In this article we computed the associations between changes in the DNA copy number (Copy Number Aberrations, CNA), and variation in gene expression, from our Colonomics data. As a novelty with regard to other works, here we took the stromal component of the sample into account. We consider important the purity of the tumor in order to accurately calculate the changes in the number of copies in tumor samples, given the diploid nature of the infiltrating stromal cells. Additionally, a sub-study was carried out by categorizing the samples analyzed according to their Consensus Molecular Subtypes (CMS). We found a great heterogeneity of CNA between the samples. The aberrations in CNA showed an impact on gene expression and contributed greatly to deregulate relevant signaling pathways in colon cancer. Finally, from a methodological perspective, we have found that the proportion of tumor stroma may bias the estimation of CNA. To avoid this effect, an adjusted cut-off definition proportional to the estimated stromal content produced more accurate results.
The article was published in the British Journal of Cancer, with Ma Henar Alonso as a lead author.