BMC Cancer Research article Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data Michael Baudis Address: Institute of Molecular Biology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Germany Email: Michael Baudis - mbaudis@gmail.com BioMed Central Open Access Published: 18 December 2007 BMC Cancer 2007, 7:226 doi:10.1186/1471-2407-7-226 This article is available from: http://www.biomedcentral.com/1471-2407/7/226 Received: 26 April 2007 Accepted: 18 December 2007 © 2007 Baudis; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Chromosomal abnormalities have been associated with most human malignancies, with gains and losses on some genomic regions associated with particular entities. Methods: Of the 15429 cases collected for the Progenetix molecular-cytogenetic database, 5918 malignant epithelial neoplasias analyzed by chromosomal Comparative Genomic Hybridization (CGH) were selected for further evaluation. For the 22 clinico-pathological entities with more than 50 cases, summary profiles for genomic imbalances were generated from case specific data and analyzed. Results: With large variation in overall genomic instability, recurring genomic gains and losses were prominent. Most entities showed frequent gains involving 8q2, while gains on 20q, 1q, 3q, 5p, 7q and 17q were frequent in different entities. Loss "hot spots" included 3p, 4q, 13q, 17p and 18q among others. Related average imbalance patterns were found for clinically distinct entities, e.g. hepatocellular carcinomas (ca.) and ductal breast ca., as well as for histologically related entities (squamous cell ca. of different sites). Conclusion: Although considerable case-by-case variation of genomic profiles can be found by CGH in epithelial malignancies, a limited set of variously combined chromosomal imbalances may be typical for carcinogenesis. Focus on the respective regions should aid in target gene detection and pathway deduction. Background The analysis of genomic abnormalities in malignant cell clones has been performed for decades. Introduced in the 1960s, the evaluation of stained metaphase preparations from tumor cells [1,2] has been widely employed in basic research as well as in clinical practice. For analysis of com- plex karyotypes, direct chromosomal inspection was recently enhanced through multicolour in-situ hybridiza- tion techniques: combinatorial multi-fluor FISH (M-FISH [3]) and multicolour spectral karyotyping (SKY [4]). In contrast to traditional or enhanced cytogenetic analy- sis, molecular-cytogenetic methods rely on tumor DNA as starting material for the exploration of genomic abnor- malities. While fluorescent in-situ hybridization (FISH [5,6]) allows for the detection of single or few numerical and structural genomic features in non-dividing cells, Comparative Genomic Hybridization (CGH [7,8]) per- mits the screening of the whole tumor genome for regional imbalances in the DNA content. Since CGH is based on the hybridization of tumor and reference DNA to standardized normal metaphase spreads, the spatial Page 1 of 15 (page number not for citation purposes)