Molecular sampling of prostate cancer: A dilemma for predicting disease progression

BMC Medical Genomics

Volumn 3, Issue , 2010, Pages

  Sboner, Andrea ^a   Demichelis, Francesca ^b   Calza, Stefano ^c,d   Pawitan, Yudi ^c   Setlur, Sunita R ^e   Hoshida, Yujin ^f,g   Perner, Sven ^b   Adami, Hans Olov ^c,h   Fall, Katja ^c,h   Mucci, Lorelei A ^e,h,j   Kantoff, Philip W ^g,j   Stampfer, Meir ^e,h,j   Andersson, Swen Olof ⁱ   Varenhorst, Eberhard ^k   Johansson, Jan Erik ⁱ   Gerstein, Mark B ^a,l   Golub, Todd R ^f,g   Rubin, Mark A ^b,f   Andrén, Ove ⁱ  

^a YALE UNIVERSITY   (United States)

^b WEILL CORNELL MEDICAL CENTER   (United States)

^c KAROLINSKA INSTITUTE   (Sweden)

^d UNIVERSITY OF BRESCIA   (Italy)

^e BRIGHAM AND WOMEN S HOSPITAL   (United States)

^f BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^g DANA FARBER CANCER INSTITUTE   (United States)

^h HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

ⁱ ÖREBRO UNIVERSITY HOSPITAL   (Sweden)

^j HARVARD MEDICAL SCHOOL   (United States)

^k LINKÖPING UNIVERSITY HOSPITAL   (Sweden)

^l Yale University   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; FORMALDEHYDE; PARAFFIN; TUMOR MARKER;

ADULT; ARTICLE; CANCER GROWTH; CLINICAL EVALUATION; CLINICAL FEATURE; CLINICAL TRIAL; COHORT ANALYSIS; COMPUTATIONAL FLUID DYNAMICS; CONTROLLED STUDY; DISEASE COURSE; GENE EXPRESSION PROFILING; GENETIC HETEROGENEITY; HUMAN; LETHALITY; LIGATION; MACHINE LEARNING; MAJOR CLINICAL STUDY; MALE; METASTASIS; MOLECULAR GENETICS; MOLECULAR MODEL; MULTICENTER STUDY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROGNOSIS; PROSTATE; PROSTATE CANCER; RISK FACTOR; SURVIVAL RATE; SWEDEN; TRANSURETHRAL RESECTION; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; PATHOLOGY; PROSTATE TUMOR;

DISEASE PROGRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MALE; PROSTATIC NEOPLASMS; TUMOR MARKERS, BIOLOGICAL;

EID: 77951723424     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-3-8     Document Type: Article

References (55)

1. Natural history of early, localized prostate cancer. J Johansson O Andrén S Andersson PW Dickman L Holmberg A Magnuson H Adami, JAMA 2004 291 2713 9 10.1001/jama.291.22.2713 15187052
2. Radical Prostatectomy Versus Watchful Waiting in Localized Prostate Cancer: the Scandinavian Prostate Cancer Group-4 Randomized Trial. A Bill-Axelson L Holmberg F Filen M Ruutu H Garmo C Busch S Nordling M Haggman S Andersson S Bratell A Spangberg J Palmgren H Adami J Johansson for the Scandinavian Prostate Cancer Group Study Number 4, J Natl Cancer Inst 2008 100 1144 1154 10.1093/jnci/djn255 18695132
3. Cancer Statistics, 2008. A Jemal R Siegel E Ward Y Hao J Xu T Murray MJ Thun, CA Cancer J Clin 2008 58 71 96 10.3322/CA.2007.0010 18287387
4. Radical prostatectomy versus watchful waiting in early prostate cancer. A Bill-Axelson L Holmberg M Ruutu M Häggman S Andersson S Bratell A Spångberg C Busch S Nordling H Garmo J Palmgren H Adami BJ Norlén J Johansson, N Engl J Med 2005 352 1977 84 10.1056/NEJMoa043739 15888698
5. A preoperative nomogram for disease recurrence following radical prostatectomy for prostate cancer. M Kattan J Eastham A Stapleton T Wheeler P Scardino, J Natl Cancer Inst 1998 90 766 771 10.1093/jnci/90.10.766 9605647
6. Contemporary update of prostate cancer staging nomograms (Partin Tables) for the new millennium. AW Partin LA Mangold DM Lamm PC Walsh JI Epstein JD Pearson, Urology 2001 58 843 848 10.1016/S0090-4295(01)01441-8 11744442
7. Nomogram incorporating PSA level to predict cancer-specific survival for men with clinically localized prostate cancer managed without curative intent. MW Kattan J Cuzick G Fisher DM Berney T Oliver CS Foster H Møller V Reuter P Fearn J Eastham PT Scardino ATTP Group, Cancer 2008 112 69 74 10.1002/cncr.23106 18000803
8. Survival in prostate carcinoma - outcomes from a prospective, population-based cohort of 8887 men with up to 15 years of follow-up: results from three countries in the population-based National Prostate Cancer Registry of Sweden. G Aus D Robinson J Rosell G Sandblom E Varenhorst, Cancer 2005 103 943 51 10.1002/cncr.20855 15651057
9. How Well Does the Gleason Score Predict Prostate Cancer Death? A 20-Year Followup of a Population Based Cohort in Sweden. O Andren K Fall L Franzen S Andersson J Johansson MA Rubin, The Journal of Urology 2006 175 1337 1340 10.1016/S0022-5347(05)00734-2 16515993
10. Recommendations for the reporting of prostate carcinoma: Association of Directors of Anatomic and Surgical Pathology. JI Epstein J Srigley D Grignon P Humphrey, Am J Clin Pathol 2008 129 24 30 10.1309/59U8R6N5R7BKCWLV 18089486
11. A Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices. J Fan JM Yeakley M Bibikova E Chudin E Wickham J Chen D Doucet P Rigault B Zhang R Shen C McBride H Li X Fu A Oliphant DL Barker MS Chee, Genome Res 2004 14 878 885 10.1101/gr.2167504 15123585
12. Quantitative Gene Expression Profiling in Formalin-Fixed, Paraffin-Embedded Tissues Using Universal Bead Arrays. M Bibikova D Talantov E Chudin JM Yeakley J Chen D Doucet E Wickham D Atkins D Barker M Chee Y Wang J Fan, Am J Pathol 2004 165 1799 1807 15509548
13. RO Duda PE Hart DG Stork, Pattern Classification New York, NY: John Wiley and Sons 2 2001
14. Gene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases. L Xu SS Shen Y Hoshida A Subramanian K Ross J Brunet SN Wagner S Ramaswamy JP Mesirov RO Hynes, Mol Cancer Res 2008 6 760 769 10.1158/1541-7786.MCR-07-0344 18505921
15. Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data. S Dudoit J Fridlyand TP Speed, Journal of the American Statistical Association 2002 97 77 87 10.1198/016214502753479248
16. VN Vapnik, Statistical Learning Theory New York, NY: Wiley-Interscience 1998
17. A Agresti, An Introduction to Categorical Data Analysis Hoboken, New Jersey: Wiley-Interscience 2 2007
18. Bias in error estimation when using cross-validation for model selection. S Varma R Simon, BMC Bioinformatics 2006 7 91 10.1186/1471-2105-7-91 16504092
19. Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. PJ Rousseeuw, Journal of Computational and Applied Mathematics 1987 20 53 65 10.1016/0377-0427(87)90125-7 (Pubitemid 18528483)
20. Evaluation of the interobserver reproducibility of Gleason grading of prostatic adenocarcinoma using tissue microarrays. A De la Taille A Viellefond N Berger E Boucher M De Fromont A Fondimare V Molinié D Piron M Sibony F Staroz M Triller E Peltier N Thiounn MA Rubin, Hum Pathol 2003 34 444 9 10.1016/S0046-8177(03)00123-0 12792917
21. Interobserver variability between expert urologic pathologists for extraprostatic extension and surgical margin status in radical prostatectomy specimens. AJ Evans PC Henry TH Van der Kwast DC Tkachuk K Watson GA Lockwood NE Fleshner C Cheung EC Belanger MB Amin L Boccon-Gibod DG Bostwick L Egevad JI Epstein DJ Grignon EC Jones R Montironi M Moussa JM Sweet K Trpkov TM Wheeler JR Srigley, Am J Surg Pathol 2008 32 1503 12 10.1097/PAS.0b013e31817fb3a0 18708939
22. Interobserver reproducibility of Gleason grading: evaluation using prostate cancer tissue microarrays. M Burchardt R Engers M Müller T Burchardt R Willers JI Epstein R Ackermann HE Gabbert A de la Taille MA Rubin, J Cancer Res Clin Oncol 2008 134 1071 8 10.1007/s00432-008-0388-0 18392850
23. Integrative molecular concept modeling of prostate cancer progression. SA Tomlins R Mehra DR Rhodes X Cao L Wang SM Dhanasekaran S Kalyana-Sundaram JT Wei MA Rubin KJ Pienta RB Shah AM Chinnaiyan, Nat Genet 2007 39 41 51 10.1038/ng1935 17173048
24. Estrogen-Dependent Signaling in a Molecularly Distinct Subclass of Aggressive Prostate Cancer. SR Setlur KD Mertz Y Hoshida F Demichelis M Lupien S Perner A Sboner Y Pawitan O Andren LA Johnson J Tang H Adami S Calza AM Chinnaiyan D Rhodes S Tomlins K Fall LA Mucci PW Kantoff MJ Stampfer S Andersson E Varenhorst J Johansson M Brown TR Golub MA Rubin, J Natl Cancer Inst 2008 100 815 825 10.1093/jnci/djn150 18505969
25. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Y Benjamini Y Hochberg, Journal of the Royal Statistical Society. Series B (Methodological) 1995 57 289 300
26. Molecular Diagnosis of Burkitt's Lymphoma. SS Dave K Fu GW Wright LT Lam P Kluin E Boerma TC Greiner DD Weisenburger A Rosenwald G Ott H Muller-Hermelink RD Gascoyne J Delabie LM Rimsza RM Braziel TM Grogan E Campo ES Jaffe BJ Dave W Sanger M Bast JM Vose JO Armitage JM Connors EB Smeland S Kvaloy H Holte RI Fisher TP Miller E Montserrat WH Wilson M Bahl H Zhao L Yang J Powell R Simon WC Chan LM Staudt the Lymphoma/Leukemia Molecular Profiling Project, N Engl J Med 2006 354 2431 2442 10.1056/NEJMoa055759 16760443
27. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. T Sorlie CM Perou R Tibshirani T Aas S Geisler H Johnsen T Hastie MB Eisen M van de Rijn SS Jeffrey T Thorsen H Quist JC Matese PO Brown D Botstein PE Lonning A Borresen-Dale, Proceedings of the National Academy of Sciences 2001 98 10869 10874 10.1073/pnas.191367098 (Pubitemid 32878711)
28. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. A Bhattacharjee WG Richards J Staunton C Li S Monti P Vasa C Ladd J Beheshti R Bueno M Gillette M Loda G Weber EJ Mark ES Lander W Wong BE Johnson TR Golub DJ Sugarbaker M Meyerson, Proc Natl Acad Sci USA 2001 98 13790 13795 10.1073/pnas.191502998 11707567
29. Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. TR Golub DK Slonim P Tamayo C Huard M Gaasenbeek JP Mesirov H Coller ML Loh JR Downing MA Caligiuri CD Bloomfield ES Lander, Science 1999 286 531 537 10.1126/science.286.5439.531 10521349
30. Mortality Results from a Randomized Prostate-Cancer Screening Trial. GL Andriole RL Grubb SS Buys D Chia TR Church MN Fouad EP Gelmann PA Kvale DJ Reding JL Weissfeld LA Yokochi ED Crawford B O'Brien JD Clapp JM Rathmell TL Riley RB Hayes BS Kramer G Izmirlian AB Miller PF Pinsky PC Prorok JK Gohagan CD Berg the PLCO Project Team, N Engl J Med 2009 360 1310 9 10.1056/NEJMoa0810696 19297565
31. Screening and Prostate-Cancer Mortality in a Randomized European Study. FH Schroder J Hugosson MJ Roobol TL Tammela S Ciatto V Nelen M Kwiatkowski M Lujan H Lilja M Zappa LJ Denis F Recker A Berenguer L Maattanen CH Bangma G Aus A Villers X Rebillard T van der Kwast BG Blijenberg SM Moss HJ de Koning A Auvinen the ERSPC Investigators, N Engl J Med 2009 360 1320 8 10.1056/NEJMoa0810084 19297566
32. A comparison of the morphological features of cancer arising in the transition zone and in the peripheral zone of the prostate. DR Greene TM Wheeler S Egawa JK Dunn PT Scardino, J Urol 1991 146 1069 76 1895423
33. Allelic loss in locally metastatic, multisampled prostate cancer. WA Sakr JA Macoska P Benson DJ Grignon SR Wolman JE Pontes JD Crissman, Cancer Res 1994 54 3273 7 7515768
34. Chromosomal anomalies in prostatic intraepithelial neoplasia and carcinoma detected by fluorescence in situ hybridization. J Qian DG Bostwick S Takahashi TJ Borell JF Herath MM Lieber RB Jenkins, Cancer Res 1995 55 5408 14 7585610
35. Evidence of independent origin of multiple tumors from patients with prostate cancer. L Cheng SY Song TG Pretlow FW Abdul-Karim HJ Kung DV Dawson WS Park YW Moon ML Tsai WM Linehan MR Emmert-Buck LA Liotta Z Zhuang, J Natl Cancer Inst 1998 90 233 7 10.1093/jnci/90.3.233 9462681
36. Heterogeneity of Gleason grade in multifocal adenocarcinoma of the prostate. R Arora MO Koch JN Eble TM Ulbright L Li L Cheng, Cancer 2004 100 2362 6 10.1002/cncr.20243 15160339
37. Characterization of ERG, AR and PTEN Gene Status in Circulating Tumor Cells from Patients with Castration-Resistant Prostate Cancer. G Attard JF Swennenhuis D Olmos AH Reid E Vickers R A'Hern R Levink F Coumans J Moreira R Riisnaes NB Oommen G Hawche C Jameson E Thompson R Sipkema CP Carden C Parker D Dearnaley SB Kaye CS Cooper A Molina ME Cox LW Terstappen JS de Bono, Cancer Res 2009 69 2912 2918 10.1158/0008-5472.CAN-08-3667 19339269
38. Characterization of TMPRSS2-ERG fusion high-grade prostatic intraepithelial neoplasia and potential clinical implications. J Mosquera S Perner EM Genega M Sanda MD Hofer KD Mertz PL Paris J Simko TA Bismar G Ayala RB Shah M Loda MA Rubin, Clin Cancer Res 2008 14 3380 5 10.1158/1078-0432.CCR-07- 5194 18519767
39. TMPRSS2-ERG fusion heterogeneity in multifocal prostate cancer: clinical and biologic implications. M Barry S Perner F Demichelis MA Rubin, Urology 2007 70 630 3 10.1016/j.urology.2007.08.032 17991527
40. Heterogeneity of TMPRSS2 Gene Rearrangements in Multifocal Prostate Adenocarcinoma: Molecular Evidence for an Independent Group of Diseases. R Mehra B Han SA Tomlins L Wang A Menon MJ Wasco R Shen JE Montie AM Chinnaiyan RB Shah, Cancer Res 2007 67 7991 7995 10.1158/0008-5472.CAN-07-2043 17804708
41. Complex patterns of ETS gene alteration arise during cancer development in the human prostate. J Clark G Attard S Jhavar P Flohr A Reid J De-Bono R Eeles P Scardino J Cuzick G Fisher MD Parker CS Foster D Berney G Kovacs CS Cooper, Oncogene 2008 27 1993 2003 10.1038/sj.onc.1210843 17922029
42. Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma. Y Hoshida A Villanueva M Kobayashi J Peix DY Chiang A Camargo S Gupta J Moore MJ Wrobel J Lerner M Reich JA Chan JN Glickman K Ikeda M Hashimoto G Watanabe MG Daidone S Roayaie M Schwartz S Thung HB Salvesen S Gabriel V Mazzaferro J Bruix SL Friedman H Kumada JM Llovet TR Golub, N Engl J Med 2008 359 1995 2004 10.1056/NEJMoa0804525 18923165
43. A Tissue Biomarker Panel Predicting Systemic Progression after PSA Recurrence Post-Definitive Prostate Cancer Therapy. T Nakagawa TM Kollmeyer BW Morlan SK Anderson EJ Bergstralh BJ Davis YW Asmann GG Klee KV Ballman RB Jenkins, PLoS ONE 2008 3 2318 10.1371/journal.pone.0002318 18846227
44. Gene Panel Model Predictive of Outcome in Men at High-Risk of Systemic Progression and Death From Prostate Cancer After Radical Retropubic Prostatectomy. JC Cheville RJ Karnes TM Therneau F Kosari J Munz L Tillmans E Basal LJ Rangel E Bergstralh IV Kovtun C Savci-Heijink EW Klee G Vasmatzis, J Clin Oncol 2008 26 3930 3936 10.1200/JCO.2007.15.6752 18711181
45. Gene expression correlates of clinical prostate cancer behavior. D Singh PG Febbo K Ross DG Jackson J Manola C Ladd P Tamayo AA Renshaw AV D'Amico JP Richie ES Lander M Loda PW Kantoff TR Golub WR Sellers, Cancer Cell 2002 1 203 209 10.1016/S1535-6108(02)00030-2 12086878
46. Gene Expression Alterations in Prostate Cancer Predicting Tumor Aggression and Preceding Development of Malignancy. YP Yu D Landsittel L Jing J Nelson B Ren L Liu C McDonald R Thomas R Dhir S Finkelstein G Michalopoulos M Becich J Luo, J Clin Oncol 2004 22 2790 2799 10.1200/JCO.2004.05.158 15254046
47. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. J Lapointe C Li JP Higgins M van de Rijn E Bair K Montgomery M Ferrari L Egevad W Rayford U Bergerheim P Ekman AM DeMarzo R Tibshirani D Botstein PO Brown JD Brooks JR Pollack, Proc Natl Acad Sci USA 2004 101 811 816 10.1073/pnas.0304146101 14711987
48. Gene expression profiling predicts clinical outcome of prostate cancer. GV Glinsky AB Glinskii AJ Stephenson RM Hoffman WL Gerald, J Clin Invest 2004 113 913 923 15067324
49. Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer. GV Glinsky O Berezovska AB Glinskii, J Clin Invest 2005 115 1503 1521 10.1172/JCI23412 15931389
50. TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. F Demichelis K Fall S Perner O Andren F Schmidt SR Setlur Y Hoshida J Mosquera Y Pawitan C Lee H Adami LA Mucci PW Kantoff S Andersson AM Chinnaiyan J Johansson MA Rubin, Oncogene 2007 26 4596 4599 10.1038/sj.onc.1210237 17237811
51. Duplication of the fusion of TMPRSS2 to ERG sequences identifies fatal human prostate cancer. G Attard J Clark L Ambroisine G Fisher G Kovacs P Flohr D Berney CS Foster A Fletcher WL Gerald H Moller V Reuter JS De Bono P Scardino J Cuzick CS Cooper, Oncogene 2008 27 253 263 10.1038/sj.onc.1210640 17637754
52. Prevalence of TMPRSS2-ERG fusion prostate cancer among men undergoing prostate biopsy in the United States. J Mosquera R Mehra MM Regan S Perner EM Genega G Bueti RB Shah S Gaston SA Tomlins JT Wei MC Kearney LA Johnson JM Tang AM Chinnaiyan MA Rubin MG Sanda, Clin Cancer Res 2009 15 4706 4711 10.1158/1078-0432.CCR-08-2927 19584163
53. Prostate cancer of transition zone origin lacks TMPRSS2-ERG gene fusion. CC Guo G Zuo D Cao P Troncoso BA Czerniak, Mod Pathol 2009 22 866 871 10.1038/modpathol.2009.57 19396154
54. Isolation of rare circulating tumour cells in cancer patients by microchip technology. S Nagrath LV Sequist S Maheswaran DW Bell D Irimia L Ulkus MR Smith EL Kwak S Digumarthy A Muzikansky P Ryan UJ Balis RG Tompkins DA Haber M Toner, Nature 2007 450 1235 1239 10.1038/nature06385 18097410
55. Detection of Mutations in EGFR in Circulating Lung-Cancer Cells. S Maheswaran LV Sequist S Nagrath L Ulkus B Brannigan CV Collura E Inserra S Diederichs AJ Iafrate DW Bell S Digumarthy A Muzikansky D Irimia J Settleman RG Tompkins TJ Lynch M Toner DA Haber, N Engl J Med 2008 359 366 377 10.1056/NEJMoa0800668 18596266