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Detailed genomic variant analysis for cancer patient stratification and treatment prognosis

  • Full or part time
  • Application Deadline
    Friday, March 15, 2019
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

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

Applicants who wish to pursue a degree at the CEITEC PhD programme must hold the equivalent of a Master’s degree (MSc) in similar field (four or five year undergraduate degree). The application can be submitted before obtaining the Master’s degree, however, the applicant should obtain the degree within five month after the application deadline.
Keywords: Next Generation Sequencing, NGS, cancer

Funding Notes

Admission for studies, student registration for the full-time study programme and proper fulfilment of student duties constitute the student’s right to a regular scholarship of 22 000 CZK (850 EUR). Information is available at View Website

Living costs and other practicalities available at View Website

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