BMC Cancer 2007, 7:226 http://www.biomedcentral.com/1471-2407/7/226 of the project, the author has been supported through a grant from the Claussen-Simon-Stiftung. References 1. Patau K: The identification of individual chromosomes, espe- cially in man. Am J Hum Genet 1960, 12:250-276. 2. Crossen PE: Giemsa banding patterns of human chromo- somes. Clin Genet 1972, 3:169-179. 3. Speicher MR, Gwyn Ballard S, Ward DC: Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 1996, 12:368-375. 4. Veldman T, Vignon C, Schrock E, Rowley JD, Ried T: Hidden chro- mosome abnormalities in haematological malignancies detected by multicolour spectral karyotyping. Nat Genet 1997, 15:406-410. 5. Cremer T, Lichter P, Borden J, Ward DC, Manuelidis L: Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-spe- cific library probes. Hum Genet 1988, 80:235-246. 6. Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC: Delineation of individual human chromosomes in metaphase and inter- phase cells by in situ suppression hybridization using recom- binant DNA libraries. Hum Genet 1988, 80:224-234. 7. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Wald- man F, Pinkel D: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992, 5083:818-821. 8. Joos S, Scherthan H, Speicher MR, Schlegel J, Cremer T, Lichter P: Detection of amplified DNA sequences by reverse chromo- some painting using genomic tumor DNA as probe. Hum Genet 1993, 90(6):584-589. 9. Bentz M, Plesch A, Stilgenbauer S, Dohner H, Lichter P: Minimal sizes of deletions detected by comparative genomic hybridi- zation. Genes Chromosomes Cancer 1998, 2:172-175. 10. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P: Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997, 4:399-407. 11. 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, Albertson DG: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 2:207-211. 12. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO: Genome-wide analysis of DNA copy-number changes using cDNA microar- rays. Nat Genet 1999, 1:41-46. 13. Nowell PC, Hungerford DA: A minute chromosome in chronic granulocytic leukemia. Science 1960, 132:1497. 14. Rowley JD: Letter: A new consistent chromosomal abnormal- ity in chronic myelogenous leukaemia identified by quina- crine fluorescence and Giemsa staining. Nature 1973, 5405:290-293. 15. Manolov G, Manolova Y: Marker band in one chromosome 14 from Burkitt lymphomas. Nature 1972, 237:33-34. 16. Mrozek K, Heerema NA, Bloomfield CD: Cytogenetics in acute leukemia. Blood Rev 2004, 18:115-136. 17. Mitelman Database of Chromosome Aberrations in Cancer [http://cgap.nci.nih.gov/Chromosomes/Mitelman] 18. Speicher MR, du Manoir S, Schrock E, Holtgreve-Grez H, Schoell B, Lengauer C, Cremer T, Ried T: Molecular cytogenetic analysis of formalin-fixed, paraffin-embedded solid tumors by compar- ative genomic hybridization after universal DNA-amplifica- tion. Hum Mol Genet 1993, 11:1907-1914. 19. Knuutila S, Bjorkqvist AM, Autio K, Tarkkanen M, Wolf M, Monni O, Szymanska J, Larramendy ML, Tapper J, Pere H, El-Rifai W, Hemmer S, Wasenius VM, Vidgren V, Zhu Y: DNA copy number amplifica- tions in human neoplasms: review of comparative genomic hybridization studies. Am J Pathol 1998, 152:1107-1123. 20. Knuutila S, Aalto Y, Autio K, Bjorkqvist AM, El-Rifai W, Hemmer S, Huhta T, Kettunen E, Kiuru-Kuhlefelt S, Larramendy ML, Lushnikova T, Monni O, Pere H, Tapper J, Tarkkanen M, Varis A, Wasenius VM, Wolf M, Zhu Y: DNA copy number losses in human neo- plasms. Am J Pathol 1999, 155:683-694. 21. Gebhart E, Liehr T: Patterns of genomic imbalances in human solid tumors (Review). Int J Oncol 2000, 16:383-399. 22. Gebhart E: Genomic imbalances in human leukemia and lym- phoma detected by comparative genomic hybridization (Review). Int J Oncol 2005, 27:593-606. 23. Struski S, Doco-Fenzy M, Cornillet-Lefebvre P: Compilation of published comparative genomic hybridization studies. Cancer Genet Cytogenet 2002, 135:63-90. 24. Myllykangas S, Himberg J, Bohling T, Nagy B, Hollmen J, Knuutila S: DNA copy number amplification profiling of human neo- plasms. Oncogene 2006, 25:7324-7332. 25. Progenetix – cytogenetic abnormalities in human cancer [http://www.progenetix.net] 26. Baudis M, Cleary ML: Progenetix.net: an online repository for molecular cytogenetic aberration data. Bioinformatics 2001, 12:1228-1229. 27. Baudis M: Online database and bioinformatics toolbox to sup- port data mining in cancer cytogenetics. Biotechniques 2006, 40(3):269-272. 28. Schwaenen C, Nessling M, Wessendorf S, Salvi T, Wrobel G, Radl- wimmer B, Kestler HA, Haslinger C, Stilgenbauer S, Dohner H, Bentz M, Lichter P: Automated array-based genomic profiling in chronic lymphocytic leukemia: development of a clinical tool and discovery of recurrent genomic alterations. Proc Natl Acad Sci USA 2004, 4:1039-1044. 29. International Classification of Diseases for Oncology (ICD- O), Edition. In World Health Organization Third edition. Edited by: Fritz A, Percy C, Jack A, Sobin LH, Parkin MD. Geneva; 2000. 30. Speicher MR, Schoell B, du Manoir S, Schrock E, Ried T, Cremer T, Storkel S, Kovacs A, Kovacs G: Specific loss of chromosomes 1, 2, 6, 10, 13, 17, and 21 in chromophobe renal cell carcinomas revealed by comparative genomic hybridization. Am J Pathol 1994, 145:356-364. 31. Wild P, Giedl J, Stoehr R, Junker K, Boehm S, van Oers J, Zwarthoff E, Blaszyk H, Fine S, Humphrey P, Dehner L, Amin M, Epstein J, Hart- mann A: Genomic aberrations are rare in urothelial neo- plasms of patients 19 years or younger. J Pathol 2006. 32. Clausen OP, Aass HC, Beigi M, Purdie KJ, Proby CM, Brown VL, Mat- tingsdal M, Micci F, Kolvraa S, Bolund L, Deangelis PM: Are Keratoa- canthomas Variants of Squamous Cell Carcinomas? A Comparison of Chromosomal Aberrations by Comparative Genomic Hybridization. J Invest Dermatol 2006. 33. van Beers EH, van Welsem T, Wessels LF, Li Y, Oldenburg RA, Dev- ilee P, Cornelisse CJ, Verhoef S, Hogervorst FB, van't Veer LJ, Ned- erlof PM: Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differen- tial sets of genomic aberrations. Cancer Res 2005, 65:822-827. 34. The Perl Directory at Perl.org [http://www.perl.org] 35. UCSC Genome Bioinformatics [http://genome.ucsc.edu] 36. Bioconductor – open source software for bioinformatics [http://www.bioconductor.org] 37. The R Project for Statistical Computing [http://www.r- project.org] 38. GD.pm Perl interface to GD graphics library [http:// stein.cshl.org/WWW/software/GD/] 39. GD open source code library for the dynamic creation of images [http://www.libgd.org] 40. Vos CB, ter Haar NT, Rosenberg C, Peterse JL, Cleton-Jansen AM, Cornelisse CJ, van de Vijver MJ: Genetic alterations on chromo- some 16 and 17 are important features of ductal carcinoma in situ of the breast and are associated with histologic type. Br J Cancer 1999, 81:1410-1418. 41. Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG: Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006, 6:96. 42. Aubele M, Auer G, Braselmann H, Nahrig J, Zitzelsberger H, Quinta- nilla-Martinez L, Smida J, Walch A, Hofler H, Werner M: Chromo- somal imbalances are associated with metastasis-free survival in breast cancer patients. Anal Cell Pathol 2002, 24:77-87. 43. Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A, Fleming T, Eiermann W, Wolter J, Pegram M, Baselga J, Norton L: Use of chemotherapy plus a monoclonal antibody against Page 13 of 15 (page number not for citation purposes)