Title: “Epigenomic and Transcriptomic Analysis of Breast Cancer”
The aim of this project is a better understanding of the role of epigenetic modifications in breast cancer. More specifically we want to focus on modifications of the DNA methylome.
For this purpose DNA methylation data were acquired from almost 250 tissues samples (236 carcinoma and 12 normal) using the Illumina Infinium 450K Bead Chip technology. Because it is a recent technology there is not any consensus on the way to normalize the data. So we are first going to develop a pipeline for the preprocess of our data in a way that maximize biological significance. Then we want to use the CpG methylation pattern to cluster patients. To confirm and refine our results we also plan to realize a whole genome DNA methylation analysis on a few samples using MethylCap-Seq technology.
An RNA-Seq analysis is also planned on a few samples of each cluster obtained during the DNA methylation analysis. The aim is on one hand to refine breast cancer taxonomy for better survival predictions. On the other hand we also want to get a better understanding of the link between DNA methylation and gene expression. For this purpose we are going to infer causal models from methylation and expression data.
In conclusion we want to use to power of bioinformatics and machine learning to extract biological information from methylation data. The aims are on one hand to refine breast cancer taxonomy and on the other hand to get a better understanding of the link between DNA methylation modifications and cancer.