72847 - Applied Genomics

Learning outcomes

At the end of the course, the student acquires the theoretical and practical bases for autonomously conducting genomic analyzes, in particular: i) reconstruction and characterization of eukaryotic and prokaryotic genomes; ii) reconstruction and analysis of transcriptomes; iii) identification of the interactions between proteins, DNA and RNA; iv) identification of epigenetic modifications; v) identification of regulation modules; vi) identification of pathological variants, for diagnosis and prognosis, and reconstruction of the molecular mechanisms of pathologies; vii) personalized intervention strategies based on the genomic characteristics of the individual

Course contents

Genome analysis:

• Modern definition of the genome
• Gene expression regulation, epigenetic modifications.
• Major and recent sequencing platforms.
• Application of sequencing technologies to the reconstruction of the eukaryotic and prokaryotic genome, to the analysis of genome variation in different individuals and populations, to the reconstruction and analysis of the transcriptome, for mapping interactions between genomic DNA and proteins, for the identification of epigenetic modifications (e.g. cytosine methylation), for the identification of long-range interactions between genomic loci

Applications:

• Molecular diagnosis
• Association between genome and diagnosis/prognosis
• Genome-wide association studies
• Quantitative traits
• Strategies for the personalisation of therapies based on individual genomic characteristics

Laboratory module. The practical part of the course consists of exercises on the use of the UCSC genome browser to learn how to access and analyze genome-wide data, and on the use of the web-server Galaxy for the analysis of sequencing data.

Readings/Bibliography

Articles and reviews indicated by the teacher.

Teaching methods

Lectures and PC work assignments. Practical use of UCSC genome browser and of Galaxy for accessing and analyzing genomic data

Assessment methods

The exam assesses if the student knows the organization of eukaryotic and prokaryotic genomes, the genomic analysis techniques and their application to medicine and pharmacology, and how to analyze gene expression and its regulation. The exam will also assess if the student knows how to access UCSC Genome database, and how to retrieve and analyze genomic data using the UCSC genome browser and Galaxy.

The exam consists of: a) an evaluation of the methodologies described in the laboratory; b) a written exam on the course arguments, and c) an optional oral exam.
The maximum score is 30.

Teaching tools

PC, internet, videoprojector, board.

Bioinformatic laboratory at the Biotecnology Education Center at Battiferro teaching complex.

Office hours

See the website of Fabrizio Ferrè