London School of Hygiene & Tropical Medicine

The overall module aim is to give participants a critical understanding of current methods and interpretations of pathogen genomics as a preparation for future research or translation of findings.

Intended learning outcomes

Upon successful completion of the module, a student should be able to:

• Analyse pathogen genome sequence data accessed from diverse sources to produce descriptive summaries.
• Apply freely available bioinformatic tools for relating genome sequence data to the biology of particular pathogens.
• Identify methods to analyse genome sequences from population samples of pathogen isolates to address epidemiological issues.
• Demonstrate how detailed information on individual genes and their functions relates to large genome-scale analyses of pathogens.
• Assess how local data fit into globally accessible genome databases to give a stronger understanding of pathogens.

Session Content

The module is expected to cover the following topics:

• Pathogen genome structure and annotation (includes: genome content and chromosomal arrangements; generating and assembling genome sequences; browsing and analysing genome sequences; principles of comparative genomics). 
• Population and evolutionary genomics of pathogens (includes: population structure and epidemiological history; phylogenomics; recombination and lateral gene transfer; signatures and causes of natural selection). 
• Use of pathogen genome data and analyses in public health (includes: tracking emerging and endemic infections, geographical and temporal spread of pathogens, selection and spread of resistance to drugs and vaccines). 
• Centralised genomic and bioinformatic research and resources (includes: primary genome databases; derived genome databases and community resources; overview of facilities and pathogen research at Wellcome Trust Sanger Institute). 
• Computer practicals will relate to the above subjects and include the use of freely available software for genome sequence data analysis and for interpretation and integration of transcript and phenotypic data at the genomic scale.

Mode of delivery

This module is delivered predominantly face-to-face. Where specific teaching methods (lectures, seminars, discussion groups) are noted in this module specification these will be delivered by predominantly face-to-face sessions. There will be a combination of live and interactive activities (synchronous learning) as well as self-directed study (asynchronous learning).

Assessment

The assessment for this module has been designed to measure student learning against the module's intended learning outcomes (ILOs) as listed above. The grade for summative assessment(s) only will go towards the overall award GPA. 

The assessment for this module will be in sessions on campus. There are two sub-components to the assessment: 

Computer Practical. An assessment of understanding and skills gained from computer practical sessions will involve a computer practical examination using ideas and processes that have been covered during the module. This will be conducted during the final week of the module and will comprise 50% of the assessment marks for the module. 

Written answers on analytical interpretation. An assessment of data interpretation will involve examination of published research results, and giving written answers to questions about the analyses and meaning of the findings. This will be conducted in the final week of the module and will comprise 50% of the assessment marks for the module

Credits

• CATS: 15
• ECTS: 7.5

Module specification

For full information regarding this module please see the module specification.