| Lehrinhalte |
(*)PART 1 – Introduction to genomics
1. The Human Genome Project
- Definition of bioinformatics/genomics
- The Human Genome Project - the start of genomics
- Sequencing the human genome
- Assembly: paired-end and shotgun sequencing
- Main conclusions of the human genome project
2. Genomic variation
- Genomic variation
- From SNPs to copy number variants and their evolution
- HapMap project
- Uses of SNPs
3. Genome projects/ Comparative genomics
- Methods to detect genomic variation
- Sequencing Projects
- Understanding a genome sequence
- Structural features of a genome
4. Emerging sequencing technologies
- New sequencing technologies (NGS)
- Principles of next generation sequencing technologies
- Commercial platforms
- Uses of NGS
- Individual genomes
5. Application of genomics
- 3 study cases - why is genomics important?
- Genetics perspective - cure diseases
- Synthetic biology: build your own genome
- Evolutionary biology: Where do we come from?
- Commercializing genomics
- Ethical aspects
PART 2 – Introduction to databases (computer lab based)
1. Accessing information about DNA, proteins, diseases, and literature using the NCBI database
- Introduction into databases in general
- Overview of the NCBI website
- Accessing information: accession numbers, RefSeq, FASTA sequence, genome assembly
- NCBI databases: Gene, CCDS, Taxonomy, Nucleotide, Protein
- NCBI-based database to get information about genetic diseases: OMIM
- NCBI-based database for literature search: Pubmed
2. Polymorphisms, PCR, primer design and genotyping
- Definition of SNP, allele, genotype, haplotype
- dbSNP database and Hardy-Weinberg Equilibrium
- What is a PCR and how does it work?
- Primer design with Primer3Plus
- Design of restriction enzyme digests and genotyping assay using NEBCutter
- Polymorphisms associated with cancer using COSMIC database
- Polymorphisms within a population using gnomAD database
3. Genome Browsers and sequence alignments
- Two genome browsers: UCSC, ENSEMBL
- Definitions: homologs, paralogs, orthologs
- BLAST – Basic local alignment search tool
- How to use BLAST: pairwise and database sequence alignments
- Scoring Matrices
- How to interpret BLAST results
- Primer-BLAST
- Multiple sequence alignments using Clustal Omega
4. Protein analysis
- Introduction to proteins and protein structure
- Protein databases to get general information: UniProt, ExPASy (ProtParam)
- 3D structure of proteins using the Protein Data Bank (PDB)
- Analyze 3D protein structures using JmolS
- Mapping genomic variants to protein sequence and structure with VarMap
- The Human Protein Atlas
5. Revision and final report
- Clinical Report about a rare genetic variant/disease is used to practice the use of all databases and tools again discussed in the computer lab sessions. Students report their results within in a ‘Final Report’.
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