Course content:
1.) Knowledge bases in molecular biology
Central Dogma and ENCODE project: genes, proteins, active RNA molecules and regulatory elements
UCSD Genome Browser, GeneCards and Uniprot knowledge bases. NGL – an example of protein structure visualization application.
From a network of gene and protein interactions to the clinical phenotype.
Knowledge bases of physiological pathways of genetic, metabolic, and protein interactions and applications for their visualization
Knowledgebase of genetic inheritance in human and application for the integration of clinical genotype and phenotype information.
2.) Determining a genotype: genome and exome sequencing
The modern sequencing methodology - data collection, and the key role played by computers in their processing.
The alignment between sequencing fragments and the template genome and its visualization.
The basics of variant impact estimation and their impact on the patological phenotype . The position of the variants relative to the active genomic elements.
Mutations in exons and missense mutations in proteins.
Alignment of protein sequences from different species and conservation of positions on the protein sequence.
3)Regulation and gene expression
Gene expression and its regulation in health and disease.
High throughput methods for gene expression analysis (ChIPSeq, methylation analysis, microarrays; RNASeq and mass spectrometry).
The Cancer Genome Atlas. Somatic mutations and gene expression in cancer.
4) Variation in human genotype and phenotype
Variation in human genotype (polymorphisms, genetic predisposition, and inheritance; de novo and somatic mutations.
Databases of common and clinical variations in human genotype
Analysis and exchange of knowledge about patological genotype and phenotypes
5) Molecular diagnostics:
Knowledge gained by high throughput methods and its integration in clinical practice
CRISPR-cas9 methodology and genetic engineering and its application in medicine