BMC Cancer 2007, 7:226 http://www.biomedcentral.com/1471-2407/7/226 Table 1: Distribution of 5918 malignant epithelial tumors by clinico-pathological entities, sorted by frequency of occurrence. Diagnosis Breast carcinoma Prostate carcinoma Gastric carcinoma Ovarian carcinoma Colorectal adenocarcinoma (CRC) Hepatocellular adenocarcinoma (HCC) Head-neck squamous cell carcinoma (HNSCC) Thyroid carcinoma Non-small cell lung carcinoma (NSCLC) Cervical carcinoma Esophagus carcinoma (ES) Renal carcinoma (RCC) Nasopharynx carcinoma (NPC) Bladder carcinoma Neuroendocrine ca. and carcinoid (NE) Melanocytic (MEL) Pancreas adenocarcinoma (PAC) Cholangio carcinomas Small cell lung carcinoma (SCLC) Endometrial carcinoma Vulva carcinoma Squamous malignancies of the skin (SQS) ICD-O-3 codes(1) Locus code(s) No. of cases 81xx ... 86xx C50 814x C61 81xx ... 86xx C16 81xx ... 86xx C56 8140, 8480 C17, C18 817x C22 8070 C01, C09, C06, C10, C12, C13, C14, C30, C32 81xx ... 87xx C73 81xx ... 86xx, excl. 8041, 8045, 824x C34 81xx ... 86xx C53 81xx ... 86xx C15 81xx ... 86xx C64 8010, 8070 C11 81xx ... 86xx C67 824x (all) 872x ... 877x (all) 814x C25 816x C221, C24 8041, 8045 C34 81xx ... 86xx C55 81xx ... 86xx C51 807x C44 667 600 529 449 430 371 339 314 254 226 209 195 177 169 138 99 88 63 63 56 53 52 377 tumors from entities with <50 cases were omitted from this list. (1) ICD codes and locus codes are listed as used for automatic assignment of cases to the disease groups; groups do not necessarily contain cases assigned to the whole range of ICD codes. imbalance status ("1" = gain, "-1" = loss, "2" = high level gain) for each of 862 chromosomal bands (UCSC Genome Bioinformatics [35], Golden Path mapping, May 2004 edition), or subsets thereof. For statistical analysis, software packages available as part of the Bioconductor [36] project for the R programming language [37] were used. Visualization of genomic imbal- ance profiles was performed by custom Perl routines using the GD.pm interface [38] to the GD graphics library [39]. As a robust measure for genomic instability, the number of chromosomes per case with one or more imbalanced segments was determined. Results and Discussion In the base data set comprised of 5918 malignant cases analyzed by CGH, breast carcinomas and precursor lesions constituted the largest subgroup, followed by neo- plasias of the prostate gland and stomach (Table 1). The median aberration number per case (number of chromo- somes with at least one abnormal segment) showed a wide range (Figure 1), from 0 (squamous skin neoplasias, thyroid carcinomas) to 12 (small cell lung carcinomas; SCLC). For some of the entities at the low end of this spec- trum, a certain bias through frequent biopsies at early stages can be suspected (e.g. tumors of skin, thyroid, pros- tate), although pre-maligant tumors had been excluded from the analysis. Imbalance hot spots in clinico-pathological entities In the overall aberration profile, gains on chromosomal band 8q24 represented the most common imbalance, fol- lowed by gains involving regions on 20q, 1q, 3q, 17q, 7(q) and 5p, as well as other changes (Figure 2). In the following overview, the most frequent regions involved in genomic imbalances are listed, with detailed locus and frequency information for regional hot-spots. Since overall aberration frequencies vary greatly between entities, no absolute cut-off values (e.g. 10% or 20%) were used when selecting these regions. Instead, genomic regions with clear separation from overall background in the imbalance histograms were selected for each entity and sorted in descending frequency of occurrence. Gains and losses were evaluated separately. For each entity, few outstanding observations are dis- cussed and selected literature is provided. Histologic sub- types are only mentioned in few entities. Because not all involved regions can be discussed here with respect to putative genetic targets, a selection of well characterized oncogenes and tumor suppressor genes with involvement in epithelial neoplasias is provided as part of Table 2. Page 3 of 15 (page number not for citation purposes)