Module Specification
An online version of this specification is available to prospective students at
http://www.lshtm.ac.uk/study/currentstudents/studentinformation/msc_module_handbook/section3_moduledescript/in
dex.html
GENERAL INFORMATION
Module name
Pathogen Genomics
Module code
3460
Module Organiser
Professor David Conway
Contact email
David.Conway@lshtm.ac.uk
Home Faculty
Faculty of Infectious & Tropical Diseases
Level
This module is at Level 7 (postgraduate Masters ‘M’ level) of the QAA
Framework for Higher Education Qualifications in England, Wales & Northern
Ireland (FHEQ)
Credit
LSHTM award 15 credits on successful completion of this module
Accreditation
Not currently accredited by any other body
Keywords
Pathogens, bacterial, parasitic, epidemiology, molecular genetics,
bioinformatics
AIMS, OBJECTIVES AND AUDIENCE
Overall aim
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
By the end of this module, students should be able to:
Target audience

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.
LSHTM MSc students, particularly MBID and Medical Microbiology.
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CONTENT
Session content
The module is expected to include sessions addressing the following topics
(though please note that these may be subject to change):

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).

Functional genomics and transcriptomics of pathogens (includes:
methods for quantitative transcriptome analysis in experimental and
clinical studies; genomic perspectives on mutagenesis or gene silencing
studies).

Population and evolutionary genomics of pathogens (includes:
population structure and epidemiological history; phylogenomics;
recombination and lateral gene transfer; signatures and causes of natural
selection).

Centralised genomic and bioinformatic research and resources
(includes: primary genome databases; derived genome databases and
community resources; overview of facilities and pathogen research
programmes at Wellcome Trust Sanger Institute).

Computer practicals will relate to the above subjects and include use of
freely available software for genome sequence data analysis and for
interpretation and integration of transcript and phenotypic data at the
genomic scale.
TEACHING, LEARNING AND ASSESSMENT
Study resources
provided or required
Teaching and learning
methods
Assessment details

Computer teaching laboratory 2 days per week for 4 weeks.

Course handbook.

Session notes for each lecture and computer practical.

Reader – Includes key review papers and research papers.

Lectures

Computer practicals

Field trip to WTSI Genome Campus (1 full day)

Private study – reading

Private study – computer data browsing and software practice
A computer practical task involving some data analysis and interpretation of a
short applied research problem. This will be conducted during one morning, and
a short document presenting findings and explanations will be written for
assessment during the afternoon of the same day (during the last week of the
module).
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Assessment dates
Assessments will take place on the final day of the module. Hand in of the essay
will be on the same day.
For students who are required to re-sit, or granted a deferral or new attempt,
the next assessment date/deadline will be the standard School-recommended
date in mid/ late September 2016.
Language of study and
assessment
English (please see ‘English language requirements’ above regarding the
standard required for entry).
TIMING AND MODE OF STUDY
Duration
The module runs for 5 weeks at 2.5 days per week; this module runs between
Wednesday lunchtime and Friday afternoon.
Dates
For 2015-16, the module will start on Wednesday 20 April 2016 and finish on
Friday 20 May 2016.
Timetable slot
The module runs in LSHTM timetable slot E
Mode of Study
The module is taught face-to-face in London. Both full-time and part-time
students follow the same schedule. For full-time students, other LSHTM
modules are available in the other half of the week for the C and D slots.
Learning time
Learning time for the module should total 150 hours, consisting of
approximately:

Contact time ≈ 70 hours

Directed self-study ≈ 20 hours

Self-directed learning ≈ 30 hours

Assessment, review & revision ≈ 30 hours
APPLICATION, ADMISSION AND FEES
Pre-requisites
Robust understanding of molecular biology of infectious disease agents. This
should be equivalent to that which would be gained from study of at least 2 of
the following modules in Molecular Biology during Term 2:

Molecular Biology and Recombinant DNA Techniques;

Advanced Training in Molecular Biology;

Molecular Biology: Research Progress and Applications.
Taking of these earlier modules is not mandatory if students can demonstrate
equivalent background knowledge gained from study elsewhere.
English language
requirements
A strong command of the English language is necessary to benefit from
studying the module. Applicants whose first language is not English or whose
prior university studies have not been conducted wholly in English must fulfil
LSHTM’s English language requirements, with an acceptable score in an
approved test taken in the two years prior to entry. Applicants may be asked to
take a test even if the standard conditions have been met.
Student numbers
Student numbers are typically approx. 24 per year; numbers may be capped
due to facilities or staffing
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Student selection
Preference will be given to LSHTM MSc students, particularly those on the
Medical Microbiology, MBID, Medical Parasitology or TMIH MSc courses, and
LSHTM research degree students. Other applicants meeting the entry criteria
will usually be offered a place in the order applications are received, until any
cap on numbers is reached. Applicants may be placed on a waiting list and
given priority the next time the module is run. Full Registration (full
participation) by LSHTM research degree students is required for this module,
although the assessment for research degrees students is optional.
Fees
For registered LSHTM MSc students, fees for the module are subsumed within
MSc fees (given on individual course prospectus pages).
If registering specifically for this module, as a stand-alone short course,
individual module fees will apply.
Tuition fees must be paid in full before commencing the module, or by any fee
deadline set by the Registry.
Scholarships
Scholarships are not available at individual module level. Some potential
sources of funding are detailed on the LSHTM website.
Admission deadlines
For 2015-2016:

For registered LSHTM MSc students, the module choice deadline (for Term
2 and 3 modules) is Friday 20 November 2015.

If registering specifically for this module, applications may be made at any
time but, as places are limited, applications ahead of the MSc deadline are
strongly advised. All applications should be submitted at the latest 8 weeks
prior to the start of the module. Formal registration will take place on the
morning of the first day of the module.
ABOUT THIS DOCUMENT
This module specification applies for the academic year 2015-16
Last revised 8 August 2014 by David Conway; Minor amendments 20 July 15 SDB
London School of Hygiene & Tropical Medicine, Keppel St., London WC1E 7HT.
www.lshtm.ac.uk
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