Course description

A 3-day short course taught in London by biologists, bioinformaticians, and genetic epidemiologists in the Faculty of Infectious and Tropical Diseases (LSHTM), Bloomsbury Research Institute, and Wellcome Trust Sanger Institute.

Overview

Infectious diseases, such as HIV-AIDS, malaria, pneumonia and tuberculosis, account for 25% of global mortality and more than half of all deaths in children under the age of 5. The genetic epidemiology of these diseases can be complex, especially as they may involve several genomes, including the host, pathogen(s) and a vector.

High throughput genotyping and sequencing technologies are providing insights into these genomes, thereby revolutionising genetic epidemiological studies and biomedical research. It is now possible to genotype millions of point mutations (SNPs) using genotyping chips, facilitating large-scale genome-wide studies of association (GWAS) and genic selection, particularly in humans. Similarly, the application of second generation sequencing technologies (e.g. Illumina HiSeq2000) is leading to whole genome information on large numbers of pathogens, making it feasible to track their evolution over time and space, as well as identify variants correlated with phenotypes such as infection behaviour.

To take full advantage of these new genomic technologies requires the ability to analyse large amounts of data using methods from bioinformatics, population genetics and statistics – the focus of this course. Specifically, this course offers hands-on experience of processing sequencing data to construct genomes, identifying genomic variants and applying phylogenetic, GWAS and population genetic analyses to them. The course covers the fundamentals of GWAS and selection analysis, and post-genome translation, in human and pathogen settings. High profile examples, including malaria, TB and MRSA, will be used to illustrate the concepts, and there is a strong emphasis on how to implement the methods in practice, with the majority of sessions computer-based.

Prerequisites

This course focuses on bioinformatic, population genetic, statistical and genetic epidemiological methods for analysing large genetic datasets. Participants would be expected have some familiarity with molecular biology, and relevant statistical concepts such as a linear regression.

Course Objectives

By the end of the course participants will be able to:

Process raw sequence into a set of informative variants, through mapping to a reference genome or using de novo or reference-free assembly approaches;
Perform a population genetic analysis using sequence or genotyping data, including the construction of phylogenetic trees and identification of genomic regions under selection;
Design a GWAS and analyse the resulting data.

Teaching Methods and Course Materials

The course consists of lectures and computer practical sessions, presented in a computing laboratory. All materials will be provided on a pen-drive or CD-ROM. This device will contain all analysis software, allowing them to be run from a laptop. The course is limited to 30 participants.

Teaching Programme

The programme will include the following concepts: