Table 1.
A panel of 24 locus-specific FISH probes directed against 24 different regions localized in 20 different human chromosomes were used to validate the results obtained with the SNP arrays.
Figure 1.
Metastatic colorectal cancer genome for the 23 CRC patients studied.
In panel A an overall view of both the gained (blue areas) and lost (red areas) chromosome regions across the genome are shown for the 23 patients genotyped on the Affymetrix 500k SNP array platform. In panel B a summary plot showing the frequency of CN gains (plotted above zero values in the x-axis) and losses (plotted below zero values the x-axis) detected for each individual chromosome, is displayed. Those chromosome regions most frequently showing recurrent losses and gains by SNP arrays were localized in chromosomes 1p, 8p, 17p and 18, and involved the whole chromosome 7 and the 8q, 13q and 20q chromosome regions, respectively.
Figure 2.
Representative karyotype of a primary metastatic colorectal tumor as determined by the Affymetrix 500K SNP array genotyping platform, showing summary results for those chromosome gains/losses more frequently detected in the colorectal tumor samples analyzed (n = 23).
Table 2.
Most frequently detected small regions (<1300 kb) of gain and loss in primary sporadic colorectal tumors genotyped on the Affymetrix 500K SNP array platform (n = 23).
Table 3.
Most frequently detected extensively altered chromosome regions with CN changes (>1500 kb) in primary sporadic colorectal tumors genotyped on the Affymetrix 500K SNP array platform (n = 23).
Table 4.
Most frequently detected high-level amplified chromosome regions (average log2 copy number ratio ≥0.22) containing genes commonly associated with cancer in primary sporadic colorectal tumors genotyped on the Affymetrix 500K SNP array platform (n = 23).
Table 5.
Primary colorectal cancer with liver metastasis (n = 23): correlation between the numerical changes detected by each individual iFISH probe used and the CN changes identified for the corresponding single nucleotide polymorphisms (SNPs) through SNP array studies.
Figure 3.
Expression levels of MYC, MAP4K and BIRC7 mRNA as assessed by RQ-PCR in metastatic CRC tumors and their corresponding paired normal tissue (n = 18).
Note that MYC and BIRC7 mRNA levels from metastatic CRC tumours samples are significantly higher than in their paired normal tissues (p<0.0001). By contrast, MAP4K mRNA levels in metastatic CRC tumors are significantly lower than normal (p<0.0001).