Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens

Journal of Molecular Diagnostics

Volumn 18, Issue 3, 2016, Pages 395-406

  Knudsen, Beatrice S ^a   Kim, Hyung L ^a   Erho, Nicholas ^b   Shin, Heesun ^b   Alshalalfa, Mohammed ^b   Lam, Lucia L C ^b   Tenggara, Imelda ^c   Chadwich, Karen ^e   Van Der Kwast, Theo ^f   Fleshner, Neil ^e   Davicioni, Elai ^b   Carroll, Peter R ^c   Cooperberg, Matthew R ^c,d   Chan, June M ^c,d   Simko, Jeffry P ^c  

^a CEDARS SINAI MEDICAL CENTER   (United States)

^b GenomeDx Biosciences Inc   (Canada)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY HEALTH NETWORK   (Canada)

^f PRINCESS MARGARET HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

ARTICLE; CANCER PATIENT; CANCER PROGNOSIS; CANCER STAGING; CONTROLLED STUDY; GENE EXPRESSION; HUMAN; HUMAN TISSUE; MALE; NEEDLE BIOPSY; NEEDLE CORE BIOPSY; PROSTATE BIOPSY; PROSTATE CANCER; PROSTATECTOMY; RNA ANALYSIS; TRANSCRIPTOME WIDE EXPRESSION ANALYSIS; TRANSCRIPTOMICS; TUMOR VOLUME; BIOLOGY; CANCER GRADING; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENETICS; LARGE CORE NEEDLE BIOPSY; PROCEDURES; PROGNOSIS; PROSTATIC NEOPLASMS;

BIOPSY, LARGE-CORE NEEDLE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HUMANS; MALE; NEOPLASM GRADING; NEOPLASM STAGING; PROGNOSIS; PROSTATIC NEOPLASMS; TRANSCRIPTOME;

EID: 84963986381     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2015.12.006     Document Type: Article

References (31)

1. R. Siegel, D. Naishadham, and A. Jemal Cancer statistics, 2012 CA Cancer J Clin 62 2012 10 29
2. R. Siegel, J. Ma, Z. Zou, and A. Jemal Cancer statistics, 2014 CA Cancer J Clin 64 2014 9 29
3. K. Wojno, J. Hornberger, P. Schellhammer, M. Dai, and T. Morgan The clinical and economic implications of specimen provenance complications in diagnostic prostate biopsies J Urol 193 2015 1170 1177
4. A.J. Chang, K.A. Autio, M. Roach, and H.I. Scher High-risk prostate cancer: classification and therapy Nat Rev Clin Oncol 11 2014 308 323
5. R. Xie, J.-Y. Chung, K. Ylaya, R.L. Williams, N. Guerrero, N. Nakatsuka, C. Badie, and S.M. Hewitt Factors influencing the degradation of archival formalin-fixed paraffin-embedded tissue sections J Histochem Cytochem 59 2011 356 365
6. M.C. Haffner, T. Mosbruger, D.M. Esopi, H. Fedor, C.M. Heaphy, D.A. Walker, N. Adejola, M. Gürel, J. Hicks, A.K. Meeker, M.K. Halushka, J.W. Simons, W.B. Isaacs, A.M. De Marzo, W.G. Nelson, and S. Yegnasubramanian Tracking the clonal origin of lethal prostate cancer J Clin Invest 123 2013 4918 4922
7. J. Lindberg, A. Kristiansen, P. Wiklund, H. Grönberg, and L. Egevad Tracking the origin of metastatic prostate cancer Eur Urol 67 2015 819 822
8. P.C. Boutros, M. Fraser, N.J. Harding, R. de Borja, D. Trudel, E. Lalonde, and et al. Spatial genomic heterogeneity within localized, multifocal prostate cancer Nat Genet 47 2015 736 745
9. D. Abdueva, M. Wing, B. Schaub, T. Triche, and E. Davicioni Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays J Mol Diagn 12 2010 409 417
10. N. Erho, A. Crisan, I.A. Vergara, A.P. Mitra, M. Ghadessi, C. Buerki, E.J. Bergstralh, T. Kollmeyer, S. Fink, Z. Haddad, T. Sierocinski, K.V. Ballman, T.J. Triche, P.C. Black, R.J. Karnes, G. Klee, E. Davicioni, and R.B. Jenkins Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy PLoS One 8 2013 e66855
11. M. Alshalalfa, M. Schliekelman, H. Shin, N. Erho, and E. Davicioni Evolving transcriptomic fingerprint based on genome-wide data as prognostic tools in prostate cancer Biol Cell 107 2015 232 244
12. R. Karnes, E. Bergstralh, E. Davicioni, M. Ghadessi, C. Buerki, A. Mitra, A. Crisan, N. Erho, L. Lam, R. Carlson, Z. Haddad, T. Triche, T. Kollmeyer, K. Ballman, P. Black, G. Klee, and R. Jenkins Validation of a genomic classifier that predicts metastasis following radical prostatectomy in an at risk patient population J Urol 190 2013 2047 2053
13. E.A. Klein, K. Yousefi, Z. Haddad, V. Choeurng, C. Buerki, A.J. Stephenson, J. Li, M.W. Kattan, C. Magi-Galluzzi, and E. Davicioni 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 Eur Urol 67 2014 778 786
14. A.E. Ross, F.Y. Feng, M. Ghadessi, N. Erho, A. Crisan, C. Buerki, D. Sundi, A.P. Mitra, I.A. Vergara, D.J. Thompson, T.J. Triche, E. Davicioni, E.J. Bergstralh, R.B. Jenkins, R.J. Karnes, and E.M. Schaeffer A genomic classifier predicting metastatic disease progression in men with biochemical recurrence after prostatectomy Prostate Cancer Prostatic Dis 17 2014 64 69
15. R.B. Den, K. Yousefi, E.J. Trabulsi, A. Firas, C. Voleak, F.Y. Feng, A.P. Dicker, C.D. Lallas, L.G. Gomella, E. Davicioni, and R.J. Karnes Genomic classifier identifies men with adverse pathology after radical prostatectomy who benefit from adjuvant radiation therapy J Clin Oncol 33 2015 944 951
16. J.R. Prensner, Z. Shuang, N. Erho, M. Schipper, M.K. Lyer, S.M. Dhanasekaran, and C. Magi-Galluzzi RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1 Lancet Oncol 15 2014 1469 1480
17. E. Lalonde, A. Ishkanian, J. Sykes, M. Fraser, H. Ross-Adams, N. Erho, and M. Dunning Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study Lancet Oncol 15 2014 1521 1532
18. E.A. Klein, M.R. Cooperberg, C. Magi-Galluzzi, J.P. Simko, S.M. Falzarano, T. Maddala, J.M. Chan, J. Li, R.J. Pelham, I. Tenggara-Hunter, F.L. Baehner, D. Knezevic, P.G. Febbo, S. Shak, M.W. Kattan, M. Lee, and P.R. Carroll A 17-gene assay to predict prostate cancer aggressiveness in the context of Gleason grade heterogeneity, tumor multifocality, and biopsy undersampling Eur Urol 66 2014 550 560
19. J. Cuzick, G.P. Swanson, G. Fisher, A.R. Brothman, D.M. Berney, J.E. Reid, D. Mesher, V.O. Speights, E. Stankiewicz, P. Scardino, A. Younus, D.D. Flake, S. Wagner, A. Gutin, J.S. Lanchbury, and S. Stone Prognostic value of an RNA expression signature derived from cell cycle proliferation genes in patients with prostate cancer: a retrospective study Lancet Oncol 12 2011 245 255
20. K.L. Penney, J.A. Sinnott, K. Fall, Y. Pawitan, Y. Hoshida, P. Kraft, J.R. Stark, M. Fiorentino, S. Setlur, J.-E. Johansson, H.-O. Adami, M.A. Rubin, M. Loda, T.R. Golub, O. Andrén, M.J. Stampfer, and L.A. Mucci mRNA expression signature of Gleason grade predicts lethal prostate cancer J Clin Oncol 29 2011 2391 2396
21. S.A. Tomlins, M. Alshalalfa, E. Davicioni, N. Erho, K. Yousefi, S. Zhao, Z. Haddad, R.B. Den, A.P. Dicker, B.J. Trock, A. DeMarzo, A. Ross, E.M. Schaeffer, E.A. Klein, C. Magi-Galluzzi, R.J. Karnes, R.B. Jenkins, and F.Y. Feng Characterization of 1,577 primary prostate cancers reveals novel biological and clinicopathological insights into molecular subtypes Eur Urol 68 2015 555 567
22. S.R. Piccolo, Y. Sun, J.D. Campbell, M.E. Lenburg, A.H. Bild, and W.E. Johnson A single-sample microarray normalization method to facilitate personalized-medicine workflows Genomics 100 2012 337 344
23. W.E. Johnson, C. Li, and A. Rabinovic Adjusting batch effects in microarray expression data using empirical Bayes methods Biostatistics 8 2007 118 127
24. B.S. Taylor, N. Schultz, H. Hieronymus, A. Gopalan, Y. Xiao, B.S. Carver, V.K. Arora, P. Kaushik, E. Cerami, B. Reva, M. Wilson, A. Heguy, J.A. Eastham, P.T. Scardino, C. Sander, C.L. Sawyers, and W.L. Gerald Integrative genomic profiling of human prostate cancer Cancer Cell 18 2010 11 22
25. J.C. Brase, M. Johannes, H. Mannsperger, M. Falth, J. Metzger, L.A. Kacprzyk, T. Andrasiuk, S. Gade, M. Meister, H. Sirma, G. Sauter, R. Simon, T. Schlomm, T. Beissbarth, U. Korf, R. Kuner, and H. Sultmann TMPRSS2-ERG-specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-beta signaling BMC Cancer 11 2011 507
26. S.A. Tomlins, A. Bjartell, A.M. Chinnaiyan, G. Jenster, R.K. Nam, M.A. Rubin, and J.A. Schalken ETS gene fusions in prostate cancer: from discovery to daily clinical practice Eur Urol 56 2009 275 286
27. A. Lachmann, H. Xu, J. Krishnan, S.I. Berger, A.R. Mazloom, and A. Ma'ayan ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments Bioinformatics 26 2010 2438 2444
28. N.M. Corcoran, M.K. Hong, R.G. Casey, A. Hurtado-Coll, J. Peters, L. Harewood, S.L. Goldenberg, C.M. Hovens, A.J. Costello, and M.E. Gleave Upgrade in Gleason score between prostate biopsies and pathology following radical prostatectomy significantly impacts upon the risk of biochemical recurrence BJU Int 108 8 Pt 2 2011 E202 E210
29. M. Bibikova, J.M. Yeakley, E. Chudin, J. Chen, E. Wickham, J. Wang-Rodriguez, and J.-B. Fan Gene expression profiles in formalin-fixed, paraffin-embedded tissues obtained with a novel assay for microarray analysis Clin Chem 50 2004 2384 2386
30. M. Frank, C. Döring, D. Metzler, S. Eckerle, and M.-L. Hansmann Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays Virchows Arch 450 2007 699 711
31. R. Pillai, R. Deeter, and C.T. Rigl Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimens J Mol Diagn 13 2011 48 56