MSc in Clinical Epidemiology

PROGRAMME BROCHURE
2015

Division of Community Health

Faculty of Medicine and Health Sciences
Stellenbosch University

www.sun.ac.za/clinepi

September 2014

Clinical Epidemiology is the science of applying the best available research evidence
to patient care. It uses the methods of epidemiology to find scientifically valid answers
to questions concerning diagnosis, prevention, therapy, prognosis and aetiology, thus
improving the evidence-base for the care of individual patients.

The course offers rigorous methodological training for those with a background or
experience in a health-related discipline who wish to pursue a career in clinical
research or evidence-based practice. The programme would be of interest to
potential researchers who require robust training in research techniques, including
advanced concepts and methods of epidemiology.
CONTENTS

PAGE

1. Overview of course structure

2. Admission requirements

3. Structured modules: objectives and content

i.

Fundamentals of epidemiology

ii.

Biostatistics I

iii.

Research proposal writing and grantsmanship

iv.

Systematic reviews and meta-analysis

10

v.

Randomised controlled trials

11

vi.

Biostatistics II

12

vii.

Writing and reviewing scientific papers

13

viii.

Diagnosis and screening

14

ix.

Clinical guidelines

15

x.

Teaching Evidence-based Health Care

16

xi.

Infectious disease epidemiology

17

xii.

Economic evaluation of health care

18

xiii.

Health systems and services research

19

xiv.

Qualitative research methods for health

20

4. Research project

21

5. Bursaries

23

6. What do MSc Clinical Epidemiology students say?

24

7. Contact details

24

Information summarised in this document is subject to change.

1. OVERVIEW OF COURSE STRUCTURE

This is a 180 credit programme which consists of modules (120 credits) and a
research project (60 credits).

Types of learning activities

Modules

Credits
1 credit = 10 hours
120

Research project

60

Nature and duration of programme

The programme is offered on a part-time basis over a minimum period of two years.

Language specification
English

Modules
Students need to do 10 modules, of which eight are compulsory and two elective.
Compulsory modules

Biostatistics I
Biostatistics II
Diagnosis and Screening
Fundamentals of Epidemiology
Randomised controlled trials
Research Proposal Writing and Grantsmanship
Systematic Reviews and Meta-analysis
Writing and Reviewing Scientific Papers

Elective modules (choose two)

Clinical Guidelines
Teaching evidence-based health care
Infectious disease epidemiology
Economic evaluation in health care
Health systems and services research
Qualitative research methods for Health

Information summarised in this document is subject to change.

Duration of a module: Semester (February June or July November)

When are core modules offered?
Semester 1

Semester 2

Fundamentals of epidemiology

Research proposal writing and grantsmanship

Year 1

Systematic reviews and meta-analysis

Biostatistics I

Biostatistics II

Diagnosis and screening

Year 2
Writing and reviewing scientific papers

Clinical trials

When are elective modules offered?

Semester 1 (year 2)
Clinical guidelines
Teaching Evidence-based health care
Health systems and services research

Semester 2 (year 1 and 2)

Qualitative research methods for health
Economic evaluation in health care
Infectious disease epidemiology

Module structure
Modules are offered using a combination of face-to-face teaching and e-learning using
Sun Learn, Stellenbosch Universitys online learning environment. Typically a module
consists of
40 hours classroom time
80 hours self-study: reading / formal assignments / projects
Module assessment

50%: 2-3 formative assessments

50%: summative assessment

Continuous and summative assessment of modules will be conducted through written

examinations, oral presentations, written assignments and participation in discussions. A
pass mark of 50% is required for each module, with a 45% sub-minimum on formative
and summative assessments. The student will be required to participate successfully and
to integrate knowledge in projects, reports and assignments. An external examiner is
appointed for every module. A candidate who fails any module may be denied the right to
reregister for the programme.
Please note that we have to enforce strict deadlines for all assignments. Assignments handed in
after the due date and time will not be marked. University guidelines related to misconduct and
dishonesty will apply.

Information summarised in this document is subject to change.

Attendance
Students should inform the module convener if they are going to be absent for more than
one session in a block or in the semester.
Students missing sessions must make their own arrangements to obtain material they
have missed.
Students should ensure that the examination weeks are kept free of any competing
engagements.
Semester timetables should be consulted well in advance.
Communication
Students should ensure that the programme administrator has all their contact details,
including any change in email address. Communication will take place using Sun Learn
and email.
Short courses
Some of the modules are available as short courses. Should a prospective full degree
student have completed a short course offered by the programme, the student can apply
for recognition of prior learning when entering the full degree programme.

Research project
o Equal to one peer reviewed publication
o The completed research project must be submitted in the prescribed format and will be
assessed by both internal and external examiners.
o Do familiarise yourself with the University Ethics and research integrity guidelines and
procedures.

General:
All students should consult Part 1 of the University Calendar for general information
related to studying with Stellenbosch University such as the code of conduct guiding the
relationship between the supervisor and student, responsibilities of students, supervisors,
etc.
http://www.sun.ac.za/university/yearbook/

Information summarised in this document is subject to change.

2. ADMISSION REQUIREMENTS
To be eligible for application to the MSc (Clinical Epidemiology) programme

The candidate shall hold an MB, ChB or equivalent degree; or a four-year

professional bachelors degree in a health-related discipline; or a BScHons degree
in Medical Sciences of this University or another recognised university or an
equivalent qualification approved by Senate.*
Mathematics at National Senior Certificate (NSC) level
Computer literacy
Fluency in written and spoken English
Students will be selected on the basis of academic merit.

* Application by international students will be reviewed for equivalence of degree.

Application procedures:
Full details of the application procedure is available on the programme website
www.sun.ac.za.clinepi
Applications should include:
Completed application form
Letter of motivation
Academic Record
Proof of computer literacy
Matric certificate

Information summarised in this document is subject to change.

3. STRUCTURED MODULES: OBJECTIVES AND CONTENTS

i. Fundamentals of epidemiology
Conveners: Sade Adeniyi (Centre for Evidence-based Health Care) and Mark Engel
(University of Cape Town)
Requirements: Course entry requirements as outlined on page 6
Objectives
At the end of the course students will understand
the history and development of clinical epidemiology
how to frame research questions
the principles, strengths and weaknesses of various study designs
the different data sources
measures of disease occurrence, measures of effect and association
random error, bias, confounding and effect modification in epidemiological studies
and how to deal with these issues
how to determine causal links between exposure (treatment) and outcome
epidemiological concepts related to Infectious diseases, occupational health and
chronic diseases

Contents

History and contribution of epidemiology

Development of clinical epidemiology
Framing research questions
Strength and weaknesses of various study designs
Data sources for clinical epidemiology
Diagnosis and screening
Measures of disease frequency/occurrence
Measures of effect/association
Random error
Bias
Confounding and effect modification
External validity
Causation
Epidemiological concepts related to infectious diseases, occupational health and
chronic diseases

Information summarised in this document is subject to change.

ii. Biostatistics I
Convener: Tonya Esterhuizen (Centre for Evidence-based Health Care)
Requirements: Course entry requirements as outlined on page 6
Objectives
At the end of this course students will be able to:
Summarize statistical data using tables, graphs and appropriate summary statistics.
Interpret significance tests and confidence intervals.
Compare two samples using the student t test for continuous variables and the chisquared test for categorical data, in both paired and unpaired cases, calculate
confidence intervals for the main results, and summarize the conclusions from such
an analysis.
Compare two samples using non-parametric tests, in both paired and unpaired
cases, and summarize the conclusions from such an analysis.
Use statistical software to present and analyze data.

Contents

Descriptive statistics
Probability and distributions
Hypothesis testing, confidence intervals and non-parametric methods for:
o One group
o Two groups
Implementing methods using statistical software

Information summarised in this document is subject to change.

iii. Research proposal writing and grantsmanship

Conveners: Tonya Esterhuizen (Centre for Evidence-based Health Care)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
By the end of the course students will be equipped with the tools needed to write and
implement a protocol for a clinical research project.

Contents
The focus of this course will be on the principles of quantitative research methodology
Select a topic and develop a well formulated research question
Conduct a literature review including literature searching (different information
sources, how to structure a database search, how to conduct a search effectively
and efficiently)
Reference management using for example Endnote
Sampling techniques
Sample size and power calculations
Data collection strategies including questionnaire design and development
Data analysis plan and data management
Create a statistical analysis plan detailing the major steps in the statistical design
and analysis of a study
Ethics and preparing an application to research ethics committees
Research integrity
Appropriate funding bodies and procedures for grant applications and their
assessment
Grant proposal writing
Grantsmanship
Compiling a biosketch

Information summarised in this document is subject to change.

iv. Systematic reviews and meta-analysis

Conveners: Taryn Young and Anel Schoonees (Centre for Evidence-based Health Care)
and Tamara Kredo (SA Cochrane Centre, SA Medical research Council)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
This module will enable students to understand the methods for conducting a systematic
review to answer a clearly defined question about an intervention.

Contents

Rationale for research synthesis

Types of systematic reviews including Cochrane Reviews
Accessing systematic reviews
Formulating a review question
Searching for evidence
Study selection and data extraction
Assessing risk of bias and quality of the evidence (GRADE)
Synthesizing the evidence including narrative and quantitative methods
Investigating publication bias
Using systematic reviews - Incorporating evidence into practice

Information summarised in this document is subject to change.

10

v. Randomised controlled trials

Conveners: Hassan Mohamed (Community Health)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
To understand the design, conduct and practicalities of successful randomized controlled
trials

Contents
Principles of comparative trials in investigating effectiveness, efficacy and safety of
treatments

Main features of different types of trials (strength and weakness of each design
together with the implications for sample size requirements, analytic methods,
interpretation and reporting)
Ethics
Good Clinical Practice and regulatory requirements
Principles of trial conduct
Reporting

Basic statistical methods used in randomized controlled trials

How to select and apply appropriate statistical measures

Presenting and interpreting results

Practicalities

Recruitment strategies
Data management
Trial governance
Quality assurance and control
Participant retention

Information summarised in this document is subject to change.

11

vi. Biostatistics II
Conveners: Tonya Esterhuizen (Centre for Evidence-based Health Care)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
At the end of this module, participants would be able to:
Select and use appropriate statistical methods in the analysis of simple datasets
and apply these methods by computer using a statistical package
Present findings based on statistical analysis in clear, concise and understandable
manner
Understand and interpret output from statistical analyses carried out by computer, in
relation to research and other questions being asked
o Analysis of variance
o linear regression
o logistic regression
o survival analysis

Contents

ANOVA
Correlation
Simple and multiple linear regression
Logistic regression
Survival analysis
Adjusting for confounding

Information summarised in this document is subject to change.

12

vii. Writing and reviewing scientific papers

Conveners: Charles Wiysonge and Taryn Young (Centre for Evidence-based Health Care)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
By the end of the module students would have
a thorough grasp of the principles of critical appraisal as it applies to health care
and the application and implementation of evidence in practice and policy.
knowledge of the required structure, language and approach to writing a scientific
paper or report.

Contents

Phrasing answerable questions

Critical appraisal of scientific papers covering the following research methodologies:

o
o
o
o
o
o
o

Randomized controlled trials (evaluating effects of treatment)

Cohort studies
Case control studies
Cross-sectional studies
Diagnostic studies
Systematic reviews
Economic evaluation of a health care intervention

Writing a paper
o
o
o
o
o
o
o

Approaching a writing project

Structure of a paper
Effective presentation of data
Scientific language and style
Reviewing and improving your writing
Submitting the manuscript for publication
Other (dealing with editors and reviewers, plagiarism, correcting proofs, legal
issues)

Information summarised in this document is subject to change.

13

viii. Diagnosis and screening

Conveners: Charles Okwundu (Centre for Evidence-based Health Care), Megan Rensburg
and A Zemlin (Chemical Pathology)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
At the end of the course students will understand
the principles and practice of disease screening
the principles and practice of diagnostics
Contents
Screening

Validity of a test
Receiver operator curves
Reliability of test
Likelihood ratios
Predictive values
Deciding on a screening programme (criteria of test, disease and screening
programme)
Implementing and evaluating screening programmes (special biases)
Adverse effects of screening

Diagnosis

Test accuracy
Multiple test
Designing a diagnostic accuracy study
Critical appraisal of diagnostic studies
Systematic review of diagnostic studies

Information summarised in this document is subject to change.

14

ix. Clinical guidelines

Conveners: Tamara Kredo (SA Cochrane Centre, SA Medical research Council) and
Quinette Louw (Division of Physiotherapy)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
After completing the course, students will be able to

describe the principles of development of evidence based guidelines

outline the steps of guideline development
describe the rationale for guideline adaptation
outline the steps of guideline adaptation
critically appraise guidelines
describe the barriers and enablers of implementation strategies
select appropriate interventions for an implementation plan
select measures to use as audit tools to demonstrate practice change
develop a guideline implementation plan

Contents

Rationale for developing and using evidence informed guidelines

Guideline adaptation and development
Decision analysis in guideline development
Adapting and developing locally appropriate guidelines (community/hospital/private
sector-based)
Critical appraisal of guidelines
Guideline implementation
Evaluating the effectiveness of a guideline implementation plan by identifying and
applying appropriate clinical audit measures

Information summarised in this document is subject to change.

15

x. Teaching Evidence-based Health Care

Conveners: Susan v Schalkwyk (Centre for Health Professions Education) and Taryn
Young (Centre for Evidence-based Health Care)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
By the end of this course participants will:

Be able to describe current concepts of how people learn

Be able to write learning outcomes for teaching EBHC to a particular audience
Be able to describe various teaching methods which promote active learning
Have experienced some of the methods which promote active learning
Have delivered and evaluated a teaching module in EBHC for a particular target
audience and setting by:
o Developing and selecting relevant teaching materials
o Employing appropriate methods of teaching
o Developing and using appropriate assessment and evaluation tools.

Contents

How people learn

Learning outcomes and how to write them
Methods of instruction to facilitate learning
Evaluating your teaching
Presentation skills
o Graphic presentation of data
o Use of slides
o Oral presentation skills
Developing a teaching plan and delivering the lesson
o Select the EBHC topic (from one of the 5 As) for your audience and setting
o Plan the teaching interaction
o Develop and select appropriate materials
o Deliver the lesson(s)
o Reflection, eliciting feedback and (summative) reporting.

Information summarised in this document is subject to change.

16

xi. Infectious disease epidemiology

Conveners: Jean Nachega (Centre Infectious Diseases) and Peter Nyasulu (Monash
South Africa)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
After completion of the module the student will be able to:

describe and understand the main epidemiological characteristics of the major

infectious diseases
describe how these epidemiological characteristics can be utilized to develop and
evaluate strategies to prevent epidemics or endemic transmission of the major
infections
investigate an outbreak
discuss transmission dynamics and mathematical modelling of epidemics
discuss routine and sentinel surveillance
discuss the role of observational studies in infectious disease epidemiology
discuss how experimental studies are used to evaluate efficacy and effectiveness of
treatment and control measures

Content
- definitions and nomenclature
- outbreak investigation
- transmission dynamics
- disease surveillance
- epidemiological studies and modelling
- vaccination efficacy and effectiveness
- epidemiology applied to HIV/AIDS, TB, STIs and other communicable diseases.

Information summarised in this document is subject to change.

17

xii. Economic evaluation of heath care

Conveners: Lungiswa Nkonki (Community Health)
Requirements: Fundamentals of Epidemiology and Biostatistics I
Objectives
At the end of the module students will be able to understand and apply fundamental
economic evaluation methods, in particular to
i)
to gain insights into theory and application of economic evaluation in health
care;
ii)
to develop an understanding of economic evaluation techniques, their
application and analysis;
iii)
to develop skills in designing and conducting cost analysis, costeffectiveness analysis, cost-utility analysis and cost-benefit analyses with an
aim of informing policy formulation and implementation process.

Contents

Principles of economic evaluation

Costing
Discounting, annualisation
Cost benefit analysis
Cost effectiveness analysis
Cost utility analysis
Uncertainty and sensitivity analysis
Modelling in economic evaluation

Information summarised in this document is subject to change.

18

xiii. Health Systems and Services Research

Conveners: Lilian Dudley (Community Health)
Requirements: Course entry requirements as outlined on page 6
Objectives
After completion of the module the student will be able to

Apply appropriate scientific principles and methods to the evaluation of health care;
Evaluate dimensions of effectiveness, efficiency, humanity and equity of health
services;
Conduct a programme evaluation in health care;
Assess the quality of health care;
Conduct a health survey;
Understand and interpret health systems and services research publications.

Contents

Introduction to health care evaluation and health services research

Measurement of effectiveness, efficiency, equity and humanity in health care
Health programme evaluation
Measurement of quality of health care
Health survey design

Information summarised in this document is subject to change.

19

xiv. Qualitative Research Methods for Health

Conveners: Donald Skinner (Community Health)
Requirements: Course entry requirements as outlined on page 6
Objectives
After completion of the module the student will be able to

Understand the role and philosophy of qualitative methods with the broader research
framework
Be able to write a qualitative protocol
Be able do a qualitative interview, understand the running of focus groups and be able
to observation research
Be able to transcribe an interview and to prepare the material for analysis
Be able to analyse qualitative data using a content analysis approach
Be able to write a qualitative report
Be able to critique a qualitative paper

Contents
The module is intended as an overview of qualitative methodology and to provide direct
practical training in qualitative tools. As such the module will cover
the background and philosophy behind qualitative methods,
an introduction and experience in the three major methods of data collection and
analysis,
other key methodological issues such as sampling and ethical issues
The assignments for the course take the participant through all phases of a very small
qualitative study, including design of the study, data collection and analysis.

Information summarised in this document is subject to change.

20

4. RESEARCH PROJECT (60 CREDITS)

The research project must be conducted on a relevant research question using a
quantitative research design. Each student must have a supervisor who is affiliated with
Stellenbosch University and can, in addition, have an external co-supervisor.
MClinEpi - Research project flow diagram
Clear research question
Identify a supervisor and
complete agreement

Inform MClinEpi programme

committee of your proposed
project
Develop a timeline for your
project

Develop research protocol

See University Provisions for

research assignments of
structured masters
programmes

Finalise the protocol and get

supervisor to approve it

Prepare and submit to MClinEpi

committee for scientific approval and
then for Ethics submission

See the university guideline on

preparation for Ethics
committee approval
http://sun025.sun.ac.za/portal/p
age/portal/Health_Sciences/En
glish/Centres%20and%20Instit
utions/Research_Development
_Support/Ethics/Application_pa
ckage

Ethics approval obtained

Conduct research

3 monthly progress reports to

MClinEpi programme
committee

Supervisor

Write up research report

Adhere to reporting guidelines

http://www.equatornetwork.org/

Submit for examination once

supervisor has approved it

The conduct of the research needs to adhere to research integrity and ethical principles of
Stellenbosch University. Students are responsible to be familiar with these policies:
SU Policy on Academic Integrity: The Prevention and Handling of Plagiarism
Framework Policy for the Assurance and Promotion of Ethically Accountable
Research at Stellenbosch University
Useful resources:
http://www.singaporestatement.org/
http://publicationethics.org/international-standards-editors-and-authors

Information summarised in this document is subject to change.

21

The research project must be submitted as a completed manuscript for a (preferably

subsidy-bearing) peer-reviewed scientific journal (i.e. that appears on the list of the
approved scientific journals of the Department of Higher Education and Training) with the
candidate as first author. This must comply with requirements as set out in the Instructions
for authors of the relevant scientific journal including word count and referencing style and
should align with good reporting guidelines http://www.equator-network.org/.
The final submission should include the following:
Declaration
See Provisions for research assignments of structured masters programmes for the
format.
Part A: Completed manuscript
The completed manuscript must comply with requirements as set out in the Instructions for
authors of the relevant scientific journal including word count and referencing style. The
word count is typically 3000-4000. Supervisors will assist candidates to identify an
appropriate journal. The article does not have to be submitted to the journal in order to
meet academic requirements.
Part B: Appendices
These will vary with the study but should typically include:
a. Relevant journal Instructions to Authors
b. Questionnaire/data capture instrument(s) (as prepared originally for protocol)
c. Ethics consent form(s) (as prepared originally for protocol)
d. Selected tables or figures, with brief explanatory text, that would be useful for the
examiner to see as part of the analyses, but which could not be included in the article due
to word restrictions. This should not simply be a collection of analysis printouts but should
be readable as an addendum with reference to the article.
e. Any technical appendices needed for example, laboratory techniques, statistical
formulae.
f. Acknowledgements
Submission process
Two copies of the dissertation must be submitted, in temporary binding to the MSc Clinical
Epidemiology Programme Coordinator. The submission deadline for December graduation
is 1 September, and for March graduation it is 1 December.
NOTE: The programme coordinator must be informed 3 months in advance of the intention
to hand in the research project.
We encourage MClinEpi students to submit their research projects for publication. In doing
so, do be reminded that the Division of Community Health, Stellenbosch University, should
be stated as an affiliation. If you have more than one affiliation, the Division of Community
Health should be stated as a secondary affiliation.
Kindly also acknowledge MClinEpi as follows This research project has been conducted
as part of the academic requirements of the MSc in Clinical Epidemiology
www.sun.ac.za/clinepi, Stellenbosch University.
The Faculty offers incentives to those who publish (for further info, Sasley Beukes can be
contacted: sasleyb@sun.ac.za).

Information summarised in this document is subject to change.

22

5. BURSARIES
SURMEPI (Stellenbosch University Rural Medical Education Partnership Initiative)
http://surmepi.sun.ac.za/ is offering bursaries for Masters and PhD students conducting
research in rural or underserved areas, or on relevant aspects of healthcare in rural or
underserved areas. Bursaries are allocated on a competitive basis, based on academic
merit and financial need.
Novartis offers bursaries to students registered for full programme only i.e. students doing
the components making up the 180 credits. Bursary funds can be used towards course
related expenses such as class fees, textbooks, STATA software licenses and living
expenses. For more information on the application procedure contact the MClinEpi
administrator.
General bursaries: do look in the general University bursary booklet

SURMEPI
Stellenbosch University Rural Medical Education Partnership Initiative
Aims:
To increase the number and quality of health care workers in rural areas
Retain health care workers over time and in areas where they are most
needed
Increase the capacity for regionally relevant research
Pioneering innovative
medical education models
to improve capacity, retention
and recruitment
of medical graduates
in Sub-Saharan Africa
http://surmepi.sun.ac.za/

Information summarised in this document is subject to change.

23

6. WHAT DO MSC CLINICAL EPIDEMIOLOGY STUDENTS SAY?

Graduating with a M.-degree in Clinical Epidemiology defines a turning point in my career.
While working as a doctor in primary health care I felt a strong need to learn more about
practicing evidence-based medicine and understanding clinical research and literature.
The course provided these vital skills but also gave trained me in planning and executing a
study. Furthermore, the course provided a great framework for understanding biostatistics,
taught me to write-up and present results and presented a wonderful opportunity to
network with people who share my interest in research.
The MSc in Clinical Epidemiology has been a most enlightening and empowering
experience. Enlightening as it revealed my glaring inadequacies in my understanding of
evidence-based medicine and how to implement it and empowering as it has now provided
me with the tools to evaluate scientific research and articles and critique them objectively.
It has also allowed me to assist postgraduate students with developing and designing their
research projects. I certainly would have liked to have followed this course many years
ago.

7. CONTACT DETAILS
Programme coordinator
Prof Taryn Young
Faculty of Medicine and Health Sciences, Stellenbosch University
Tel: +27 21 938 9452/9157
Email: tyoung@sun.ac.za
Programme administrator
Division of Community Health
Faculty of Medicine and Health Sciences, Stellenbosch University
Tel: +27 21 938 9157
Fax: +27 21 938 9723
E-mail: mclinepi@sun.ac.za
International office
Co-ordinator: Postgraduate International Students
Mrs Rachel Pullen
Tel: +27 21 938 9086
E-mail: crp@sun.ac.za
Postgraduate office
Coordinator: Postgraduate Studies
Ms Yolokazi Ntungwa
Tel: +27 21 938 9811
Fax: +27 21 933 6330
E-mail: yolokazi@sun.ac.za

Information summarised in this document is subject to change.

24