Introductory description
The module runs in Term 2 and will introduce students to probabilistic models and statistical methods used in the analysis of genetic data.
This module is available for students on a course where it is a listed option and as an Unusual Option to students who have completed the prerequisite modules.
Pre-requisites:
Statistics Students: ST218 Mathematical Statistics A AND ST219 Mathematical Statistics B
Non-Statistics Students: ST220 Introduction to Mathematical Statistics
Module web page
Module aims
Students will gain a basic understanding of the probabilistic models underlying the field of population genetics, and be exposed to practical applications of common statistical tests.
Outline syllabus
This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.
Discrete-time reproductive models - Wright-Fisher, Moran. Coalescent limit. Properties of the standard coalescent, models of mutation, summary statistics and tests for neutrality, e.g. Tajima's D. Hardy-Weinberg laws, recombination, linkage mapping, linkage disequilibrium, association testing, an overview of genome-wide association studies.
Learning outcomes
By the end of the module, students should be able to:
- Describe simple discrete-time reproductive models and use them to derive the standard coalescent model
- Apply the predictions of coalescent theory to test for departures from neutrality, using simple datasets of DNA sequence variation
- Use simple datasets to evaluate the evidence for associations between genetic loci and Mendelian diseases
- Discuss the practical issues involved in scaling up association testing to whole genomes.
Indicative reading list
View reading list on Talis Aspire
Subject specific skills
Formulation of models for population genetic data, model-based predictions of genetic diversity, parameter estimation and hypothesis testing from DNA sequence data, genome-wide association studies
Transferable skills
Inference from data, assessment of uncertainty, evaluation of evidence, academic writing, computation
Study time
| Type |
Required |
Optional |
| Lectures |
30 sessions of 1 hour (20%)
|
2 sessions of 1 hour
|
| Private study |
90 hours (60%)
|
|
| Assessment |
30 hours (20%)
|
|
| Total |
150 hours |
|
Private study description
Weekly revision of lecture notes and materials, wider reading, practice exercises and preparing for examination.
Costs
No further costs have been identified for this module.
You do not need to pass all assessment components to pass the module.
Assessment group D3
|
Weighting |
Study time |
Eligible for self-certification |
|
Assignment 1
|
10%
|
15 hours
|
Yes (extension)
|
|
Due in Term 2 Week 7.
The assignment will contain a number of questions for which solutions and / or written responses will be required.
The number of words noted below refers to the amount of time in hours that a well-prepared student who has attended lectures and carried out an appropriate amount of independent study on the material could expect to spend on this assignment. 500 words is equivalent to one page of text, diagrams, formula or equations; your ST341 Assignment 1 should not exceed 15 pages in length.
|
|
|
Assignment 2
|
10%
|
15 hours
|
Yes (extension)
|
|
Due in Term 2 Week 10.
The assignment will contain a number of questions for which solutions and / or written responses will be required.
The number of words noted below refers to the amount of time in hours that a well-prepared student who has attended lectures and carried out an appropriate amount of independent study on the material could expect to spend on this assignment. 500 words is equivalent to one page of text, diagrams, formula or equations; your ST341 Assignment 2 should not exceed 15 pages in length.
|
|
|
In-person Examination
|
80%
|
|
No
|
|
The examination paper will contain four questions, of which the best marks of THREE questions will be used to calculate your grade.
- Answerbook Pink (12 page)
- Students may use a calculator
|
Assessment group R1
|
Weighting |
Study time |
Eligible for self-certification |
|
In-person Examination - Resit
|
100%
|
|
No
|
|
The examination paper will contain four questions, of which the best marks of THREE questions will be used to calculate your grade.
~Platforms - Moodle
- Answerbook Pink (12 page)
- Students may use a calculator
|
Feedback on assessment
Marked assignments will be available for viewing at the support office within 20 working days of the submission deadline. Cohort level feedback and solutions will be provided, and students will be given the opportunity to receive feedback via face-to-face meetings.
Solutions and cohort level feedback will be provided for the examination.
Past exam papers for ST341
Anti-requisite modules
If you take this module, you cannot also take:
-
ST418-15 Statistical Genetics and Advanced Topics
Courses
This module is Optional for:
-
Year 3 of
UCSA-G4G1 Undergraduate Discrete Mathematics
-
Year 3 of
UCSA-G4G3 Undergraduate Discrete Mathematics
-
Year 4 of
UCSA-G4G2 Undergraduate Discrete Mathematics with Intercalated Year
-
USTA-G300 Undergraduate Master of Mathematics,Operational Research,Statistics and Economics
-
Year 3 of
G300 Mathematics, Operational Research, Statistics and Economics
-
Year 4 of
G300 Mathematics, Operational Research, Statistics and Economics
This module is Option list A for:
-
USTA-G1G3 Undergraduate Mathematics and Statistics (BSc MMathStat)
-
Year 3 of
G1G3 Mathematics and Statistics (BSc MMathStat)
-
Year 4 of
G1G3 Mathematics and Statistics (BSc MMathStat)
-
USTA-G1G4 Undergraduate Mathematics and Statistics (BSc MMathStat) (with Intercalated Year)
-
Year 4 of
G1G4 Mathematics and Statistics (BSc MMathStat) (with Intercalated Year)
-
Year 5 of
G1G4 Mathematics and Statistics (BSc MMathStat) (with Intercalated Year)
-
Year 3 of
USTA-GG14 Undergraduate Mathematics and Statistics (BSc)
-
Year 4 of
USTA-GG17 Undergraduate Mathematics and Statistics (with Intercalated Year)
-
Year 3 of
USTA-Y602 Undergraduate Mathematics,Operational Research,Statistics and Economics
-
Year 4 of
USTA-Y603 Undergraduate Mathematics,Operational Research,Statistics,Economics (with Intercalated Year)
This module is Option list B for:
-
Year 3 of
USTA-G304 Undergraduate Data Science (MSci)
-
Year 4 of
USTA-G303 Undergraduate Data Science (with Intercalated Year)
This module is Option list D for:
-
Year 4 of
USTA-G300 Undergraduate Master of Mathematics,Operational Research,Statistics and Economics
-
Year 5 of
USTA-G301 Undergraduate Master of Mathematics,Operational Research,Statistics and Economics (with Intercalated
This module is Option list E for:
-
Year 4 of
USTA-G300 Undergraduate Master of Mathematics,Operational Research,Statistics and Economics
-
Year 5 of
USTA-G301 Undergraduate Master of Mathematics,Operational Research,Statistics and Economics (with Intercalated
This module is Option list F for:
-
Year 3 of
USTA-G300 Undergraduate Master of Mathematics,Operational Research,Statistics and Economics
-
USTA-G301 Undergraduate Master of Mathematics,Operational Research,Statistics and Economics (with Intercalated
-
Year 3 of
G30H Master of Maths, Op.Res, Stats & Economics (Statistics with Mathematics Stream)
-
Year 4 of
G30H Master of Maths, Op.Res, Stats & Economics (Statistics with Mathematics Stream)