Diagnostics of gliomas based on circulating cell-free tumor DNA

Gliomas are incurable despite progress in surgery, radiotherapy and chemotherapy. Specific diagnosis of the type of glioma, early detection of molecular progression, characterization of critical mutations or epigenetic characteristics in individual patient give hope to improve treatment results. It is planned to develop a comprehensive diagnostic test based on analysis of the material obtained from the tumor via surgery or biopsy (targeted NGS of 700 genes). The Gliomed project will elaborate a liquid biopsy-type method based on tumor cfDNA in blood, which could be a quick and minimally invasive alternative to biopsy. The additional aims of the study are: comprehensive molecular characteristics of tumor genome and transcriptome as well as use of 3-D in vitro glioma cultures, i.a., under hypoxic conditions for screening of the content of stem cells and assessment of cells susceptibility to therapy in the environment of neoplastic niche.

The results will contribute to better understanding of glioma biology, will allow identification of new molecular biomarkers, potential therapeutic targets and will provide a practical model to investigate a response to treatment under hypoxia. Molecular diagnostic test would improve treatment results by therapy individualization and liquid biopsy will improve safety, comfort and enable to monitor disease course and treatment in a new way.

Cyfronet tasks

The Cyfronet team will undertake a series of bioinformatics and biostatistics analyses on tumor data. Information acquired from MR imaging and NGS sequencing of glioma cases will be thoroughly investigated to give answer to a set of challenging questions related to this type of tumor. The result of these analyses, collaboratively conducted with other project partners, will be the new liquid biopsy test validation.

Cyfronet will also act as the provider of adequate data storage space and computational power, to match the requirements of large-scale analyses to be undertaken in the course of the project. The tools available in the PLGrid Infrastructure will help the Gliomed researchers in efficient management of research data and analysis results.

Partners

• Medical University of Silesia (Katowice)
• Medical University of Warsaw
• Nencki Institute of Experimental Biology, Polish Academy of Sciences (Warsaw)
• Academic Computer Centre Cyfronet AGH (Krakow)
• Regional Science and Technology Center (Podzamcze)
• Oncogene Diagnostics Sp. z o.o. (Krakow)

Projekt współfinansowany przez Narodowe Centrum Badań i Rozwoju w ramach strategicznego programu badań naukowych i prac rozwojowych “Profilaktyka i leczenie chorób cywilizacyjnych - STRATEGMED ”