PMC

mRNA expression levels of a short list of seven candidate genes for early onset CRC. Log transformed mRNA expression values plotted against age. Red bullets indicate copy number gain, green bullets indicate loss and grey bullets indicate normal copy number. Box plots for each of the patient groups are indicated for each gene.

Genes mapping to the chromosome bands with copy number aberrations associated with early onset CRC. Chromosomal sites gained or lost with statistical significance in the early compared to the late onset tumor group are shown in red or green boxes, respectively. Chromosomes with no aberrations or aberrations in centromere regions only, are shaded. Genes which have expression levels corresponding to chromosomal aberration, and concurrently located within the statistically significant regions are indicated within the boxes. Genes which also have significantly different expression level between early onset and late onset groups are further marked with green or red background.

Genomic profile across all chromosomes from 40 tumor samples. A) Copy number profile across all 40 colorectal carcinomas, including early onset (n = 23) and late onset (n = 17) tumors. Percentage of samples with gains is shown in red and losses in green. Gains and losses in the short arm of acrocentric chromosomes are not considered and further discussed. The centromere positions are indicated by dashed lines, and changes recorded at the p-arms and q-arms are shown to the left and right of the dashed lines, respectively. B) Copy number profiles of early onset (solid) as compared to late onset (line) colorectal carcinomas.

Study design comparing the tumor genomes of early onset and late onset colorectal cancer patients. Tumor samples from early onset and late onset CRC patients were analyzed with aCGH (DNA/genome level) and the data were integrated with the mRNA expression (RNA/transcriptome level) of the same samples. About 10 000 genes show corresponding DNA and RNA level. Exclusion of genes located outside chromosomal regions with statistically significant difference between the two patient groups resulted in 107 genes, summarized in Additional file . Further, exclusion of genes whose mRNA expression levels were not statistically significant between patients groups resulted in a short list of seven potential predisposing genes, as summarized in Table 3.