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  • Oncogenomics
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Genome-wide screening for complete genetic loss in prostate cancer by comparative hybridization onto cDNA microarrays

Abstract

We demonstrate that comparative genomic hybridization (CGH) onto cDNA microarrays may be used to carry out genome-wide screens for regions of genetic loss, including homozygous (complete) deletions that may represent the possible location of tumour suppressor genes in human cancer. Screening of the prostate cancer cell lines LNCaP, PC3 and DU145 allowed the mapping of specific regions where genome copy number appeared altered and led to the identification of two novel regions of complete loss at 17q21.31 (500 kb spanning STAT3) and at 10q23.1 (50–350 kb spanning SFTPA2) in the PC3 cell line.

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References

  • Aurich-Costa J, Vannier A, Gregoire E, Nowak F and Cherif D . (2001). Genes Chromosomes Cancer, 30, 143–160.

  • Bednarek AK, Keck-Waggoner CL, Daniel RL, Laflin KJ, Bergsagel PL, Kiguchi K, Brenner AJ and Aldaz CM . (2001). Cancer Res., 61, 8068–8073.

  • Bromberg JF . (2001). Bioessays, 23, 161–169.

  • Cai WW, Mao JH, Chow CW, Damani S, Balmain A and Bradley A . (2002). Nat. Biotechnol., 20, 393–396.

  • Chapman RS, Lourenco PC, Tonner E, Flint DJ, Selbert S, Takeda K, Akira S, Clarke AR and Watson CJ . (1999). Genes Dev., 13, 2604–2616.

  • Chekmareva MA, Hollowell CM, Smith RC, Davis EM, LeBeau MM and Rinker-Schaeffer CW . (1997). Prostate, 33, 271–280.

  • Clark J, Edwards S, John M, Flohr P, Gordon T, Maillard K, Giddings I, Brown C, Bagherzadeh A, Campbell C, Shipley J, Wooster R and Cooper CS . (2002). Genes Chromosomes Cancer, 34, 104–114.

  • Cleveland WS . (1979). J. Am. Stat. Assoc., 74, 829–936.

  • Cleveland WS and Devlin SJ . (1988). J. Am. Stat. Assoc., 83, 596–610.

  • Dammann R, Li C, Yoon JH, Chin PL, Bates S and Pfeifer GP . (2000). Nat. Genet., 25, 315–319.

  • England NL, Cuthbert AP, Trott DA, Jezzard S, Nobori T, Carson DA and Newbold RF . (1996). Carcinogenesis, 17, 1567–1575.

  • Forozan F, Mahlamaki EH, Monni O, Chen Y, Veldman R, Jiang Y, Gooden GC, Ethier SP, Kallioniemi A and Kallioniemi OP . (2000). Cancer Res., 60, 4519–4525.

  • Friend SH, Bernards R, Rogelj S, Weinberg RA, Rapaport JM, Albert DM and Dryja TP . (1986). Nature, 323, 643–646.

  • Hahn SA, Schutte M, Hoque AT, Moskaluk CA, da Costa LT, Rozenblum E, Weinstein CL, Fischer A, Yeo CJ, Hruban RH and Kern SE . (1996). Science, 271, 350–353.

  • Heiskanen MA, Bittner ML, Chen Y, Khan J, Adler KE, Trent JM and Meltzer PS . (2000). Cancer Res., 60, 799–802.

  • Hyytinen ER, Saadut R, Chen C, Paull L, Koivisto PA, Vessela RL, Frierson Jr HF and Dong JT . (2002). Genes Chromosomes Cancer, 34, 306–312.

  • Kamb A, Gruis NA, Weaver-Feldhaus J, Liu Q, Harshman K, Tavtigian SV, Stockert E, Day III RS, Johnson BE and Skolnick MH . (1994). Science, 264, 436–440.

  • Khubchandani KR and Snyder JM . (2001). FASEB J., 15, 59–69.

  • Li J, Yen C, Liaw D, Podsypanina K, Bose S, Wang SI, Puc J, Miliaresis C, Rodgers L, McCombie R, Bigner SH, Giovanella BC, Ittmann M, Tycko B, Hibshoosh H, Wigler MH and Parsons R . (1997). Science, 275, 1943–1947.

  • Minami M, Inoue M, Wei S, Takeda K, Matsumoto M, Kishimoto T and Akira S . (1996). Proc. Natl. Acad. Sci. USA, 93, 3963–3966.

  • Monni O, Barlund M, Mousses S, Kononen J, Sauter G, Heiskanen M, Paavola P, Avela K, Chen Y, Bittner ML and Kallioniemi A . (2001). Proc. Natl. Acad. Sci. USA, 98, 5711–5716.

  • Morton RA, Ewing CM, Nagafuchi A, Tsukita S and Isaacs WB . (1993). Cancer Res., 53, 3585–3590.

  • Nakajima K, Yamanaka Y, Nakae K, Kojima H, Ichiba M, Kiuchi N, Kitaoka T, Fukada T, Hibi M and Hirano T . (1996). EMBO J., 15, 3651–3658.

  • Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connel JX, Zhu S, Fero M, Sherlock G, Pollack JR, Brown PO, Botsein D and van de Rijn M . (2002). The Lancet, 359, 1301–1307.

  • Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW and Albertson DG . (1998). Nat. Genet., 20, 207–211.

  • Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D and Brown PO . (1999). Nat. Genet., 23, 41–46.

  • Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kumura K, Law S, Myambo K, Palmer J, Ylstra B, Yue JP, Gray JW, Jain AN, Pinkel D and Albertson DG . (2001). Nat. Genet., 29, 263–264.

  • Sozzi G, Veronese ML, Negrini M, Baffa R, Cotticelli MG, Inoue H, Tornielli S, Pilotti S, De Gregorio L, Pastorino U, Pierotti MA, Ohta M, Huebner K and Croce CM . (1996). Cell, 85, 17–26.

  • Spiotto MT and Chung TD . (2000a). Prostate, 42, 88–98.

  • Spiotto MT and Chung TD . (2000b). Prostate, 42, 186–195.

  • Srivastava M, Bubendorf L, Srikantan V, Fossom L, Nolan L, Glasman M, Leighton X, Fehrle W, Pittaluga S, Raffeld M, Koivisto P, Willi N, Gasser TC, Kononen J, Sauter G, Kallioniemi OP, Srivastava S and Pollard HB . (2001). Proc. Natl. Acad. Sci. USA, 98, 4575–4580.

  • Uchida T, Wang C, Sato T, Gao J, Takashima R, Irie A, Ohori M and Koshiba K . (1999). Int. J. Cancer, 84, 19–23.

  • Yang YH, Buckley MJ and Speed TP . (2001). Brief Bioinform. JID-100912837, 2, 341–349.

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Acknowledgements

We thank Cancer Research UK and National Cancer Research Institute for funding this work and Christine Bell for typing the manuscript.

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Correspondence to Colin S Cooper.

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Clark, J., Edwards, S., Feber, A. et al. Genome-wide screening for complete genetic loss in prostate cancer by comparative hybridization onto cDNA microarrays. Oncogene 22, 1247–1252 (2003). https://doi.org/10.1038/sj.onc.1206247

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