Decipher®Prostate Key Data

    Decipher outperforms conventional clinical tools: Studies show that Decipher is a significant & independent predictor of metastasis after prostatectomy, outperforming conventional clinical tools such as Gleason score.

    Decipher reclassifies men after surgery: In clinical studies of intermediate & high-risk men after surgery, Decipher reclassified 60% of men to lower risk categories. 98.5% of patients reclassified to low risk by Decipher did not develop metastasis within 5 years of radical prostatectomy.

    Decipher helps identify which patients may benefit from multimodal therapy: Recent research demonstrates that Decipher low risk men may be managed safely with observation until PSA rise & Decipher high risk men may benefit from early radiation. Decipher high-risk men who received adjuvant radiation experienced an 80% reduction in incidence of metastasis compared to those receiving salvage radiation.

    Decipher changes treatment decisions: On average, 39% of physicians changed patient treatment recommendations after reviewing Decipher results resulting in a 50% reduction recommendations for radiation therapy in those identified as low risk by Decipher.

Decipher Biopsy Publications

Clinical Validation

1. Nguyen P.L., Martin N.E., Choeurng V., Palmer-Aronsten B., Kolisnik T., Beard C.J., Orio P.F., Nezolosky M.D., Chen Y-W., Shin H., Davicioni E., Feng F.Y. Utilization of Biopsy-based Genomic Classifier to Predict Distant Metastasis after Definitive Radiation and Short-Course ADT for Intermediate and High Risk Prostate Cancer. Prostate Cancer Prostatic Dis. 2017. Jan; doi: 10.1038/pcan.2016.58. In press.

2. Lee H.J., Yousefi K., Haddad Z., Abdollah F., Lam L.L.C., Shin H., Alshalalfa M., Godebu E., Wang S., Shabaik A., Davicioni E., Kane C.J. Evaluation of a Genomic Classifier in Radical Prostatectomy Patients with Lymph Node Metastasis. Research and Reports in Urology. 2016 Jun; 8:77-84. doi: 10.2147/RRU.S99997. eCollection 2016.

3. Klein E.A., Haddad Z., Yousefi K., Lam L.L., Wang Q., Choeurng V., Palmer-Aronsten B., Buerki C., Davicioni E., Li J., Kattan M.W., Stephenson A.J., Magi-Galluzzi, C. Decipher Genomic Classifier Measured on Prostate Biopsy Predicts Metastasis Risk. Urology. 2016 Apr; 90:148-52. doi: 10.1016/j.urology.2016.01.012.

Feasibility

4. Radtke J.P., Takhar M., Bonekamp D., Kesch C., Erho N., du Plessis M., Buerki C., Ong K., Davicioni E., Hohenfellner M., Hadaschik B.A. Transcriptome Wide Analysis of Magnetic Resonance Imaging-targeted Biopsy and Matching Surgical Specimens from High-risk Prostate Cancer Patients Treated with Radical Prostatectomy: The Target Must Be Hit. European Urology Focus. 2017. PII: S2405-4569(17)30010-X. doi: 10.1016/j.euf.2017.01.005.

5. Stoyanova R., Pollack A., Takhar M., Lynne C., Parra N., Lam L.C., Alshalalfa M., Buerki C., Castillo R., Jorda M., Al-deen Ashab H., Kryvenko O.N., Punnen S., Parekh D.J., Abramowitz M.C., Gillies R.J., Davicioni E., Erho N., Ishkanian A. Association of Multiparametric MRI Quantitative Imaging Features with Prostate Cancer Gene Expression in MRI-targeted Prostate Biopsies. Oncotarget. 2016 Jul; 7(33):53362-53376. doi: 10.18632/oncotarget.10523.

6. Knudsen B.S., Kim H.L., Erho N., Shin H., Alshalalfa M, Lam L.L., Tenggara I., Chadwich K., Van Der Kwast T., Fleshner N., Davicioni E., Carroll P.R., Cooperberg M.R., Chan J.M., Simko J.P. Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens. Journal of Molecular Diagnostics. 2016 May; 18(3):395-406. doi: 10.1016/j.jmoldx.2015.12.006. *Featured figure on cover of JMD

Decipher RP Publications

Clinical Validation

1. Dalela D., Santiago-Jimenez M., Yousefi K., Karnes J.R., Ross A.E., Den R.B., Freedland S., Schaeffer E.M., Dicker A.P., Menon M., Davicioni E., Abdollah F. Genomic Classifier augments the role of pathological features in identifying optimal candidates for adjuvant radiation therapy in patients with prostate cancer: Development and internal validation of a multivariable prognostic model. Journal of Clinical Oncology. 2017. In press.

2. Spratt D.E., Yousefi K., Deheshi S., Ross A.E., Den R.B., Schaeffer E.M., Trock B.J., Zhang J., Glass A.G., Dicker A.P., Abdollah F., Zhao S.G., Lam L.L.C., Du Plessis M., Choeurng V., Haddad Z., Buerki C., Davicioni E., Weinmann S., Freedland S.J., Klein E.A., Karnes R.J., Feng F.Y. Individual Patient Level Meta-analysis of the Performance of the Decipher Genomic Classifier in High Risk Men Post-Prostatectomy to Predict Development of Metastatic Disease. Journal of Clinical Oncology. 2017. In press.

3. Klein E.A., Santiago-Jiménez M., Yousefi K., Robbins B.A, Schaeffer E.M., Trock B.J., Tosoian J., Haddad Z., Ra S., Karnes R.J., Jenkins R.B., Cheville J.C., Den R.B., Dicker A.P., Davicioni E., Freedland S.J., Ross A.E. Molecular analysis of low grade prostate cancer utilizing a genomic classifier of metastatic potential. Journal of Urology. 2017 Jan; 197(1):122-128. doi: 10.1016/j.juro.2016.08.091. In press.

4. Ross A.E., Den R.B., Yousefi K., Trock B.J., Tosoian J., Davicioni E., Thompson D.J.S., Choeurng V., Haddad Z., Tran P.T., Trabulsi E.J., Gomella L.G., Lallas C.D., Abdollah F., Feng F.Y., Klein E.A., Dicker A.P., Freedland S.J., Karnes R.J., Schaeffer E.M. Efficacy of Post-Operative Radiation in a Prostatectomy Cohort Adjusted for Clinical and Genomic Risk. Prostate Cancer Prostatic Dis. 2016 Sept; 19(3):277-82. doi: 10.1038/pcan.2016.15.

5. Freedland S.J., Choeurng V., Howaerd L., De Hoedt A., Du Plessis M., Yousefi K., Lam L.L., Buerki C., Ra S., Robbins B., Trabulsi E.J., Shah N.L., Abdollah F., Feng F.Y., Davicioni E., Dicker A.P., Karnes R.J., Den R.B. Utilization of a genomic classifier for prediction of metastasis following salvage radiation therapy after radical prostatectomy. European Urology. 2016 Oct; 70(4):588-596. doi: 10.1016/j.eururo.2016.01.008

6. Glass A.G., Leo M.C., Haddad Z., Yousefi K., Du Plessis M., Chen C., Choeurng V., Abdollah F., Robbins B., Ra A., Richert-Boe K.E., Buerki C., Pearson K., Davicioni E., Weinmann S. Validation of a genomic classifier for predicting post-prostatectomy recurrence in a community-based healthcare setting. Journal of Urology. 2016 Jun; 195(6):1748-53. doi: 10.1016/j.juro.2015.11.044.

7. Ross A.E., Johnson M.H., Yousefi K., Davicioni E., Netto G.J., Marchionni L., Fedor H.L., Glavaris S., Choeurng V., Buerki C., Erho N., Lam L.L., Humphreys E.B., Faraj S., Bezerra S.M., Han M., Partin A.W., Trock B.J., Schaeffer E.M. Tissue Based Genomics Augments Post-Prostatectomy Risk Stratification in a Natural History Cohort of Intermediate- and High-Risk Men. European Urology. 2016 Jan; 69(1): 157-65. doi: 10.1016/j.eururo.2015.05.042. PMID: 26058959

8. Zhao S.G., Evans J.R., Kothari V., Sun G., Larm A., Mondine V., Schaeffer E.M., Ross A.E., Klein E.A., Den R.B., Dicker A.P., Karnes R.J., Erho N., Nguyen P.L., Davicioni E., Feng F.Y. The landscape of prognostic outlier genes in high-risk prostate cancer. Clinical Cancer Research. 2016 Apr 1;22(7):1777-86. doi: 10.1158/1078-0432.

9. Faisal F.A., Sundi D., Tosoian J.J., Choeurng V., Alshalalfa M., Ross A.E., Klein E., Den R., Dicker A., Erho N., Davicioni E., Lotan T.L., Schaeffer E.M. Racial Variations in Prostate Cancer Molecular Subtypes and AR Signalling Reflect Anatomic Tumor Location. European Urology. 2015 Jul;70(1):14-7. doi:10.1016/j.eururo.2015.09.031.

10. Yamoah K., Johnson M.H., Choeurng V., Faisal F.A., Yousefi K., Haddad Z., Ross A.E., Alshalafa M., Den R., Lal P., Feldman M., Dicker A.P., Klein E.A., Davicioni E., Rebbeck T.R., Schaeffer E.M. Novel Biomarker Signature That May Predict Aggressive Disease in African American Men with Prostate Cancer. Journal of Clinical Oncology. 2015 Sep; 33(25): 2789-96. doi: 10.1200/JCO.2014.59.8912.

11. Den R.B., Yousefi K., Trabulsi E.J., Abdollah F., Choeurng V., Feng F.Y., Dicker A.P., Lallas C.D., Gomella L.G., Davcioni E., Karnes R.J. A Genomic Classifier Identifies Men with Adverse Pathology after Radical Prostatectomy who Benefit from Adjuvant Radiation Therapy. Journal of Clinical Oncology. 2015 Mar; 33(8): 944-51. doi: 10.1200/JCO.2014.59.0026

12. Klein E.A., Yousefi K., Haddad Z., Choeurng V., Buerki C., Stephnson A.J., Li J., Kattan M.W., Magi-Galluzzi C., Davicioni E. A Genomic Classifier Improves Prediction of Metastatic Disease within 5 Years After Surgery in Node-Negative High-Risk Prostate Cancer Patients Managed by Radical Prostatectomy without Adjuvant Therapy. European Urology. 2015 Apr; 67(4): 778-86. doi: 10.1016/j.eururo.2014.10.036.

13. Cooperberg M.R., Davicioni E., Crisan A., Jenkins R.B., Ghadessi M., Karnes R.J. Combined Value of Validated Clinical and Genomic Risk Stratification Tools for Predicting Prostate Cancer Mortality in a High-risk Prostatectomy Cohort. European Urology. 2015 Feb; 67(2): 326-33. doi: 10.1016/j.eururo.2014.05.039.

14. Den R.B., Feng F.Y., Showalter T.N., Mishra M.V., Trabulsi E.J., Lallas C.D., Gomella L.G., Kelly W.K., Birbe R.C., McCue P.A., Ghadessi M., Yousefi K., Davicioni E., Knudsen K.E., Dicker A.P. Genomic Prostate Cancer Classifier Predicts Biochemical Failure and Metastases in Patients After Postoperative Radiation Therapy. Int J Radiat Oncol Biol Phys. 2014 Aug; 89(5): 1038-46. doi: 10.1016/j.ijrobp.2014.04.052.

15. Prensner J.R., Zhao S., Erho N., Schipper M., Iyer M.K., Dhanasekaran S.M., Magi-Galluzzi C., Mehra R., Sahu A., Siddiqui J., Davicioni E., Den R.B., Dicker A.P., Karnes R.J., Wei J.T., Klein E.A., Jenkins R.B., Chinnaiyan A.M., Feng F.Y. RNA Biomarkers Associated with Metastatic Progression in Prostate Cancer: a Multi-Institutional High-Throughput Analysis of SChLAP1. Lancet Oncol. 2014 Dec; 15(13): 1469-80. doi: 10.1016/S1470-2045(14)71113-1.

16. Ross A.E., Feng F.Y., Ghadessi M., Erho N., Crisan A., Buerki C., Sundi D., Mitra A.P., Vergara I.A., Thompson D.J.S., Triche T.J., Davicioni E., Bergstralh E.J., Jenkins R.B., Karnes R.J., Schaeffer, E.M. A Genomic Classifier Predicting Metastatic Disease Progression in Men with Biochemical Recurrence after Prostatectomy. Prostate cancer and prostatic diseases. 2014 Mar; 17(1): 64-9. doi: 10.1038/pcan.2013.49.

17. Karnes R.J., Bergstralh E.J., Davicioni E., Ghadessi M., Buerki C., Mitra A.P., Crisan A., Erho N., Vergara I.A., Lam L.L., Carlson R., Thompson D.J.S., Haddad Z., Zimmermann B., Sierocinski T., Triche T.J., Kollmeyer T., Ballman K.V., Black P.C., Klee G.G, Jenkins R.B. Validation of a Genomic Classifier that Predicts Metastasis Following Radical Prostatectomy in an At Risk Patient Population. The Journal of Urology. 2013 Dec; 190(6): 2047-53. doi: 10.1016/j.juro.2013.06.017.

18. Erho N., Crisan A., Vergara I.A., Mitra A.P, Ghadessi M., Buerki C., Bergstralh E.J., Kollmeyer T., Fink S., Haddad Z., Zimmermann B., Siercinski T., Ballman K.V., Triche T.J., Black P.C., Karnes R.J., Klee G., Davicioni E., Jenkins R.B. Discovery and Validation of a Prostate Cancer Genomic Classifier that Predicts Early Metastasis Following Radical Prostatectomy. PLoS One. 2013 Jun;8(6):e66855. doi: 10.1371/journal.pone.0066855.

Clinical Use

19. Den R.B., Santiago-Jimenez M., Alter J., Schliekelman M., Wagner J.R., Renzulli J.F., Lee D.I., Brito C.G., Monahan K., Gburek B., Kella N., Vallabhan G., Abdollah F., Trabulsi E.J., Lallas C.D., Gomella L.G., Woodlief T.L., Haddad Z., Lam L.L.C., Deheshi S., Wang Q., Choeurng V., Du Plessis M., Jordan J., Parks B., Shin H., Buerki C., Yousefi K., Davicioni E., Patel V.R., Shah N.L. Decipher correlation patterns post-prostatectomy: Initial experience from 2,342 prospective patients. Prostate Cancer and Prostatic Disease. 2016 Dec;19(4):374-379. doi: 10.1038/pcan.2016.38. In press.

Clinical Utility

20. Gore J.L., Du Plessis M., Santiago-Jimenez M., Yousefi K., Thompson D.J.S., Karsh L., Lane B., Franks M., Chen D.Y.T., Bandyk M., Bianco F.J., Brown G., Clark W., Kibel A.S., Kim H., Lowrance W., Manoharan M., Maroni P., Perrapato S., Sieber P., Trabulsi E.J., Waterhouse R., Davicioni E., Lotan Y., Lin D.W. Decipher Test Impacts Decision-Making among Patients Considering Adjuvant and Salvage Treatment following Radical Prostatectomy: Interim Results from the Multicenter Prospective PRO-IMPACT Study. Cancer. 2017. In press

21. Lobo J.M, Trifiletti D.M., Sturz V.N., Dicker A.P., Buerki C., Davicioni E., Cooperberg M.R., Karnes R.J., Jenkins R.B., Den R.B., Showalter T.N. Cost effectiveness of the Decipher genomic classifier to guide individualized decisions for early radiation therapy after prostatectomy for prostate cancer. Clinical Genitourinary Cancer. 2017. pii: S1558-7673(16)30246-4. doi: 10.1016/j.clgc.2016.08.012.

22. Nguyen P., Shin H., Yousefi K., Thompson D.J., Hornberger J., Hyatt A.S., Badani K.K., Morgan T., Feng, Y.F. Impact of a Genomic Classifier of Metastatic Risk on Post-Prostatectomy Treatment Recommendations by Radiation Oncologists and Urologists. Urology 2015 Jul; 86(1): 35-40. Featured on the cover of Urology July 2015. doi: 10.1016/j.urology.2015.04.004.

23. Michalopolous S.N., Kella N, Payne R., Yohannes P., Singh A., Hettinger C., Yousefi K., Hornberger J. Influence of a Genomic Classifier on Post-Operative Treatment Decisions in High-Risk Prostate Cancer Patients: Results from the PRO-ACT Study. Curr Med Res Opin. 2014 Aug; 30(8): 1547-56. doi: 10.1185/03007995.2014.919908.

24. Lobo J.M., Dicker A.P., Buerki C., Davicioni E., Karnes R.J., Jenkins R.B., Patel N., Den R.B., Showalter T.N. Evaluating Clinical Impact of a Genomic Classifier in Prostate Cancer Using Individualized Decision Analysis. PLoS One. 2015 Apr; 10(3):e0116866. doi: 10.1371/journal.pone.0116866.

25. Badani K.K., Thompson D.J., Brown G., Holmes D., Kella N., Albala D., Singh A., Buerki C., Davicioni E., Hornberger J. Effect of a Genomic Classifier Test on Clinical Practice Decisions for Patients with High-Risk Prostate Cancer After Surgery. British Journal of Urology Intl. 2014 Mar; 115(3):419-29. doi: 10.1111/bju.12789.

26. Badani K.K., Thompson D.J.S., Buerki C., Davicioni E., Garrison J., Ghadessi M., Mitra A.P., Wood P.J., Hornberger J. Impact of a Genomic Classifier of Metastatic Risk on Postoperative Treatment Recommendations for Prostate Cancer Patients: A Report from the DECIDE Study Group. Oncotarget. 2013 Apr; 4(4): 600-9. doi: 10.18632/oncotarget.918.

Analytical Validation

27. Abdueva D., Wing M., Schaub B., Triche T., Davicioni E., Quantitative Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays. The Journal of molecular diagnostics. 2010 Jul; 12(4): 409-17. doi: 10.2353/jmoldx.2010.090155.

Decipher GRID Publications

1. Itkonen H.M., Brown M., Urbanucci A., Tredwell G, Lau C.H., Barfeld S., Hart C., Guldvik I.J., Takhar M., Heemers H.V., Erho N., Bloch K., Davicioni E., Derua R., Waelkens E., Mohler J.L., Clarke N., Swinnen J.V., Keun H.C., Rekvig O.P., Mills I.G. Lipid degradation promotes prostate cancer cell survival. Oncotarget. 2017. In press. (Accepted March 1st)

2. Zhao S.G., Chang S.L., Erho N., Yu M., Lehrer J., Alshalalfa M., Speers C., Cooperberg M.R., Kim W., Ryan C. J., Den R.B., Freedland S.J., Posadas E., Sandler H., Klein E.A., Black P., Seiler R., Tomlins S.A., Chinnaiyan A.M., Jenkins R.B., Davicioni E., Ross A.E., Schaeffer E.M., Nguyen P.L., Carroll P.R., Karnes R.J., Spratt D.E., Feng F.Y. Luminal and basal subtyping of prostate cancer is prognostic and predicts response to androgen deprivation therapy. JAMA Oncology. 2017. In press.

3. Mo F., Lin D., Takhar M., Ramnarine V.R., Dong X., Bell R.H., Volik S.V., Wang K., Xue H., Wang Y., Haegert A., Anderson S., Brahmbhatt S., Erho N., Wang X., Gout P.W., Morris J., Karnes R.J., Den R.B., Klein E.A., Schaeffer E.M., Ross A., Ren S., Sahinal S.C., Li Y., Xu X., Wang J., Wang J., Gleave M.E., Davicioni E., Sun Y., Wang Y., Collins C.C. Stromal Gene Expression is Predictive for Metastatic Primary Prostate Cancer. European Urology. 2017. In press.

4. Torres A., Alshalalfa M., Tomlins S.A, Erho N., Gibb E.A., Chelliserry J., Lim L., Lam L.L.C., Faraj S.F, Bezerra S.M., Davicioni E., Yousefi K., Ross A.E., Netto G.J., Schaeffer E.M., Lotan T.M. Comprehensive Determination of Prostate Tumor ETS Gene Status in Clinical Samples Using the CLIA Decipher® Assay. Modern Pathology. 2017. In press.

5. Pellegrini K.L., Sanda M.G., Patil D., Long Q., Santiago-Jiménez M., Takhar M., Erho N., Yousefi K., Davicioni E., Klein E.A., Jenkins R.B., Karnes R.J., Moreno C.S. Evaluation of a 24-Gene Signature for Prognosis of Metastatic Events and Prostate Cancer-Specific Mortality. BJU International. 2017. Jan. doi: 10.1111/bju.13779. In press.

6. Alshalalfa A, Verhaegh G.W., Gibb E.A., Santiago-Jiménez M., Erho N., Jordan J., Yousefi K., Lam L.L.C, Kolisnik T., Chellisery J., Seiler R., Ross A.E, Karnes R.J., Schaeffer E.M., Lotan T.T., Den R.B., Freedland S.J., Davicioni E., Klein E. A, Schalken J.A. Low PCA3 expression is a marker of poor differentiation in localized prostate tumors: Exploratory analysis from 12,076 patients. Oncotarget. 2017. doi: 10.18632/oncotarget.15133. In press

7. Nouri M., Caradec J., Lubik A.A., Li N., Hollier B.G., Takhar M., Altimirano-Dimas M., Chen M., Roshan-Moniri M., Butler M., Lehman M., Bishop J., Truong S., Huang S.C., Cochrane D., Cox M., Collins C., Gleave M., Erho N., Alshalafa M., Davicioni E., Nelson C., Gregory-Evans S., Karnes R.J, Jenkins R.B., Klein E.A., Buttyan R. Therapy-Induced Developmental Reprogramming of Prostate Cancer Cells and Acquired Therapy Resistance. Oncotarget. 2017. Jan. doi: 10.18632/oncotarget.14850. In press.

8. Kim H., Kalchman I., Santiago-Jiménez M., Lehrer J., Guo J., Hermann G., Yamoah K., Alshalalfa M., Huang H.C., Ross A.E., Schaeffer E.M., Davicioni E., Erho N., Yousefi K., Den R.B. Transcriptome evaluation of the relationship between body mass index and prostate cancer outcomes. Cancer. 2017. Jan. doi: 10.1002/cncr.30580. In press.

9. Wahl D.R., Mehra R., Santiago-Jiménez M., Yousefi K., Davicioni E., Speers C., Feng F.Y., Nguyen P., Lawrence T., Osborne J.R., Spratt D.E. Pan-Cancer Analysis of Genomic Sequencing among the Elderly. IJROBP. 2017. In press.

10. Tse B.W., Volpert M., Ratther E., Stylianou N., Nouri M., McGowan K., Lehman M.L., McPherson S.J., Roshan-Moniri M., Butler M.S., Caradec J., Gregory-Evans C.Y., McGovern J., Das R., Takhar M., Erho N., Alshalafa M., Davicioni E., Schaeffer E.M., Jenkins R.B., Ross A.E., Karnes R.J., Den R.B., Fazli L., Gregory P.A., Gleave M.E., Williams E.D., Rennie P.S., Buttyan R., Gunter J.H., Selth L.A., Russell P.J., Nelson C.C., Hollier B.G. Neuropilin-1 is upregulated in the adaptive response of prostate tumors to androgen-targeted therapies and is prognostic of metastatic progression and patient mortality. Oncogene. 2017. doi: 10.1038/onc.2016.482. In press

11. Das R., Gregory P.A., Fernandes R.C., Denis I., Wang Q., Townley S. L., Zhao S., Hanson A. R., Pickering M.A., Armstrong H.K., Lokman N.A., Davicioni E., Jenkins R.B., Karnes R.J., Ross A.E., Den R.B., Klein E., Chi K.N., Ramshaw H.S., Williams E.D., Zoubeidi A., Goodall G.J., Feng F.Y., Butler L.M., Tilley W.D., Selth L. A. GATA2-regulated miR-194 targets Suppressor of Cytokine Signaling 2 to promote prostate cancer metastasis. Cancer Research. 2017. In press.

12. White N.M., Zhao S.G., Zhang J., Rozycki E.B., Dang H.X., McFadden S.D., Eteleeb A.M., Alshalalfa M., Vergara I.A., Erho N., Arbeit J.M., Karnes R.J., Den R.B., Davicioni E., Maher C.A. Multi-institutional Analysis Shows that Low PCAT-14 Expression Associates with Poor Outcomes in Prostate Cancer. Eur Urol. 2017 Feb; 71(2): 257-266. doi:10.1016/j.eururo.2016.07.012.

13. Benzon B., Zhao S.G., Haffner M.C., Takhar M., Erho N., Yousefi K., Hurley P., Bishop J.L., Tosoian J., Ghabili K., Alshalalfa M., Glavaris S., Simons B.W., Tran P., Davicioni E., Karnes R.J., Boudadi K., Antonarakis E.S., Schaeffer E.M., Drake C.G., Feng F., Ross A.E. Correlation of B7-H3 with androgen receptor, immune pathways and poor outcome in prostate cancer: an expression-based analysis. Prostate Cancer and Prostatic Disease. 2016 Nov. doi: 10.1038/pcan.2016.49. In press.

14. Kim H., Alshalalfa M., Hoffman-Censits J., Lallas C.D., Davicioni E., Lin J., Birbe R., Erho N., Lehrer J., Al-Deen Ashab H., Takhar M., Olson A., Lam L.L.C., Kelly W.K., Knudsen K.E., Thangavel C., Seiler R., Feng F.Y., Schaeffer E.M., Trabulsi E.J., Gomella L.G., Hurwitz M.D., Dicker A.P., Den R.B. Potential impact on clinical decision making via a genome-wide expression profiling: a case report. Urology Case Reports. 2016 Oct; 9:51-54. eCollection 2016.

15. Zhao S.G., Chang L.S., Spratt D.E., Erho N., Yu M., Al-Deen Ashab H., Alshalalfa M., Speers C., Tomlins S.A., Davicioni E., Dicker A.P., Carroll P.C., Cooperberg M.R., Freedland S.J., Karnes R.J., Ross A., Schaeffer E.M., Den R.B., Nguyen P.L., Feng F.Y. The Development and Validation of a 24-gene Predictor of Response to Post-operative Radiation Therapy in Prostate Cancer: A Matched Retrospective Analysis. Lancet Oncology. 2016 Nov; 17(11):1612-1620. doi: 10.1016/S1470-2045(16)30491-0.

16. McNair C., Urbanucci A., Comstock C., Augello M., Goodwin J., Launchbury R., Zhao S., Schiewer M., Ertel A., Karnes R., Davicioni E., Wang L., Wang Q., Mills I., Feng F., Li W., Carroll J.S., Knudsen K. Cell-cycle coupled expansion of AR activity promotes cancer progression. Oncogene. 2016 Sept. doi: 10.1038/onc.2016.334.

17. You S., Knudsen B.S., Erho N., Alshalalfa M., Takhar M., Al-Deen Ashab H., Davicioni E., Karnes R.J., Klein E.A., Den R.B., Ross A.E., Schaeffer E.M., Garraway I.P, Kim J., Freeman M.R. Integrated classification of prostate cancer reveals a novel luminal subtype with poor outcome. Cancer Res. 2016 Sep; 76(17):4948-58. doi: 10.1158/0008-5472.CAN-16-0902.

18. Johnson M.H., et al., SPINK1 defines a molecular subtype of prostate cancer in men with more rapid progression in an at-risk, natural history radical prostatectomy cohort. Journal of Urology. 2016 Nov; 196(5):1436-1444. doi: 10.1016/j.juro.2016.05.092.

19. Spans L., et al., Genomic and epigenomic analysis of high-risk prostate cancer reveals changes in hydroxymethylation and TET1. Oncotarget. 2016 Mar; 7(17):24326-24338. doi: 10.18632/oncotarget.8220.

20. Hu B.R., et al., AXIN2 expression predicts prostate cancer recurrence and regulates invasion and tumor growth. The Prostate. 2016 May; 76(6):597-608. doi: 10.1002/pros.23151.

21. Evans J.R., et al., Patient-Level DNA Damage and Repair Pathway Profiles and Prostatectomy for High-Risk Prostate Cancer. JAMA Oncology. 2016 Jan 7: 2(4):1-10. doi:10.1001/jamaoncol.2015.4955.

22. Faraj S.F., et al., Clinical Validation of the 2005 ISUP Gleason Grading System in a Cohort of Intermediate and High Risk Men Undergoing Radical Prostatectomy. PLoS One. 2016 Jan; 11(1):e0146189 doi: 10.1371/journal.pone.0146189. eCollection 2016.

23. Hurley P.J., et al. Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment and are Differentially Associated with Metastatic Prostate Cancer. Clin Cancer Res. 2016 Jan; 22(2):448-58. doi: 10.1158/1078-0432.CCR-15-0256.

24. Ross A.E., et al., Utility of Risk Models in Decision Making After Radical Prostatectomy: Lessons from a Natural History Cohort of Intermediate- and High-Risk Men. European Urology. 2016 Apr; pii: S0302-2838(15)00318-8. doi: 10.1016/j.eururo.2015.04.016.

25. Hurley P.J., et al., Androgen-Regulated SPARCL1 in the Tumor Microenvironment Inhibits Metastatic Progression. Cancer Res. 2015 Oct 15;75(20):4322-34. doi: 10.1158/0008-5472.CAN-15-0024.

26. Zhao S.G., et al., High-throughput transcriptomic analysis nominates proteasomal genes as age-specific biomarkers and therapeutic targets in prostate cancer. Prostate Cancer Prostatic Dis. 2015 Sep; 18(3): 229-36. doi: 10.1038/pcan.2015.22.

27. Tsai H., et al., Cyclin D1 Loss Distinguishes Prostatic Small-Cell Carcinoma from Most Prostatic Adenocarcinomas. Clin Cancer Res. 2015 Aug. doi: 10.1158/1078-0432.CCR-15-0744.

28. Goodwin J.F., et al., DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis. Cancer Cell. 2015 Jul; 28(1): 97-113. doi: 10.1016/j.ccell.2015.06.004.

29. Tomlins S.A., et al., Characterization of 1,577 Primary Prostate Cancers Reveals Novel Biological and Clinicopathological Insights into Molecular Subtypes. European Urology. 2015 Oct;68(4):555-67. doi:10.1016/j.eururo.2015.04.033.

30. Alshalalfa M., et al., Evolving Transcriptomic Fingerprint Based on Genome-Wide Data as Prognostic Tools in Prostate Cancer. Biology of the Cell. 2015 Jul; 107(7): 232-44. doi: 10.1111/boc.201400097.

31. Alshalalfa M., et al., Clinical and Genomic Analysis of Metastatic Prostate Cancer Progression in a Background of Post-Operative Biochemical Recurrence. British Journal of Urology Intl. 2015 Oct; 116(4): 556-67. doi: 10.1111/bju.13013.

32. Chakravarty D., et al., The ​Oestrogen Receptor Alpha-Regulated lncRNA ​NEAT1 is a Critical Modulator of Prostate Cancer. Nature Communications. 2014 Nov; 5:5383. doi:10.1038/ncomms6383.

33. Lalonde E., et al., Tumour Genomic and Microenvironmental Heterogeneity for Integrated Prediction of 5-Year Biochemical Recurrence of Prostate Cancer: a Retrospective Cohort Study. Lancet Oncology. 2014 Dec; 15(13): 1521-32. doi: 10.1016/S1470-2045(14)71021-6.

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40. Erho N. et al., Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and their Clinical Significance in Prostate Cancer. Journal of Oncology. 2012; 2012:541353.

Bladder Cancer

1. Kiss B., Wyatt A.W., Skuginna V., Douglas J., Mo F., Anderson S., Rotzer D., Fleischmann A., Genitsch V., Neuenschwader M., Bürki C., Davicioni E., Collins C., Thalmann G.N., Black P.C., Seiler R. ERBB2 alterations in muscle-invasive bladder cancer: Patient selection beyond protein expression for targeted therapy. Scientific Reports. 2017 Feb;7:42713 doi: 10.1038/srep42713.

2. Seiler R., Lam L.L., Erho N., Takhar M., Mitra A.P., Buerki C., Davicioni E., Skinner E.C., Daneshmand S., Black P.C. Prediction of lymph node metastasis in bladder cancer patients using whole transcriptome gene expression signatures. Journal of Urology. 2016 Oct;196(4):1036-41. doi: 10.1016/j.juro.2016.04.061.

3. Jager W., Xue H., Hayashi T., Janssen C., Awrey S., Wyatt A.W., Anderson S., Moskalev I., Haegert A., Alshalalfa M., Erho N., Davicioni E., Fazli L., Li E., Collins C., Wang Y., and Black P.C. Patient-Derived Bladder Cancer Xenografts in the Preclinical Development of Novel Targeted Therapies. Oncotarget. 2015 Aug; 6(25):21522-32.

4. Mitra A.P., Lam L.L., Ghadessi M., Erho N., Vergara I.A., Alshalalfa M., Buerki C., Haddad Z., Sierocinski T., Triche T.J., Skinner E.C., Davicioni E., Daneshmand S., Black, P.C. Discovery and Validation of Novel Expression Signature for Postcystectomy Recurrence in High-Risk Bladder Cancer. JNCI J Natl Cancer Inst. 2014 Oct; 106(11). pii: dju290. doi: 10.1093/jnci/dju290.

Reviews

Internal Reviews

1. Stoyanova R., Takhar M., Tschudi Y., Ford J.C., Solórzano G., Erho N., Balagurunathan Y., Punnen S., Davicioni E., Gillies R.J., Pollack A. Prostate Cancer Radiomics and the Promise of Radiogenomics. Translational Cancer Research. 2016. In press

2. Alshalalfa M., Shin H., Clinical and Genomic Analysis of Metastatic Prostate Cancer Progression with a Background of Postoperative Biochemical Recurrence – Beyond the Abstract. UROToday. 2015

External Reviews Discussing Decipher

1. Dall’Era M., Evans C., Genomic and Biological Markers to Select Treatment in Patients with Prostate Cancer: Choose Wisely, My Friend. Journal of Urology. 2016 Oct; pii: S0022-5347(16)31511-7. doi: 10.1016/j.juro.2016.10.048.

2. Morlacco A., Karnes R.J. Early salvage radiation therapy post-prostatectomy: key considerations. Future Oncol. 2016 Jul 8.

3. Gaudreau P-O., Stagg J., Soulières D., Saad F. The Present and Future of Biomarkers in Prostate Cancer: Proteomics, Genomics, and Immunology Advancements. Biomark Cancer. 2016 May; 8(Suppl 2):15-33. doi:10.4137/BIC.S31802.

4. Dalela D., Löppenberg B., Sood A., Sammon J., Abdollah F. Contemporary Role of the Decipher® Test in Prostate Cancer Management: Current Practice and Future Perspectives. Rev Urol. 2016; 18(1):1-9. doi: 10.4137/BIC.S31802.

5. Moschini M., Spahn M., Mattei A., Cheville J., Karnes RJ. Incorporation of tissue-based genomic biomarkers into localized prostate cancer clinics. BMC Med. 2016 Apr; 14(1):67. doi:10.1186/s12916-016-0613-7.

6. Martin, N.E. New Developments in Prostate Cancer Biomarkers. Curr Opin Oncol. 2016 May; 28(3):248-52. doi: 10.1097/CCO.0000000000000279.

7. Pisansky T.M., Salvage Radiotherapy for Postoperative Biochemical Failure of Prostate Cancer: The Path Toward Personalized Medicine. European Urology. 2016 Jan. pii: S0302-2838(16)00135-4. doi: 10.1016/j.eururo.2016.01.033.

8. Boström P.J., Bjartell A.S., Catto J.W., Eggener S.E., Lilja H., Loeb S., Schalken J., Schlomm T., Cooperberg M.R. Genomic Predictors of Outcome in Prostate Cancer. European Urology. 2015 Dec; 68(6):1033-44. doi: 10.1016/j.eururo.2015.04.008.

9. Davis, J.W., Use of Genomic Markers to Risk Stratify Men with Prostate Cancer. Trends in Urology & Men’s Health. 2015. 6(3): 36-39. doi: 10.1002/tre.461

10. Ross A.E., D’Amico A.V., Freedland S.J., Which, When and Why? Rational Use of Tissue-Based Molecular Testing in Localized Prostate Cancer. Prostate Cancer Prostatic Disease. 2015 Dec; 68(6): 1033-44. doi: 10.1038/pcan.2015.31

11. Spahn M., Boxler S., Joniau S., Moschini M., Tombal B., Karnes R.J. What is the Need for Prostatic Biomarkers in Prostate Cancer Management? Current Urology Report. 2015 Oct; 16(10):70. doi: 10.1007/s11934-015-0545-3.

12. Marrone M., Potosky A.L., Penson D., Freedman A.N. A 22 Gene-expression Assay, Decipher® (GenomeDx Biosciences) to Predict Five-year Risk of Metastatic Prostate Cancer in Men Treated with Radical Prostatectomy. PLoS Curr. 2015 Nov; 7. doi:10.1371/currents.eogt.761b81608129ed61b0b48d42c04f92a4.

13. Nguyen H.G., Welty C.J., Cooperberg M.R., Diagnostic Associations of Gene Expression Signatures in Prostate Cancer Tissue. Current Opinion in Urology. 2015 Jan; 25(1): 65-70. doi:10.1097/MOU.0000000000000131.

14. Davis J.W., Novel commercially available genomic tests for prostate cancer: a roadmap to understanding their clinical impact. BJU International. 2014 Sep; 114(3):320-2. doi: 10.1111/bju.12695