It is widely recognized that acquired genomic aberrations, leading to loss of function of tumor suppressor genes or gain of function of protooncogenes, are the driving force behind cellular neoplastic transformation (Hanahan and Weinberg, 2000). The increased knowledge of the human genome and the advances in the field of biotechnology have provided us with powerful tools for high-throughput characterization of these alterations in cancer samples. Novel microarray platforms with genome-wide coverage at escalating resolutions give promise of quickly uncovering the genetic events driving neoplastic transformation, which have previously gone undetected.
In this chapter we summarize the stateof- the-art in the fast-evolving field of genomic microarrays, highlighting some of the advantages and pitfalls of different array platforms and analyses techniques. We also review the relative contribution of this new technology to the knowledge of prostate cancer genetics, with an emphasis on its potential use in a clinical setting.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
REFERENCES
Abdulkadir, S.A., Magee, J.A., Peters, T.J., Kaleem, Z., Naughton, C.K., Humphrey, P.A., and Milbrandt, J. 2002. Conditional loss of Nkx3.1 in adult mice induces prostatic intraepi-thelial neoplasia. Mol. Cell Biol. 22: 1495–1503
Barrett, M.T., Scheffer, A., Ben Dor, A., Sampas, N., Lipson, D., Kincaid, R., Tsang, P., Curry, B., Baird, K., Meltzer, P.S., Yakhini, Z., Bruhn, L., and Laderman, S. 2004. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl. Acad. Sci. USA 101: 17765–17770
Cerveira, N., Ribeiro, F.R., Peixoto, A., Costa, V., Henrique, R., Jerónimo, C., and Teixeira, M.R. 2006. TMPRSS2-ERG gene fusion causing ERG overexpression precedes chromosome copy number changes in prostate carcinomas and paired HGPIN lesions. Neoplasia 8: 826–832
Clark, J., Edwards, S., Feber, A., Flohr, P., John, M., Giddings, I., Crossland, S., Stratton, M.R., Wooster, R., Campbell, C., and Cooper, C.S. 2003. Genome-wide screening for complete genetic loss in prostate cancer by comparative hybridization onto cDNA microarrays. Oncogene 22: 1247–1252
Epstein, J.I. 2004. Diagnosis and reporting of limited adenocarcinoma of the prostate on needle biopsy. Mod. Pathol. 17: 307–315
Gaur, U., and Aggarwal, B.B. 2003. Regulation of proliferation, survival and apoptosis by members of the TNF superfamily. Biochem. Pharmacol. 66: 1403–1408
Halvorsen, O.J., Haukaas, S.A., and Akslen, L.A. 2003. Combined loss of PTEN and p27 expression is associated with tumor cell proliferation by Ki-67 and increased risk of recurrent disease in localized prostate cancer. Clin. Cancer Res. 9: 1474–1479
Hanahan, D., and Weinberg, R.A. 2000. The hallmarks of cancer. Cell 100: 57–70
Hayat, MA. Ed. 2004–2006. Immunohistochemistry and In Situ Hybridization of Human Carcinomas. Elsevier/Academic, San Diego, CA
Hermans, K.G., van Marion, R., Van Dekken, H., Jenster, G., van Weerden, W.M., and Trapman, J. 2006. TMPRSS2:ERG fusion by translocation or interstitial deletion is highly relevant in androgen-dependent prostate cancer, but is bypassed in late-stage androgen receptor-negative prostate cancer. Cancer Res. 66: 10658–10663
Hughes, S., Yoshimoto, M., Beheshti, B., Houlston, R.S., Squire, J.A., and Evans, A. 2006. The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression. B.M.C. Genomics 7: 65
Iljin, K., Wolf, M., Edgren, H., Gupta, S., Kilpinen, S., Skotheim, R.I., Peltola, M., Smit, F., Verhaegh, G., Schalken, J., Nees, M., and Kallioniemi, O. 2006. TMPRSS2 fusions with oncogenic ETS factors in prostate cancer involve unbalanced genomic rearrangements and are associated with HDAC1 and epigenetic reprogramming. Cancer Res. 66: 10242–10246
Kallioniemi, A., Kallioniemi, O.P., Sudar, D., Rutovitz, D., Gray, J.W., Waldman, F., and Pinkel, D. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818–821
Kim, M.J., Bhatia-Gaur, R., Banach-Petrosky, W.A., Desai, N., Wang, Y., Hayward, S.W., Cunha, G.R., Cardiff, R.D., Shen, M.M., and Abate-Shen, C. 2002. Nkx3.1 mutant mice recapitulate early stages of prostate carcinogenesis. Cancer Res. 62: 2999–3004
King, C.R., and Long, J.P. 2000. Prostate biopsy grading errors: a sampling problem? Int. J. Cancer 90: 326–330
Kononen, J., Bubendorf, L., Kallioniemi, A., Barlund, M., Schraml, P., Leighton, S., Torhorst, J., Mihatsch, M.J., Sauter, G., and Kallioniemi, O.P. 1998. Tissue microarraysfor high-throughput molecular profiling of tumor specimens. Nat. Med. 4: 844–847
Kwabi-Addo, B., Giri, D., Schmidt, K., Podsypanina, K., Parsons, R., Greenberg, N., and Ittmann, M. 2001. Haploinsufficiency of the Pten tumor suppressor gene promotes prostate cancer progression. Proc. Natl. Acad. Sci. USA 98: 11563–11568
Lai, W.R., Johnson, M.D., Kucherlapati, R., and Park, P.J. 2005. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 21: 3763–3770
Liu, W., Chang, B., Sauvageot, J., Dimitrov, L., Gielzak, M., Li, T., Yan, G., Sun, J., Sun, J., Adams, T.S., Turner, A.R., Kim, J.W., Meyers, D.A., Zheng, S.L., Isaacs, W.B., and Xu, J. 2006. Comprehensive assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping array. Genes Chromosomes Cancer 45: 1018–1032
Mitelman, F. 2000. Recurrent chromosome aberrations in cancer. Mutat. Res. 462: 247–253
Paris, P.L., Albertson, D.G., Alers, J.C., Andaya, A., Carroll, P., Fridlyand, J., Jain, A.N., Kamkar, S., Kowbel, D., Krijtenburg, P.J., Pinkel, D., Schroder, F.H., Vissers, K.J., Watson, V.J., Wildhagen, M.F., Collins, C., and Van Dekken, H. 2003. High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microar-rays. Am. J. Pathol. 162: 763–770
Paris, P.L., Andaya, A., Fridlyand, J., Jain, A.N., Weinberg, V., Kowbel, D., Brebner, J.H., Simko, J., Watson, J.E., Volik, S., Albertson, D.G., Pinkel, D., Alers, J.C., van der Kwast, T.H., Vissers, K.J., Schroder, F.H., Wildhagen, M.F., Febbo, P.G., Chinnaiyan, A.M., Pienta, K.J., Carroll, P.R., Rubin, M.A., Collins, C., and Van Dekken, H. 2004. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum. Mol. Genet. 13: 1303–1313
Perner, S., Demichelis, F., Beroukhim, R., Schmidt, F.H., Mosquera, J.M., Setlur, S., Tchinda, J., Tomlins, S.A., Hofer, M.D., Pienta, K.G., Kuefer, R., Vessella, R., Sun, X.W., Meyerson, M., Lee, C., Sellers, W.R., Chinnaiyan, A.M., and Rubin, M.A. 2006. TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. Cancer Res. 66: 8337–8341
Perner, S., Mosquera, J.M., Demichelis, F., Hofer, M.D., Paris, P.L., Simko, J., Collins, C., Bismar, T.A., Chinnaiyan, A.M., De Marzo, A.M., and Rubin, M.A. 2007. TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion. Am. J. Surg. Pathol. 31: 882–888
Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.L., Chen, C., Zhai, Y., Dairkee, S.H., Ljung, B.M., Gray, J.W., and Albertson, D.G. 1998. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20: 207–211
Pollack, J.R., Perou, C.M., Alizadeh, A.A., Eisen, M.B., Pergamenschikov, A., Williams, C.F., Jeffrey, S.S., Botstein, D., and Brown, P.O. 1999. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23: 41–46
Ribeiro, F.R., Diep, C.B., Jeronimo, C., Henrique, R., Lopes, C., Eknaes, M., Lingjaerde, O.C., Lothe, R.A., and Teixeira, M.R. 2006a. Statistical dissection of genetic pathways involved in prostate carcinogenesis. Genes Chromosomes Cancer 45: 154–163
Ribeiro, F.R., Jerónimo, C., Henrique, R., Fonseca, D., Oliveira, J., Lothe, R.A., and Teixeira, M.R. 2006b. 8q gain is an independent predictor of poor survival in diagnostic needle biopsies from prostate cancer suspects. Clin. Cancer Res. 12: 3961–3970
Ribeiro, F.R., Henrique, R., Hektoen, M., Berg, M., Jerónimo, C., Teixeira, M.R., and Lothe, R.A. 2006c. Comparison of chromosomal and array-based comparative genomic hybridization for the detection of genomic imbalances in primary prostate carcinomas. Mol. Cancer 5: 33
Saramaki, O., and Visakorpi, T. 2007. Chromosomal aberrations in prostate cancer. Front. Biosci. 12: 3287–3301
Saramaki, O.R., Porkka, K.P., Vessella, R.L., and Visakorpi, T. 2006. Genetic aberrations in prostate cancer by microarray analysis. Int. J. Cancer 119: 1322–1329
Seth, A., and Watson, D.K. 2005. ETS transcription factors and their emerging roles in human cancer. Eur. J. Cancer 41: 2462–2478
Solinas-Toldo, S., Lampel, S., Stilgenbauer, S., Nickolenko, J., Benner, A., Döhner, H., Cremer, T., and Lichter, P. 1997. Matrix-based compara-tive genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20: 399–407
Tan, D.S., Lambros, M.B., Natrajan, R., and Reis-Filho, J.S. 2007. Getting it right: designing microarray (and not ‘microawry’) comparative genomic hybridization studies for cancer research. Lab. Invest. 87: 737–754
Teixeira, M.R., Ribeiro, F.R., Eknaes, M., Waehre, H., Stenwig, A.E., Giercksky, K.E., Heim, S., and Lothe, R.A. 2004. Genomic analysis of prostate carcinoma specimens obtained via ultrasound-guided needle biopsy may be of use in preopera-tive decision-making. Cancer 101: 1786–1793
Tomlins, S.A., Rhodes, D.R., Perner, S., Dhanasekaran, S.M., Mehra, R., Sun, X.W., Varambally, S., Cao, X., Tchinda, J., Kuefer, R., Lee, C., Montie, J.E., Shah, R.B., Pienta, K.J., Rubin, M.A., and Chinnaiyan, A.M. 2005. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310: 644–648
Torring, N., Borre, M., Sorensen, K.D., Andersen, C.L., Wiuf, C., and Orntoft, T.F. 2007. Genome-wide analysis of allelic imbalance in prostate cancer using the Affymetrix 50K SNP mapping array. Br. J. Cancer 96: 499–506
Van Dekken, H., Paris, P.L., Albertson, D.G., Alers, J.C., Andaya, A., Kowbel, D., van der Kwast, T.H., Pinkel, D., Schroder, F.H., Vissers, K.J., Wildhagen, M.F., and Collins, C. 2004. Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis. Genes Chromosomes Cancer 39: 249–256
van Duin, M., van Marion, R., Vissers, K., Watson, J.E., van Weerden, W.M., Schroder, F.H., Hop, W.C., van der Kwast, T.H., Collins, C., and Van Dekken, H. 2005. High-resolution array comparative genomic hybridization of chromosome arm 8q: evaluation of genetic progression markers for prostate cancer. Genes Chromosomes Cancer 44: 438–449
Verhagen, P.C., van Duijn, P.W., Hermans, K.G., Looijenga, L.H., van Gurp, R.J., Stoop, H., van der Kwast, T.H., and Trapman, J. 2006. The PTEN gene in locally progressive prostate cancer is preferentially inactivated by bi-allelic gene deletion. J. Pathol. 208: 699–707
Vijayakumar, S., Hall, D.C., Reveles, X.T., Troyer, D.A., Thompson, I.M., Garcia, D., Xiang, R., Leach, R.J., Johnson-Pais, T.L., and Naylor, S.L. 2006. Detection of recurrent copy number loss at Yp11.2 involving TSPY gene cluster in prostate cancer using array-based comparative genomic hybridization. Cancer Res. 66: 4055–4064
Wang, J., Cai, Y., Ren, C., and Ittmann, M. 2006. Expression of variant TMPRSS2/ERG fusion messenger RNAs is associated with aggressive prostate cancer. Cancer Res. 66: 8347–8351
Watson, J.E., Doggett, N.A., Albertson, D.G., Andaya, A., Chinnaiyan, A., Van Dekken, H., Ginzinger, D., Haqq, C., James, K., Kamkar, S., Kowbel, D., Pinkel, D., Schmitt, L., Simko, J.P., Volik, S., Weinberg, V.K., Paris, P.L., and Collins, C. 2004. Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancer. Oncogene 23: 3487–3494
Watson, S.K., deLeeuw, R.J., Horsman, D.E., Squire, J.A., and Lam, W.L. 2007. Cytogenetically balanced translocations are associated with focal copy number alterations. Hum. Genet. 120: 795–805
Wicker, N., Carles, A., Mills, I.G., Wolf, M., Veerakumarasivam, A., Edgren, H., Boileau, F., Wasylyk, B., Schalken, J.A., Neal, D.E., Kallioniemi, O., and Poch, O. 2007. A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. B.M.C. Genomics 8: 84
Wolf, M., Mousses, S., Hautaniemi, S., Karhu, R., Huusko, P., Allinen, M., Elkahloun, A., Monni, O., Chen, Y., Kallioniemi, A., and Kallioniemi, O.P. 2004. High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microar-rays: impact of copy number on gene expression. Neoplasia 6: 240–247
Ylstra, B., van den Ijssel, P., Carvalho, B., Brakenhoff, R.H., and Meijer, G.A. 2006. BAC to the future! or oligonucleotides: a perspective for microarray comparative genomic hybridization (array CGH). Nucleic Acids Res. 34: 445–450
Zhao, H., Kim, Y., Wang, P., Lapointe, J., Tibshirani, R., Pollack, J.R., and Brooks, J.D. 2005. Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines. Prostate 63: 187–197
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer Science + Business Media B.V
About this chapter
Cite this chapter
Ribeiro, F.R., Skotheim, R.I., Henrique, R., Teixeira, M.R. (2008). Array-Based Comparative Genomic Hybridization in Prostate Cancer: Research and Clinical Applications. In: Hayat, M.A. (eds) General Methods and Overviews, Lung Carcinoma and Prostate Carcinoma. Methods of Cancer Diagnosis, Therapy, and Prognosis, vol 2. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8442-3_30
Download citation
DOI: https://doi.org/10.1007/978-1-4020-8442-3_30
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-8441-6
Online ISBN: 978-1-4020-8442-3
eBook Packages: MedicineMedicine (R0)