional

Published
2019
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208. Echocardiographic Assessment for the Detection of Cardiotoxicity Due to Vascular Endothelial Growth Factor Inhibitor Therapy in Metastatic Renal Cell and Colorectal Cancers

Author

Nhola, Lara F., primary, Abdelmoneim, Sahar S., additional, Villarraga, Hector R., additional, Kohli, Manish, additional, Grothey, Axel, additional, Bordun, Kimberly-Ann, additional, Cheung, Matthew, additional, Best, Ryan, additional, Cheung, David, additional, Huang, Runqing, additional, Barros-Gomes, Sergio, additional, Pitz, Marshall, additional, Singal, Pawan K., additional, Jassal, Davinder S., additional, and Mulvagh, Sharon L., additional

Published
2019
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212. TMPRSS2-ERG Controls Luminal Epithelial Lineage and Antiandrogen Sensitivity in PTEN and TP53-Mutated Prostate Cancer

Author

Blee, Alexandra M., primary, He, Yundong, additional, Yang, Yinhui, additional, Ye, Zhenqing, additional, Yan, Yuqian, additional, Pan, Yunqian, additional, Ma, Tao, additional, Dugdale, Joseph, additional, Kuehn, Emily, additional, Kohli, Manish, additional, Jimenez, Rafael, additional, Chen, Yu, additional, Xu, Wanhai, additional, Wang, Liguo, additional, and Huang, Haojie, additional

Published
2018
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216. Burden of Metastatic Castrate Naive Prostate Cancer Patients, to Identify Men More Likely to Benefit from Early Docetaxel: Further Analyses of CHAARTED and GETUG-AFU15 Studies

Author

Gravis, Gwenaelle, primary, Boher, Jean-Marie, additional, Chen, Yu-Hui, additional, Liu, Glenn, additional, Fizazi, Karim, additional, Carducci, Michael A., additional, Oudard, Stephane, additional, Joly, Florence, additional, Jarrard, David M., additional, Soulie, Michel, additional, Eisenberger, Mario J., additional, Habibian, Muriel, additional, Dreicer, Robert, additional, Garcia, Jorge A., additional, Hussain, Maha H.M., additional, Kohli, Manish, additional, Vogelzang, Nicholas J., additional, Picus, Joel, additional, DiPaola, Robert, additional, and Sweeney, Christopher, additional

Published
2018
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217. High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing

Author

Zhang, Peng, primary, Xia, Ji-Han, additional, Zhu, Jing, additional, Gao, Ping, additional, Tian, Yi-Jun, additional, Du, Meijun, additional, Guo, Yong-Chen, additional, Suleman, Sufyan, additional, Zhang, Qin, additional, Kohli, Manish, additional, Tillmans, Lori S., additional, Thibodeau, Stephen N., additional, French, Amy J., additional, Cerhan, James R., additional, Wang, Li-Dong, additional, Wei, Gong-Hong, additional, and Wang, Liang, additional

Published
2018
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219. A transcriptome analysis of castration resistant prostate cancer metastases in a prospective cohort study reveals high expression of AKT pathway genes predictive of long term response to abiraterone acetate/prednisone.

Author

Kohli, Manish, primary, Dehm, Scott, additional, Bhargava, Vipul, additional, Gormley, Michael, additional, Sinnwell, Jason P., additional, Tan, Winston, additional, Hillman, David W., additional, Li, Ying, additional, Jimenez, Rafael E., additional, Weinshilboum, Richard M., additional, Kalari, Krishna R., additional, Wang, Liguo, additional, and Sicotte, Hugues, additional

Published
2018
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220. Patterns of PSA versus clinically progressive disease in the E3805 CHAARTED trial.

Author

Bryce, Alan Haruo, primary, Chen, Yu-Hui, additional, Liu, Glenn, additional, Carducci, Michael Anthony, additional, Jarrard, David Frazier, additional, Garcia, Jorge A., additional, Dreicer, Robert, additional, Hussain, Maha, additional, Eisenberger, Mario A., additional, Kohli, Manish, additional, Hahn, Noah M., additional, Plimack, Elizabeth R., additional, Vogelzang, Nicholas J., additional, Picus, Joel, additional, DiPaola, Robert S., additional, Harshman, Lauren Christine, additional, and Sweeney, Christopher, additional

Published
2018
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221. A meta-analysis of randomized controlled trials for efficacy and safety of vascular endothelial growth factor tyrosine kinase inhibitors (VEGF-TKIs) adjuvant therapy in high-risk renal cell cancer (RCC).

Author

Riaz, Irbaz Bin, primary, Malik, Saad, additional, Husnain, Muhammad, additional, Sipra, Qurat Ul Ain Riaz, additional, Faridi, Warda, additional, Gondal, Farva R., additional, Xie, Hao, additional, Yadav, Siddhartha, additional, and Kohli, Manish, additional

Published
2018
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222. Chemohormonal Therapy in Metastatic Hormone-Sensitive Prostate Cancer: Long-Term Survival Analysis of the Randomized Phase III E3805 CHAARTED Trial

Author

Kyriakopoulos, Christos E., primary, Chen, Yu-Hui, additional, Carducci, Michael A., additional, Liu, Glenn, additional, Jarrard, David F., additional, Hahn, Noah M., additional, Shevrin, Daniel H., additional, Dreicer, Robert, additional, Hussain, Maha, additional, Eisenberger, Mario, additional, Kohli, Manish, additional, Plimack, Elizabeth R., additional, Vogelzang, Nicholas J., additional, Picus, Joel, additional, Cooney, Matthew M., additional, Garcia, Jorge A., additional, DiPaola, Robert S., additional, and Sweeney, Christopher J., additional

Published
2018
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226. Prognostic value of chromogranin-a (CGA) compared to circulating tumor cells (CTCs) in metastatic castration resistant prostate cancer (mCRPC).

Author

Giridhar, Karthik, primary, Sanhueza, Cristobal T., additional, Hillman, David W., additional, Alkhateeb, Hassan, additional, Carlson, Rachel, additional, Tan, Winston, additional, Quevedo, Fernando, additional, Pagliaro, Lance C., additional, Costello, Brian Addis, additional, and Kohli, Manish, additional

Published
2018
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227. PTEN Loss Promotes Intratumoral Androgen Synthesis and Tumor Microenvironment Remodeling via Aberrant Activation of RUNX2 in Castration-Resistant Prostate Cancer

Author

Yang, Yinhui, primary, Bai, Yang, additional, He, Yundong, additional, Zhao, Yu, additional, Chen, Jiaxiang, additional, Ma, Linlin, additional, Pan, Yunqian, additional, Hinten, Michael, additional, Zhang, Jun, additional, Karnes, R. Jeffrey, additional, Kohli, Manish, additional, Westendorf, Jennifer J., additional, Li, Benyi, additional, Zhu, Runzhi, additional, Huang, Haojie, additional, and Xu, Wanhai, additional

Published
2018
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231. Whole Blood mRNA Expression-Based Prognosis of Metastatic Renal Cell Carcinoma

Author

Giridhar, Karthik, primary, Sosa, Carlos, additional, Hillman, David, additional, Sanhueza, Cristobal, additional, Dalpiaz, Candace, additional, Costello, Brian, additional, Quevedo, Fernando, additional, Pitot, Henry, additional, Dronca, Roxana, additional, Ertz, Donna, additional, Cheville, John, additional, Donkena, Krishna, additional, and Kohli, Manish, additional

Published
2017
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233. Aberrations in circulating ceramide levels are associated with poor clinical outcomes across localised and metastatic prostate cancer

Author

Lin, Hui-Ming, Huynh, Kevin, Kohli, Manish, Tan, Winston, Azad, Arun A., Yeung, Nicole, Mahon, Kate L., Mak, Blossom, Sutherland, Peter D., Shepherd, Andrew, Mellett, Natalie, Docanto, Maria, Giles, Corey, Centenera, Margaret M., Butler, Lisa M., Meikle, Peter J., and Horvath, Lisa G.

Abstract

Background: Dysregulated lipid metabolism is associated with more aggressive pathology and poorer prognosis in prostate cancer (PC). The primary aim of the study is to assess the relationship between the plasma lipidome and clinical outcomes in localised and metastatic PC. The secondary aim is to validate a prognostic circulating 3-lipid signature specific to metastatic castration-resistant PC (mCRPC). Patients and methods: Comprehensive lipidomic analysis was performed on pre-treatment plasma samples from men with localised PC (N= 389), metastatic hormone-sensitive PC (mHSPC)(N= 44), or mCRPC (validation cohort, N= 137). Clinical outcomes from our previously published mCRPC cohort (N= 159) that was used to derive the prognostic circulating 3-lipid signature, were updated. Associations between circulating lipids and clinical outcomes were examined by Cox regression and latent class analysis. Results: Circulating lipid profiles featuring elevated levels of ceramide species were associated with metastatic relapse in localised PC (HR 5.80, 95% CI 3.04–11.1, P= 1 × 10−6), earlier testosterone suppression failure in mHSPC (HR 3.70, 95% CI 1.37–10.0, P= 0.01), and shorter overall survival in mCRPC (HR 2.54, 95% CI 1.73–3.72, P= 1 × 10−6). The prognostic significance of circulating lipid profiles in localised PC was independent of standard clinicopathological and metabolic factors (P< 0.0002). The 3-lipid signature was verified in the mCRPC validation cohort (HR 2.39, 95% CI 1.63–3.51, P= 1 × 10−5). Conclusions: Elevated circulating ceramide species are associated with poorer clinical outcomes across the natural history of PC. These clinically actionable lipid profiles could be therapeutically targeted in prospective clinical trials to potentially improve PC outcomes.

Published
2021
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234. Additional file 4: Figure S1. of Measure transcript integrity using RNA-seq data

Author

Liguo Wang, Jinfu Nie, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette, Surendra Dasari, Vedell, Peter, Poulami Barman, Liewei Wang, Weinshiboum, Richard, Jen, Jin, Haojie Huang, Kohli, Manish, and Kocher, Jean-Pierre

Abstract

Concordance between RIN and median TIN score for 20 peripheral blood mononuclear cell (PBMC) samples [4]. The PBMC samples were stored at room temperature for 0 h (blue), 12 h (green), 24 h (orange), 48 h (purple) and 84 h (red). Each time point contains 4 individuals (replicates). r, Pearson correlation coefficient. (PDF 143 kb)

Published
2016
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235. Additional file 12: Figure S9. of Measure transcript integrity using RNA-seq data

Author

Liguo Wang, Jinfu Nie, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette, Surendra Dasari, Vedell, Peter, Poulami Barman, Liewei Wang, Weinshiboum, Richard, Jen, Jin, Haojie Huang, Kohli, Manish, and Kocher, Jean-Pierre

Abstract

Relationship between 5â ˛UTR (untranslated regoin) size and TIN score for 12 Glioblastoma (GBM) samples. (a)-(c) three samples with RIN value of 10; (d)-(e), two samples with RIN value of 8; (f)-(h) three samples with RIN value of 6; (i)-(k) three samples with RIN value of 4; (l) one sample with RIN value of 2. r, Pearson correlation coefficient. r, Pearson correlation coefficient. Linear regression lines fitted to data are indicated as black dashed lines. (PDF 7140 kb)

Published
2016
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236. Additional file 9: Figure S6. of Measure transcript integrity using RNA-seq data

Author

Liguo Wang, Jinfu Nie, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette, Surendra Dasari, Vedell, Peter, Poulami Barman, Liewei Wang, Weinshiboum, Richard, Jen, Jin, Haojie Huang, Kohli, Manish, and Kocher, Jean-Pierre

Subjects
complex mixtures
Abstract

Smoothed scatter plots showing correlation between TIN score and transcript size. (a)-(c) three samples with RIN value of 10; (d)-(e), two samples with RIN value of 8; (f)-(h) three samples with RIN value of 6; (i)-(k) three samples with RIN value of 4; (l) one sample with RIN value of 2. Blue, orange and red represents low, median and high density of data points, respectively. Transcripts with no read coverage or smaller then 100 nucleotide were removed. r, Pearson correlation coefficient. Linear regression lines fitted to data are indicated as black dashed lines. (PDF 6875 kb)

Published
2016
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237. Additional file 20: Figure S14. of Measure transcript integrity using RNA-seq data

Author

Liguo Wang, Jinfu Nie, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette, Surendra Dasari, Vedell, Peter, Poulami Barman, Liewei Wang, Weinshiboum, Richard, Jen, Jin, Haojie Huang, Kohli, Manish, and Kocher, Jean-Pierre

Subjects
Condensed Matter::Materials Science, Physics::Accelerator Physics, Astrophysics::Earth and Planetary Astrophysics, Nuclear Experiment, Astrophysics::Galaxy Astrophysics
Abstract

Venn diagram showing the overlapping between 665 DEGs (before TIN correction) and 289 DEGs (after TIN correction). DEG, differentially expressed gene. (PDF 101 kb)

Published
2016
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238. Additional file 3: Figure S2. of miR-375 induces docetaxel resistance in prostate cancer by targeting SEC23A and YAP1

Author

Wang, Yuan, Lieberman, Rachel, Pan, Jing, Zhang, Qi, Meijun Du, Zhang, Peng, Nevalainen, Marja, Kohli, Manish, Niraj Shenoy, Meng, Hui, You, Ming, and Wang, Liang

Abstract

Representative immunohistochemistry analysis of xenograft tumor tissues. Cells with active caspase-3 were shown in brown color. A, B and C are representative images for a lower fraction of apoptotic cells, a higher fraction of apoptotic cells, and negative controls, respectively. (PPTX 1067 kb)

Published
2016
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239. Additional file 7: Figure S4. of Measure transcript integrity using RNA-seq data

Author

Liguo Wang, Jinfu Nie, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette, Surendra Dasari, Vedell, Peter, Poulami Barman, Liewei Wang, Weinshiboum, Richard, Jen, Jin, Haojie Huang, Kohli, Manish, and Kocher, Jean-Pierre

Abstract

Evaluating TIN (x-axis) metric using transcript level RNA fragment size (y-axis) for 12 Glioblastoma (GBM) samples [5]. (a)-(c) Three samples with RIN value of 10 (red); (d)-(e), two samples with RIN value of 8 (purple); (f)-(h) three samples with RIN value of 6 (orange); (i)-(k) three samples with RIN value of 4 (blue); (l) one sample with RIN value of 2 (cyan). Each dot represents 50 transcripts. Black curves indicate locally weighted polynomial regression curves. r, Pearson correlation coefficient. (PDF 1490 kb)

Published
2016
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240. Additional file 6: Figure S3. of Measure transcript integrity using RNA-seq data

Author

Liguo Wang, Jinfu Nie, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette, Surendra Dasari, Vedell, Peter, Poulami Barman, Liewei Wang, Weinshiboum, Richard, Jen, Jin, Haojie Huang, Kohli, Manish, and Kocher, Jean-Pierre

Subjects
equipment and supplies
Abstract

Evaluating RIN and median TIN score using sample level RNA fragment size as benchmark. Only 28 mCRPC samples with RINâ

Published
2016
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241. Additional file 2: Figure S1. of miR-375 induces docetaxel resistance in prostate cancer by targeting SEC23A and YAP1

Author

Wang, Yuan, Lieberman, Rachel, Pan, Jing, Zhang, Qi, Meijun Du, Zhang, Peng, Nevalainen, Marja, Kohli, Manish, Niraj Shenoy, Meng, Hui, You, Ming, and Wang, Liang

Subjects
animal structures, viruses, fungi, embryonic structures
Abstract

Higher miR-375 suppresses cell proliferation in PC cells. Overexpression of miR-375 by transfection with 200 nM miR-375 mimic inhibited cell growth when compared to miRNA negative control in PC-3 and DU145 cells at 72Â h after transfection. (Pâ

Published
2016
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242. Additional file 8: Figure S5. of Measure transcript integrity using RNA-seq data

Author

Liguo Wang, Jinfu Nie, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette, Surendra Dasari, Vedell, Peter, Poulami Barman, Liewei Wang, Weinshiboum, Richard, Jen, Jin, Haojie Huang, Kohli, Manish, and Kocher, Jean-Pierre

Abstract

Barplot showing Pearson correlation coefficients between TIN and RNA fragment size. 12 Glioblastoma (GBM) samples were stratified by RIN score; RIN = 10 (red), RIN = 8 (purple), RIN = 6 (orange), RIN = 4 (blue) and RIN = 2 (cyan). (PDF 120 kb)

Published
2016
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243. Plasma cell-free DNA-based predictors of response to abiraterone acetate/prednisone and prognostic factors in metastatic castration-resistant prostate cancer

Author

Du, Meijun, Tian, Yijun, Tan, Winston, Wang, Liewei, Wang, Liguo, Kilari, Deepak, Huang, Chiang-Ching, Wang, Liang, and Kohli, Manish

Abstract

Background: The combination of abiraterone acetate and prednisone (AA/P) is used to treat metastatic prostate cancer, but molecular predictors of treatment response are not well elucidated. We evaluated plasma circulating tumor DNA- (ctDNA-) based copy number alterations (CNAs) to determine treatment-related predictive and prognostic biomarkers for metastatic castration-resistant prostate cancer (mCRPC). Methods: Serial plasma specimens were prospectively collected from 88 chemotherapy-naive mCRPC patients before and after 12 weeks of AA/P treatment. Sequencing-based CNA analyses were performed on 174 specimens. We evaluated CNA-associated 12-week responses for primary resistance, time to treatment change (TTTC) for secondary resistance, and overall survival for prognosis (P< 0.05). Associations with primary resistance were analyzed using the Fisher exact test. Kaplan–Meier survival curves and Cox regression analyses were used to determine the associations of CNAs with acquired resistance and overall survival. Results: ctDNA reduced by 3.89% in responders and increased by 0.94% in nonresponders (P= 0.0043). Thirty-one prostate cancer-related genes from whole genome CNAs were tested. ARand ARenhancer amplification were associated with primary resistance (P= 0.0039) and shorter TTTC (P= 0.0003). ZFHX3deletion and PIK3CAamplification were associated with primary resistance (P= 0.026 and P= 0.017, respectively), shorter TTTC (P= 0.0008 and P= 0.0016, respectively), and poor survival (P= 0.0025 and P= 0.0022, respectively). CNA-based risk scores combining selected significant associations (AR, NKX3.1, and PIK3CA)at the univariate level with TTTC were predictive of secondary resistance (P= 0.0002). and established prognoses for survival based on CNAs in ZFHX3, RB1, PIK3CA, and OPHN1(P= 0.002). Multigene risk scores were more predictive than individual genes or clinical risk factors (P< 0.05). Conclusion: Plasma ctDNA CNAs and risk scores can predict mCRPC-state treatment and survival outcomes.

Published
2020
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244. Androgen Receptor Variant AR-V9 Is Coexpressed with AR-V7 in Prostate Cancer Metastases and Predicts Abiraterone Resistance

Author

Kohli, Manish, primary, Ho, Yeung, additional, Hillman, David W., additional, Van Etten, Jamie L., additional, Henzler, Christine, additional, Yang, Rendong, additional, Sperger, Jamie M., additional, Li, Yingming, additional, Tseng, Elizabeth, additional, Hon, Ting, additional, Clark, Tyson, additional, Tan, Winston, additional, Carlson, Rachel E., additional, Wang, Liguo, additional, Sicotte, Hugues, additional, Thai, Ho, additional, Jimenez, Rafael, additional, Huang, Haojie, additional, Vedell, Peter T., additional, Eckloff, Bruce W., additional, Quevedo, Jorge F., additional, Pitot, Henry C., additional, Costello, Brian A., additional, Jen, Jin, additional, Wieben, Eric D., additional, Silverstein, Kevin A.T., additional, Lang, Joshua M., additional, Wang, Liewei, additional, and Dehm, Scott M., additional

Published
2017
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247. Abstract 425: SMRT® Sequencing of full-length androgen receptor isoforms in prostate cancer reveals previously hidden drug resistant variants

Author

Kohli, Manish, primary, Ho, Yeung, additional, Hillman, David W., additional, Etten, Jamie L. Van, additional, Henzler, Christine, additional, Yang, Rendong, additional, Li, Yingming, additional, Tseng, Elizabeth, additional, Hon, Ting, additional, Clark, Tyson A., additional, Wang, Liguo, additional, Silverstein, Kevin, additional, Wang, Liewei, additional, and Dehm, Scott M., additional

Published
2017
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