Infectious Disease 'Omics

Overview - Infectious Disease 'Omics

This course has been postponed. Please register your interest for 2021.

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 five years. The genetic epidemiology of these diseases can be complex, especially as they may involve several genomes, including the host, pathogen(s) and a vector. There is also a need to look beyond the genome to consider other ‘omes, such as the transcriptome, in a more systems biology framework.

High throughput genotyping and sequencing technologies are providing insights into these genomes, metabolomes, transcriptomes and proteomes, thereby revolutionising genetic epidemiological studies and biomedical research. The use of SNP chips in large-scale genome-wide studies of association and genic selection has revolutionized the study of human disease susceptibility. Whole genome studies of pathogens using high throughput sequencing technologies is leading to the ability to track microbial evolution over time and space, as well as identify variants correlated with phenotypes such as anti-microbial resistance. Further, RNAseq methodologies are being used to measure transcript abundance and differential gene expression across isolates.

To take full advantage of new ‘omic 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 downstream methods, such as phylogenetics. Further, the course covers transcriptomic and proteomic analysis 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.


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 fee

Commercial sector: £1,000
Public/academic sector: £690

Fee deadline: 16 August 2019

Fees include course materials and some refreshments, but exclude accommodation.

Course objectives
Course objectives - Infectious Disease 'Omics


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;
  • Conduct transcriptomic and proteomic analysis, in an integrated systems biology approach
  • Perform downstream population genetic and association analysis

Teaching Programme

The programme will include the following concepts:

  • Genomic variation and technologies, data visualisation and quality control
  • Mapping to a reference pathogen genome and variant detection
  • Transcriptomics and RNA-seq
  • Assembly of pathogen genomes
  • Phylogenetic analysis and detection of genic selection
  • Exploring Host-pathogen interactions

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. This device will contain all analysis software, allowing them to be run from a laptop. The course is limited to 30 participants.


There is no formal assessment but a certificate of attendance will be provided.

How to apply
How to apply - Infectious Disease 'Omics

Applying for this course

This course has been cancelled. Please register your interest for 2021.

Please read LSHTM's Admissions policies prior to submitting your application.

Short courses - visas, accommodation, disclaimer


The student is responsible for obtaining any visa or other permissions to attend the course, and is encouraged to start the application process as early as possible as obtaining a visa for the UK can sometimes take a long time. The Short Courses team can provide supporting documentation if requested.

Accommodation and meals

A list of hotels located in the vicinity of LSHTM, along with further resources for short term accommodation, can be found on our accommodation pages. Tea and coffee will be provided during breaks. Lunch vouchers for the LSHTM canteen will also be available.

Evening meals are not catered for at LSHTM, however there is a large choice of restaurants, cafés and shops nearby.

Important information

Please note:

  • If you have been offered a place on the course you will not be able to register without bringing formal ID (Passport) and without having obtained the correct visa if required.
  • It is essential that you read the current visa requirements for short course students.
  • LSHTM may cancel courses two weeks before the first day of the course if numbers prove insufficient.  In those circumstances, course fees will be refunded.
  • LSHTM cannot accept responsibility for accommodation, travel and other losses incurred as a result of the course being cancelled.