Postgraduate Course: Linkage and Association in Genome Analysis (PGBI11086)
Course Outline
| School | School of Biological Sciences |
College | College of Science and Engineering |
| Course type | Standard |
Availability | Available to all students |
| Credit level (Normal year taken) | SCQF Level 11 (Postgraduate) |
Credits | 20 |
| Home subject area | Postgraduate |
Other subject area | None |
| Course website |
None |
Taught in Gaelic? | No |
| Course description | This course builds on Population and Quantitative Genetics (in PGBI11001) and Statistics and Data Analysis (PGBI11003). It introduces the analytical approaches of linkage and association to dissect genetic variation and identify causative loci. |
Information for Visiting Students
| Pre-requisites | PGBI11001
Recommended PGBI11003 and PGBI11085 |
| Displayed in Visiting Students Prospectus? | No |
Course Delivery Information
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| Delivery period: 2013/14 Semester 2, Available to all students (SV1)
|
Learn enabled: Yes |
Quota: None |
|
Web Timetable |
Web Timetable |
| Course Start Date |
13/01/2014 |
| Breakdown of Learning and Teaching activities (Further Info) |
Total Hours:
200
(
Lecture Hours 36,
Supervised Practical/Workshop/Studio Hours 24,
Programme Level Learning and Teaching Hours 4,
Directed Learning and Independent Learning Hours
136 )
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| Additional Notes |
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| Breakdown of Assessment Methods (Further Info) |
Written Exam
60 %,
Coursework
40 %,
Practical Exam
0 %
|
| No Exam Information |
Summary of Intended Learning Outcomes
| On successfully completing the course, students will have an understanding of the analytical approaches of linkage and association for the dissection of genetic variation of complex traits and the identification of causative loci. They will be aware of the potential shortfalls of these techniques and be able to identify the most appropriate analyses for particular problems. They will be familiar with current practices in genome analysis for complex trait dissection and have skills required to implement them. |
Assessment Information
| Two in-course assessments (data analysis reports) (each 20%), two class tests (problem solving and essay) (each 30%). |
Special Arrangements
| None |
Additional Information
| Academic description |
Not entered |
| Syllabus |
Session Topic
1 Introduction to molecular markers: genotype calling, quality control
2 Linkage: testing for linkage, estimating recombination fraction, development of genetic maps
3 Basic concepts of QTL mapping in inbred line crosses
4 Extensions to outbred crosses and multiple QTL
5 Significance and precision: issues and the use of sampling methods.
6 Predicting power to detect QTL
7+8 QTL mapping in complex pedigrees
9 Linkage disequilibrium including patterns in natural populations
10 Introduction to association in quantitative traits
11 Basic issues in association: significance, estimation, validation, stratification
12 Stratification: Identification and analytical approaches to avoid problems
13+14 Case-control studies: odds and risk ratios, generalised linear models.
15 Use of multiple markers: haplotypes, regional estimates
16 Imputation: use of reference population data to infer additional genotypes
17 Potential causes of $ùmissing heritability&©: how likely and routes to discovery, considering rare variants, GxG, GxE, CNV, epigenetics
18 Meta analysis: combining data across many studies.
19 Post analysis investigation of results: gene identification, gene set enrichment, functional consequences.
20 Future developments: next generation sequencing
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| Transferable skills |
Not entered |
| Reading list |
Not entered |
| Study Abroad |
Not entered |
| Study Pattern |
Not entered |
| Keywords | LAGA |
Contacts
| Course organiser | Dr Sara Knott
Tel: (0131 6)50 5444
Email: s.knott@ed.ac.uk |
Course secretary | Mrs Jennifer Morris
Tel: (0131 6)50 5513
Email: jennie.morris@ed.ac.uk |
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© Copyright 2013 The University of Edinburgh - 13 January 2014 4:48 am
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