85170 - COMPUTATIONAL HUMAN GENOMICS

Scheda insegnamento

Anno Accademico 2018/2019

Conoscenze e abilità da conseguire

By the end of the course the student acquires knowledge on the main bioinformatics tools and approaches to analyse whole genome sequencing data available from publicly accessible databases. Particularly the student learns how to obtain through ftp a comprehensive catalogue of genetic data made freely available by international scientific consortia; to replicate published results as proof of concept; to develop new Perl and R scripts to address novel scientific questions and to plot and visualize the newly generated results.

Programma/Contenuti

1. Human genomics: basic concepts

2. Methodological overview

3. Useful shell commands

4. Plink software: format and data manipulation

7. Eigenstrat: Principal Component Analysis applied to genomic data

8. DAPC: Discriminant Analysis of Principal Components applied to genomic data

5. Admixture software: searching for admixture events

6. Threepop software: testing for admixture events

9. Alder: dating admixture events

10. Replication of selected studies from literature

Testi/Bibliografia

Jobling M, Hollox E, Kivisild T & Tyler-Smith C. 2013. Human evolutionary genetics (2nd ed.), Garland Science.

Metodi didattici

The course is characterized by a marked practical approach. Explanations of the theoretical aspects will be limited to the minimum necessary. On the contrary, students are encouraged to perform 'live' analyses on 'real' datasets and to interpret the obtained results in light of the most recent advances in molecular anthropology/human population genetics.

Modalità di verifica dell'apprendimento

The final examination will consist of a practical part, i.e. analysis of human genomic data with the aim to understand/interpret some aspects of the genetic/genomic history of the considered populations/individuals, and of an oral part in which the obtained results will be thoroughly discussed and evaluated.

Strumenti a supporto della didattica

All lessons will be held in a computer laboratory equipped with Linux machines. Slides/tutorials will be supplied to the students during the course.

Orario di ricevimento

Consulta il sito web di Alessio Boattini