Statistical dissection of genetic pathways involved in prostate carcinogenesis

Genes Chromosomes and Cancer

Volumn 45, Issue 2, 2006, Pages 154-163

  Ribeiro, Franclim R ^a,b   Diep, Chieu B ^b   Jerónimo, Carmen ^a,c   Henrique, Rui ^a,d   Lopes, Carlos ^a,d   Eknæs, Mette ^b   Lingjærde, Ole Christian ^e   Lothe, Ragnhild A ^b,e   Teixeira, Manuel R ^a,d  

^a PORTUGUESE ONCOLOGY INSTITUTE   (Portugal)

^b OSLO UNIVERSITY HOSPITAL   (Norway)

^c UNIVERSIDADE FERNANDO PESSOA   (Portugal)

^d UNIVERSITY OF PORTO   (Portugal)

^e UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ADVANCED CANCER; ARTICLE; CANCER GROWTH; CANCER INVASION; CARCINOGENESIS; CHROMOSOME 10Q; CHROMOSOME 13Q; CHROMOSOME 6Q; CHROMOSOME 7Q; CHROMOSOME 8P; CHROMOSOME 8Q; CHROMOSOME LOSS; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; GENETIC ANALYSIS; GENOMIC INSTABILITY; GLEASON SCORE; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; METASTASIS; PRIORITY JOURNAL; PROGNOSIS; PROSTATE CANCER; PROSTATE HYPERTROPHY; RECURRENT CANCER;

AGED; HUMANS; MALE; MIDDLE AGED; MULTIVARIATE ANALYSIS; NUCLEIC ACID HYBRIDIZATION; PROSTATIC HYPERPLASIA; PROSTATIC NEOPLASMS;

EID: 31944449020     PISSN: 10452257     EISSN: 10982264     Source Type: Journal    
DOI: 10.1002/gcc.20279     Document Type: Article

References (49)

1. Affifi A, Azen S. 1979. Statistical analysis: a computer oriented approach. New York: Academic Press, p 318-324.
2. Aldenderfer MS, Blashfield RK. 1984. Cluster analysis. Sage University paper series on quantitative applications in the social sciences. 07-044. Beverly Hills, CA: Sage.
3. Alers JC, Krijtenburg PJ, Vis AN, Hoedemaeker RF, Wildhagen MF, Hop WC, van Der Kwast TT, Schroder FH, Tanke HJ, Van Dekken H. 2001. Molecular cytogenetic analysis of prostatic adenocarcinomas from screening studies: early cancers may contain aggressive genetic features. Am J Pathol 158:399-406.
4. Alers JC, Rochat J, Krijtenburg PJ, Hop WC, Kranse R, Rosenberg C, Tanke HJ, Schroder FH, Van Dekken H. 2000. Identification of genetic markers for prostatic cancer progression. Lab Invest 80:931-942.
5. Bettendorf O, Schmidt H, Eltze E, Gockel I, Semjonow A, Burger H, Bocker W, Brandt B. 2005. Cytogenetic changes and loss of heterozygosity in atypical adenomatous hyperplasia, in carcinoma of the prostate and in non-neoplastic prostate tissue using comparative genomic hybridization and multiplex-PCR. Int J Oncol 26: 267-274.
6. Cher ML, Bova GS, Moore DH, Small EJ, Carroll PR, Pin SS, Epstein JI, Isaacs WB, Jensen RH. 1996. Genetic alterations in untreated metastases and androgen-independent prostate cancer detected by comparative genomic hybridization and allelotyping. Cancer Res 56:3091-3102.
7. Chu LW, Troncoso P, Johnston DA, Liang JC. 2003. Genetic markers useful for distinguishing between organ-confined and locally advanced prostate cancer. Genes Chromosomes Cancer 36: 303-312.
8. Diep CB, Kleivi K, Ribeiro FR, Teixeira MR, Lingjærde OC, Lothe RA. 2005. The order of genetic events associated with colorectal cancer progression deduced from meta-analysis of copy number changes. Genes Chromosomes Cancer, in press.
9. Doll JA, Zhu X, Furman J, Kaleem Z, Torres C, Humphrey PA, Donis-Keller H. 1999. Genetic analysis of prostatic atypical adenomatous hyperplasia (adenosis). Am J Pathol 155:967-971.
10. Dong JT, Chen C, Stultz BG, Isaacs JT, Frierson HF, Jr. 2000. Deletion at 13q21 is associated with aggressive prostate cancers. Cancer Res 60:3880-3883.
11. Dysvik B, Jonassen I. 2001. J-Express: exploring gene expression data using Java. Bioinformatics 17:369-370.
12. El Gedaily A, Bubendorf L, Willi N, Fu W, Richter J, Moch H, Mihatsch MJ, Sauter G, Gasser TC. 2001. Discovery of new DNA amplification loci in prostate cancer by comparative genomic hybridization. Prostate 46:184-190.
13. Etzioni R, Penson DF, Legier JM, di Tommaso D, Boer R, Gann PH, Feuer EJ. 2002. Overdiagnosis due to prostate-specific antigen screening: lessons from U.S. prostate cancer incidence trends. J Natl Cancer Inst 94:981-990.
14. Foster CS, Bostwick DG, Bonkhoff H, Damber JE, van der KT, Montironi R, Sakr WA. 2000. Cellular and molecular pathology of prostate cancer precursors. Scand J Urol Nephrol Supp 205: 19-43.
15. Fu W, Bubendorf L, Willi N, Moch H, Mihatsch MJ, Sauter G, Gasser TC. 2000. Genetic changes in clinically organ-confined prostate cancer by comparative genomic hybridization. Urology 56:880-885.
16. Gleason DF, Mellinger GT. 1974. Prediction of prognosis for prostatic adenocarcinoma by combined histological grading and clinical staging. J Urol 111:58-64.
17. Hermanek P, Hutter RVP, Sobin LH, Wagner G, Wittekind C. 1997. Prostate. In: Illustrated guide to the TNM/pTNM classification of malignant tumors. Hermanek P, Hutter RVP, Sobin LH, Wagner G, Wittekind C, editors. Heidelberg, Germany: Springer-Verlag, p 278-280.
18. Höglund M, Frigyesi A, Sall T, Gisselsson D, Mitelman F. 2005. Statistical behavior of complex cancer karyotypes. Genes Chromosomes Cancer 42:327-341.
19. Höglund M, Gisselsson D, Hansen GB, Mitelman F. 2004a. Wilms tumors develop through two distinct karyotypic pathways. Cancer Genet Cytogenet 150:9-15.
20. Höglund M, Gisselsson D, Hansen GB, White VA, Sall T, Mitelman F, Horsman D. 2004b. Dissecting karyotypic patterns in malignant melanomas: temporal clustering of losses and gains in melanoma karyotypic evolution. Int J Cancer 108:57-65.
21. Höglund M, Gisselsson D, Mandahl N, Johansson B, Mertens F, Mitelman F, Sall T. 2001. Multivariate analyses of genomic imbalances in solid tumors reveal distinct and converging pathways of karyotypic evolution. Genes Chromosomes Cancer 31:156-171.
22. Höglund M, Gisselsson D, Sall T, Mitelman F. 2002. Coping with complexity. Multivariate analysis of tumor karyotypes. Cancer Genet Cytogenet 135:103-109.
23. ISCN. 1995. An international system for human cytogenetic nomenclature. Mitelman F, editor. Basel, Switzerland: S. Karger.
24. Jemal A, Tiwari RC, Murray T, Ghafoor A, Samuels A, Ward E, Feuer EJ, Thun MJ. 2004. Cancer statistics, 2004. CA Cancer J Clin 54:8-29.
25. Jeronimo C, Usadel H, Henrique R, Oliveira J, Lopes C, Nelson WG, Sidransky D. 2001. Quantitation of GSTP1 methylation in non-neoplastic prostatic tissue and organ-confined prostate adenocarcinoma. J Natl Cancer Inst 93:1747-1752.
26. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818-821.
27. Karayi MK, Markham AF. 2004. Molecular biology of prostate cancer. Prostate Cancer Prostatic Dis 7:6-20.
28. Kasahara K, Taguchi T, Yamasaki I, Kanada M, Yuri K, Shuin T. 2002. Detection of genetic alterations in advanced prostate cancer by comparative genomic hybridization. Cancer Genet Cytogenet 137:59-63.
29. Kirchhoff M, Gerdes T, Maahr J, Rose H, Bentz M, Dohner H, Lundsteen C. 1999. Deletions below 10 megabasepairs are detected in comparative genomic hybridization by standard reference intervals. Genes Chromosomes Cancer 25:410-413.
30. Kirchhoff M, Gerdes T, Rose H, Maahr J, Ottesen AM, Lundsteen C. 1998. Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals. Cytometry 31:163-173.
31. Kraggerud SM, Szymanska J, Abeler VM, Kaern J, Eknaes M, Heim S, Teixeira MR, Trope CG, Peltomaki P, Lothe RA. 2000. DNA copy number changes in malignant ovarian germ cell tumors. Cancer Res 60:3025-3030.
32. Kumar-Sinha C, Chinnaiyan AM. 2003. Molecular markers to identify patients at risk for recurrence after primary treatment for prostate cancer. Urology 62(Suppl 1):19-35.
33. Matsuda K, Matsuyama H, Hara T, Yoshihiro S, Oga A, Kawauchi S, Furuya T, Izumi H, Naito K, Sasaki K. 2004. DNA sequence copy number aberrations in prostate cancers: a comparison of comparative genomic hybridization data between Japan and European countries. Cancer Genet Cytogenet 152:119-123.
34. Mattfeldt T, Woher H, Trijic D, Gottfried HW, Kestler HA. 2002. Chromosomal regions in prostatic carcinomas studied by comparative genomic hybridization, hierarchical cluster analysis and self-organizing feature maps. Anal Cell Pathol 24:167-179.
35. Mitelman F, Johansson B, Mertens F. 2005. Mitelman database of chromosome aberrations in cancer. Available at: http://cgap.nci. nih.gov/Chromosomes/ Mitelman.
36. Nelson WG, De Marzo AM, Isaacs WB. 2003. Prostate cancer. N Engl J Med 349:366-381.
37. Nupponen NN, Kakkola L, Koivisto P, Visakorpi T. 1998. Genetic alterations in hormone-refractory recurrent prostate carcinomas. Am J Pathol 153:141-148.
38. Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schroder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, Van Dekken H. 2003. High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol 162: 763-770.
39. Rokman A, Koivisto PA, Matikainen MP, Kuukasjarvi T, Poutiainen M, Helin HJ, Karhu R, Kallioniemi OP, Schleutker J. 2001. Genetic changes in familial prostate cancer by comparative genomic hybridization. Prostate 46:233-239.
40. Schulz WA, Elo JP, Florl AR, Pennanen S, Santourlidis S, Engers R, Buchardt M, Seifert HH, Visakorpi T. 2002. Genomewide DNA hypomethylation is associated with alterations on chromosome 8 in prostate carcinoma. Genes Chromosomes Cancer 35:58-65.
41. Stanford JL, Feng Z, Hamilton AS, Gilliland FD, Stephenson RA, Eley JW, Albertsen PC, Harlan LC, Potosky AL. 2000. Urinary and sexual function after radical prostatectomy for clinically localized prostate cancer: the Prostate Cancer Outcomes Study. JAMA 283:354-360.
42. Steineck G, Helgesen F, Adolfsson J, Dickman PW, Johansson JE, Norlen BJ, Holmberg L. 2002. Quality of life after radical prostatectomy or watchful waiting. N Engl J Med 347:790-796.
43. Steiner T, Junker K, Burkhardt F, Braunsdorf A, Janitzky V, Schubert J. 2002. Gain in chromosome 8q correlates with early progression in hormonal treated prostate cancer. Eur Urol 41:167-171.
44. Teixeira MR, Ribeiro FR, Eknaes M, Waehre H, Stenwig AE, Giercksky KE, Heim S, Lothe RA. 2004. Genomic analysis of prostate carcinoma specimens obtained via ultrasound-guided needle biopsy may be of use in preoperative decision-making. Cancer 101:1786-1793.
45. Teixeira MR, Waehre H, Lothe RA, Stenwig AE, Pandis N, Giercksky KE, Heim S. 2000. High frequency of clonal chromosome abnormalities in prostatic neoplasms sampled by prostatectomy or ultrasound-guided needle biopsy. Genes Chromosomes Cancer 28:211-219.
46. Van Dekken H, Alers JC, Damen IA, Vissers KJ, Krijtenburg PJ, Hoedemaeker RF, Wildhagen MF, Hop WC, van der Kwast TH, Tanke HJ, Schroder FH. 2003. Genetic evaluation of localized prostate cancer in a cohort of forty patients: gain of distal 8q discriminates between progressors and nonprogressors. Lab Invest 83:789-796.
47. Visakorpi T, Kallioniemi AH, Syvänen AC, Hyytinen ER, Karhu R, Tammela T, Isola JJ, Kallioniemi OP. 1995. Genetic changes in primary and recurrent prostate cancer by comparative genomic hybridization. Cancer Res 55:342-347.
48. Woher H, Gottfried HW, Mattfeldt T. 2002a. Genetic changes in stage pT2N0 prostate cancer studied by comparative genomic hybridization. BJU Int 89:310-316.
49. Wolter H, Trijic D, Gottfried HW, Mattfeldt T. 2002b. Chromosomal changes in incidental prostatic carcinomas detected by comparative genomic hybridization. Eur Urol 41:328-334.