Medical Genomics - Šárka Pospíšilová
Medical Genomics - Šárka Pospíšilová

PhD Topics

1.  Detailed genomic variant analysis for cancer patient stratification and treatment prognosis

Supervisor: Vojtěch Bystrý, Ph.D.

Annotation: Detailed molecular characterisation of the tumor or of patient predisposition in cases of hereditary forms of disease is a state of the art approach for high risk cancer patients’ diagnosis and treatment prognosis. Next Generation Sequencing (NGS) is a relatively novel analytical technique allowing for accurate detection of somatic variants presented in tumor samples and inherited germline variants.

However due to massive parallel nature of NGS data a high quality computational processing is essential for correct analysis and thus prognosis. Even though general techniques for NGS data variant detection are already quite standardised, such generic approaches tend to fail in a more problematic cases and therefore to design more detailed, disease specific analysis is of an utmost importance. The aim of the PhD study will be to improve variant calling and variant characterisation for clinical samples in problematic regions such as genes with pseudogenes or repetitive regions and to design and implement novel systems for disease specific variant prioritisation.

Student will work with NGS systems to analyse the cancer sample data for genetic abnormalities associated with the specific diseases.

RG: Šárka Pospíšilová Research Group

Keywords: Next Generation Sequencing, NGS, cancer