C7175en DNA diagnostics

Faculty of Science
Spring 2024
Extent and Intensity
2/0/0. 4 credit(s). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
doc. Mgr. Jan Lochman, Ph.D. (lecturer)
prof. RNDr. Omar Šerý, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Omar Šerý, Ph.D.
Department of Biochemistry – Chemistry Section – Faculty of Science
Supplier department: Department of Biochemistry – Chemistry Section – Faculty of Science
Prerequisites
Without preconditions.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
At the end of the course students should be able to understand and explain practical use of DNA diagnostics in human medicine, veterinary medicine etc.
Learning outcomes
At the end of the course students will understand principles of PCR methods, RealTime PCR, sequencing, next generation sequencing, restriction analysis, work with DNA databases, European Union legislation on in vitro medical devices, use of DNA diagnostics in medical practice. Students will have the theoretical knowledge of methods used in clinical laboratories for DNA diagnosis of bacterial and viral pathogens.
Syllabus
  • 1. General introduction, history of DNA diagnostics (discovery of DNA structure, discovery of PCR principle). 2. Principle of polymerase chain reaction - master mixes, template DNA, primers, buffer, dNTP, DNA polymerase, PCR steps, thermocycler, methods of multiplying DNA in vitro without using DNA polymerase. 3. Detection of amplified DNA, agarose gels, polyacrylamide gels, electrophoresis, PCR in situ, restriction analysis. 4. Real Time PCR, principle, sybrgreen, TaqMan, molecular beacons, detection of point polymorphisms, quantification by RealTime PCR, DNA isolation methods. 5. Principles and use of genotyping methods (RFLP methods, methods based on qPCR, SNaPshot method, chip technologies, CNV analysis). 6. Principles of NGS methods (library preparation, pyrosequencing, Illumina technology, Ion PGM system, nanoball sequencing). 7. Use of NGS methods in diagnostics (genome, exome, transcriptome, metagenome, resistome, targeted resequencing). 8. Modifications of PCR methods used in diagnostics, celiac disease diagnostics. 9. DNA diagnostics in medicine: legislative requirements for in vitro diagnostic medical devices (IVDR). 10. Medical virology: practical use of DNA diagnostics in direct virus detection. Detection of HIV, SARS-CoV-2, viral hepatitis, herpes viruses, papillomaviruses, etc. 11. Medical microbiology and parasitology: practical use of DNA diagnostics in direct detection of microorganisms. Detection of MTB, borrelia, chlamydia, mycoplasmas, ureaplasmas, etc.
Literature
  • PITT, Sarah J. Clinical microbiology for diagnostic laboratory scientists. Hoboken: Wiley-Blackwell, 2018, xv, 275. ISBN 9781118745854. info
  • Next generation sequencing based clinical molecular diagnosis of human genetic disorders. Edited by Lee-Jun C. Wong. Cham: Springer, 2017, viii, 364. ISBN 9783319564180. info
  • Clinical applications for next-generation sequencing. Edited by Urszula Demkow - Rafał Płoski. Amsterdam: Elsevier, 2016, xiv, 319. ISBN 9780128017395. info
  • Manual of commercial methods in clinical microbiology. Edited by Allan L. Truant. Washington: ASM Press, 2002, xix, 481. ISBN 1555811892. info
  • RAPLEY, Ralph. The nucleic acid protocols : handbook. Totowa, New Jersey: Humana Press, 1999, xxii, 1050. ISBN 0-89603-459-3. info
Teaching methods
Oral lectures with PowerPoint presentations, class discussion.
Assessment methods
Oral exam
Language of instruction
English
Further Comments
Study Materials
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2023, Autumn 2024, Spring 2025.
  • Enrolment Statistics (Spring 2024, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2024/C7175en