Cristian Ruiz Moreno
DNA methylation biomarkers for the non-invasive diagnosis for brain cancer
Professor Henk Stunnrnberg, Radboud University, Netherlands
The primary objective of this ESR project is to identify new molecular blood biomarkers (methylated DNA) for brain cancer and use them for diagnostic purposes. The secondary aim is to use these non-invasive biomarkers for brain cancer classification and staging. Blood and serum samples will be obtained from partner IRE and purified DNA will be subjected to bisulfite as well as Ox-BS NGS sequencing (MethySeq) to identify 5methylcytosine and 5hydroxymethyl cytosine modifications. In the exploratory phase, DNA from patient samples will be subjected to whole genome bisulfite and ox-bisulfite sequencing (paired-end) to obtain an unbiased coverage of the DNA present in the samples. The depth of sequencing depends on the complexity of the DNA samples. Mapping and Quality Controls will be performed according to the recommendation by the International Human Epigenome consortium (www.ihecepigenomes.org). A first pass analysis will be performed to determine the complexity as well as the extend and genomic location (promoter, enhancer, CpG-islands etc) of the DNA modifications. Targeted approaches of DNA fragments will be employed to extend the analysis on a large cohort of patient sera.