Assessment of Differentiation and Progression of Hepatic Tumors Using Array-Based Comparative Genomic Hybridization Doris Steinemann, Britta Skawran,

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Assessment of Differentiation and Progression of Hepatic Tumors Using Array-Based Comparative Genomic Hybridization Doris Steinemann, Britta Skawran, Thomas Becker, Marcel Tauscher, Anja Weigmann, Luzie Wingen, Sarah Tauscher, Tanja Hinrichsen, Sabine Hertz, Peer Flemming, Jacobus Flik, Birgit Wiese, Hans Kreipe, Peter Lichter, Brigitte Schlegelberger, Ludwig Wilkens Clinical Gastroenterology and Hepatology Volume 4, Issue 10, Pages 1283-1291 (October 2006) DOI: 10.1016/j.cgh.2006.07.010 Copyright © 2006 American Gastroenterological Association (AGA) Institute Terms and Conditions

Figure 1 Examples of genomic profiles of 1 HCA (N11), 1 HCC-G1 (N59), 1 HCC-G2 (N80), and 1 HCC-G3 (N16). Dark squares represent mean normalized T/R values for each clone computed as log2 ratio. Log2 ratios of each clone are ordered from chromosome 1 to Y according to their Mb position (ENSEMBL database, http://www.ensembl.org/Homo_sapiens/). The vertical lines separate the clones per chromosome; the dashed lines indicate centromeres. Clinical Gastroenterology and Hepatology 2006 4, 1283-1291DOI: (10.1016/j.cgh.2006.07.010) Copyright © 2006 American Gastroenterological Association (AGA) Institute Terms and Conditions

Figure 2 FISH on paraffin-embedded tissue sections from HCC cases with gains of 1q22 and 8q24 as detected by array-CGH. In cases (A) N91 and (B) N47 probes specific for 1q22 were hybridized together with centromere-specific probes for chromosome 1. Comparison of the number of signals for 1q22 (green) and cen1 (red) confirmed the gain of 1q22 in both cases. For tumors (C) N71 and (D) N37, high amplification with log ratios greater than 1 were revealed by array-CGH. Accordingly, in both cases, FISH using probes for 8q24 (green) and cen8 (red) showed a clear increase of signal numbers for 8q24 in relation to the centromere-specific probe for this chromosome. Interestingly, in tumor N37 there was a mixture of cells with no obvious amplification (arrowhead), whereas in other cells a high number of signals for 8q24 occurred in cluster-like aggregates (arrow) (original magnification: A and B, 10 × 100; C and D, 10 × 63). Clinical Gastroenterology and Hepatology 2006 4, 1283-1291DOI: (10.1016/j.cgh.2006.07.010) Copyright © 2006 American Gastroenterological Association (AGA) Institute Terms and Conditions

Figure 3 Genome-wide DNA copy number alterations of 34 HCAs and HCCs. Columns represent tumor samples; rows represent individual clones ordered by chromosome and genome positions. Chromosomal aberrations were classified as gains (green) or losses (red) when the smoothed normalized log2 ratios (as obtained by software package Smooth) were greater than 0.1 or less than −0.1, respectively. Hierarchic clustering (Euclidean distance, average linkage) was performed on all autosomal clones excluding clones with missing values in individual samples, using 1, 0, and −1 as values for gain, no aberration, and loss, respectively. The differentiation of tumors is shown by colored background at the bottom. Clinical Gastroenterology and Hepatology 2006 4, 1283-1291DOI: (10.1016/j.cgh.2006.07.010) Copyright © 2006 American Gastroenterological Association (AGA) Institute Terms and Conditions