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Kotková Lucie

Academic Title: Mgr
Groups: Doctoral Student, LEM, Staff, Master Student, Bachelor Student

Master training

Optimization of library technology for multi-parallel sequencing in the colorectal cancer diagnostics.

Personalised therapy promises prolonged and better quality survival for patients with colorectal carcinoma. Mutation status of KRAS and NRAS genes is important in patients indicated for anti-EGFR treatment (cetuximab, panitumumab) because it predicts negative response to therapy. Mutational status of BRAF is considered to be a prognostic marker. Problems of commercially available genotyping kits based on next-generation sequencing approach are long and expensive processing of one sample. Preparation of sequencing library mostly takes from two to four steps which makes it time-consuming and it carries a high risk of possible mistakes. Newly developed fastRAS method enables one-step library preparation with fewer costs for genotyping one sample, it is more user friendly, faster comparing to standard methods and robust enough to process a sample without the need of technical replicates. The method had been validated and accredited for diagnostics.

Status: Graduated from 2015 to 2017.

Bachelor training

Molecular and genetic changes in glial tumors.

Identification of genetic changes typical for particular subtypes of glioma is crucial for the improvement of diagnostics and choosing personalised therapy. This thesis describes the detection of BRAF:KIAA1549 fusion, which is considered a possible diagnostic marker for pilocytic astrocytoma. Fusion was detected by polymerase chain reaction (PCR) in 25 % of examined brain tumours (2 out of 8), in 40% of pilocytic astrocytoma (2 out of 5) specifically. Fusion was also detected by fluorescent in situ hybridization (FISH) using a specifically labelled fluorescence DNA probe. Amplification of the PDGFRA gene is common in high-grade gliomas and is considered a possible prognostic factor. Amplification of PDGFRA was detected by FISH using specifically labelled fluorescence DNA probe in 5.6 % of brain tumours (2 out of 36). From the examined subset of brain tumours FFPE samples, only 57 % (36 out of 63) provided countable signals. The significant connection between FFPE sample age and quality of the provided signal was found.

Supervisor:
Status: Graduated from 2013 to 2015.
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