72847 - APPLIED GENOMICS

Learning outcomes

At the end of the course the student has knowledge of the main experimental designs and tools applied in genetics and genomics and approaches for genetic and genomic data analysis, with an emphasis on vertebrate genomes including genetic mapping, QTL, eQTL analysis, and next generation sequencing. In particular the student is able to: understand the structure of genetic variability and its phenotypic effects, browse vertebrate genomes, apply methods to identify disease genes and QTL, use software for genomic data analysis, correctly interpret results and plan genetic studies in a proper way.

Course contents

Prerequisites:

The knowledge of genetics and molecular biology are important prerequisites to follow the course. Who might have gaps in these fields is strongly encouraged to contact the professor at the beginning of the course. Together, the student and the professor will prepare ad hoc plans to fill any gaps.

Program:

1) Foundational concepts in genetics (including population and quantitative genetics) and genomics.

2) Genome structure and variability in vertebrates

3) The transcriptional landscape of the mammalian genome

4) High throughput technologies for genotyping and next generation sequencing (NGS) platforms

5) Applications of NGS, array comparative genome hybridization

6) Linkage disequilibrium and linkage analysis, genetic mapping

7) QTL mapping, eQTL

8) Candidate gene analysis, genome wide association studies, selection signature

9) Relevant genomic projects: modENCODE, ENCODE, 1000 genome project, The Mammalian Genome Project, 10K Genome project.

10) Discussion of relevant scientific literature

Readings/Bibliography

Notes from the lectures. Scientific articles, reference and tools provided during the course.

Teaching methods

Lectures. Exercises during the course for specific aspects. Analysis of scientific papers in class. Each student plans a genomic experiment.

Assessment methods

The final exam valuates the students according to the following objectives:

1) knowledge of the foundational concepts in genetics and genomics;

2) knowledge of advanced technologies for genome analysis;

3) knowledge of advanced applications of genomic tools to answer biological questions in vertebrates;

4) capacity planning of genomic experiments.

The final exam has two levels:

1) Preparation of a genomic project: a text should be written including an appropriate introduction to the problem/question that the experiment or project would like to analyse or answer, aim of the project, a section with materials and methods, expected results and impact. The project should be submitted to the professor one week before the interview.

2) Interview based on the project submitted and other two questions according to the main objective of the course. Only students that are positively evaluated at the first level are admitted at the second level.

The final score will be based on the performance of the students at the two levels.

Teaching tools

Scientific articles, references and software are provided to the students during the course. Lecture slides are given to the students at the end of the course.

Office hours

See the website of Luca Fontanesi