Volume 131, Issue 6, Pages 1913-1924 (December 2006) Recurrent Genomic Alterations With Impact on Survival in Colorectal Cancer Identified by Genome-Wide Array Comparative Genomic Hybridization  Mi–Young Kim, Seon–Hee Yim, Mi–Seon Kwon, Tae–Min Kim, Seung–Hun Shin, Hyun–Mi Kang, Charles Lee, Yeun–Jun Chung  Gastroenterology  Volume 131, Issue 6, Pages 1913-1924 (December 2006) DOI: 10.1053/j.gastro.2006.10.021 Copyright © 2006 AGA Institute Terms and Conditions

Figure 1 Genomic signature of 59 colorectal cancer cases. (A) Genome-wide profiles of 59 CRCs are presented in individual lanes. Intensity ratios are plotted schematically in different color scale, reflecting the extent of genomic gains (red) and losses (green) as indicated on the reference color bar. A total of 2981 BAC clones were ordered (x-axis) according to map positions and chromosomal order from 1pter to Yqter. (B) Frequencies of all significant gains and losses in 59 CRCs. Red bars denote copy number gain and green bars denote copy number loss. The boundaries of individual chromosomes and the location of centromeres are indicated by the vertical bars. Gastroenterology 2006 131, 1913-1924DOI: (10.1053/j.gastro.2006.10.021) Copyright © 2006 AGA Institute Terms and Conditions

Figure 2 Verification of array CGH copy number profiles using MLPA analysis. MLPA aneuploidy test kit (P095) peak profile of (A) normal tissue DNA and (B) tumor tissue DNA of CCRC80. Twelve peaks (numbered) are the examples of copy number gain, loss, or diploid on chromosomes 13, 18, 21, and X. (C) Tumor vs normal peak ratio plot (upper box) in linear chromosomal order and relevant array CGH plots (lower boxes). Red spots (copy number gained regions in array CGH plots) consistently show regions of MLPA ratio value above 1.3 (cut-off value for copy number gain, upper broken line), green spots (copy number lost regions in array CGH plots) show regions of MLPA ratio value below .7 (cut-off value for copy number loss, lower broken line), and yellow spots (unchanged regions in array CGH plots) show regions of MLPA ratio .7 to ∼1.3. Gastroenterology 2006 131, 1913-1924DOI: (10.1053/j.gastro.2006.10.021) Copyright © 2006 AGA Institute Terms and Conditions

Figure 3 Kaplan–Meier survival curves and examples of RARs. The survival curves for the cases with or without specific genomic changes are plotted using the Kaplan–Meier method. The RARs and clinicopathologic factors associated with poor survival are presented with significance level: (A) stage, (B) RAR-L1 on 1p36, (C) RAR-L4 on 1p31, and (D) RAR-L20 on 21q22. Representative diagrams of the 2 RARs showing statistically significant association with poor survival are presented in individual lanes with corresponding sample numbers: (E) RAR-L1 and (F) RAR-L20. Gastroenterology 2006 131, 1913-1924DOI: (10.1053/j.gastro.2006.10.021) Copyright © 2006 AGA Institute Terms and Conditions

Figure 4 Expression profile of CAMTA1 in 3 colorectal cancer cell lines (RKO, HT29, and HCT116) and 44 pairs (normal/tumor) of primary CRCs by real-time quantitative PCR. Human glyceraldehyde-3-phosphate dehydrogenase was used as the internal control. (A) Plot of tumor/normal intensity ratios illustrating CAMTA1 expression level. Red broken line shows the cut-off level for the criterion of low CAMTA1 (>40% decrease in tumor tissue compared with normal tissue). Asterisks represent the CRCs with RAR-L1. (B) Kaplan–Meier survival curves according to CAMTA1 expression level. Low CAMTA1 cases showed significantly poorer survival than those with intact CAMTA1. (C) Example of missense mutation (Pro–Ser) in exon 15 of CCRC71. Mutation in exon 15 in cancer tissue is presented as a black dot. Gastroenterology 2006 131, 1913-1924DOI: (10.1053/j.gastro.2006.10.021) Copyright © 2006 AGA Institute Terms and Conditions