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Lecturer(s)
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Kuchařová Anna, Mgr. Ph.D.
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Plíhal Ondřej, RNDr. Ph.D.
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Slavkovský Rastislav, Ing. Ph.D.
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Course content
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The lectures cover the following topics: Genomics and its embedding in medicine. Genome projects. Structure of DNA and RNA, genetic information, size of genomes, basic structural regions in human DNA. Transcriptome and Gene Expression Study Methods. Structure and classification of RNA and its modification. Control of gene expression in prokaryotes and eukaryotes. Transcription factors and regulators. DNA microarrays. Functional genomics - methods of direct and reverse genetics, methods based on gene knockout and methods based on overproduction, cloning and GFP technology. Physical mapping of genomes, cytogenetic, optical methods, mapping using radiation hybrids, physical contig maps. Use of STS markers. Genome mapping based on sequencing techniques, 2nd and 3rd generation sequencing techniques. Methods of studying the human genome and transcriptome, methods based on targeted panels, labeling and enrichment. Analysis of whole genome sequencing data. De novo sequencing, Whole Genome Shotgun (WGS) sequencing, assembly and alignment of sequence data, variant calling. Sequencing of short and long fragments. File types and basic steps in data processing. Genetic markers and molecular changes in tumor cells. Oncogenes, tumor suppressors, molecular and informative genomic methods of studying tumors. Tumor formation and progression vs genomic instability and epigenetics, DNA repair defects. Genomics and translational medicine, omic approaches. Variants in genetic information and their classification by region in the genome. Point mutations, silent, large-scale rearrangements in the genome. Genetic diseases and their inheritance, examples of diseases, structural chromosome aberrations. Record of genetic variants.
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Learning activities and teaching methods
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Monologic Lecture(Interpretation, Training), Dialogic Lecture (Discussion, Dialog, Brainstorming)
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Learning outcomes
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Study of genome organization and gene functions, and the modern methods and aproaches used for.
Upon completion of the course, the student will be able to: - describe the structure and organization of the human genome; - explain the differences between coding and non-coding DNA and characterize repetitive elements of the human genome; - describe and classify the main types of RNA molecules found in human cells; - explain in detail the mechanisms of transcriptional regulation and describe the methodological approaches for transcriptomics; - explain the principles and purpose of physical genome mapping; - outline the basic principles of current genome-mapping methods, including cytogenetic and optical mapping, the construction of physical contig maps, and the use of sequence-tagged site (STS) markers; - describe and compare the principles of the main second- and third-generation sequencing technologies; - summarize the historical development of human genome sequencing, identify the principal stages of genome sequencing, assembly, and analysis, and describe the basic methodological approaches involved; - describe the principles of sequencing data analysis and explain concepts such as read depth and sequencing coverage; - define and classify the different types of genetic variants and provide examples of common genetic disorders; - define the different modes of inheritance, describe the methodological approaches used to investigate different types of genetic disease, and use standard nomenclature to describe genetic variants.
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Prerequisites
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A basic understanding of the principles of molecular biology is required, particularly the flow of genetic information, the basic mechanisms of transcription and translation, and the differences between prokaryotic and eukaryotic organisms.
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Assessment methods and criteria
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Oral exam
oral exam, in extent of the lectures
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Recommended literature
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Birren a kol. (1997). Genome analysis - Mapping Genomes. New York.
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Brdička, R. Lidský genom na rozhraní tisíciletí. Grada Publishing, Praha, 2001.
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Cantor, C.R., Smith, C.L. Genomics: The Science and Technology Behind the Human Genome Project, John Wiley and Sons, New York, 1999..
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Cullis, C.A. Plant Genomics and Proteomics. John Wiley and Sons, Inc., New York, 2004.
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Gibson, G., Muse, V.S. (2004). A Primer of Genome Science. Sinauer Associates, Inc., Sunderland.
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Hunt, S. P., Livesey, F. Functional Genomics: A Practical Approach. Oxford University Press, Oxford, 2000..
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Meksem, K., Kahl, G. (2005). The Handbook of Plant Genome Mapping. Wiley-VCH Verlag.
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Primrose, S.B. Principles of Genome Analysis: A guide to mapping and sequencing DNA from different organisms. Blackwell Science Inc., 1998..
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Rashidi, H.H., Buehler, L.K. Bioinformatics Basics. CRC Press, Boca Raton, 2000..
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