Postgraduate Course: Linkage and Association in Genome Analysis (PGBI11086)
Course Outline
| School | School of Biological Sciences |
College | College of Science and Engineering |
| Credit level (Normal year taken) | SCQF Level 11 (Postgraduate) |
Availability | Available to all students |
| SCQF Credits | 20 |
ECTS Credits | 10 |
| Summary | 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. |
| Course description |
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 ¿missing 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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Information for Visiting Students
| Pre-requisites | PGBI11001
Recommended PGBI11003 and PGBI11085 |
| High Demand Course? |
Yes |
Course Delivery Information
|
| Academic year 2015/16, Available to all students (SV1)
|
Quota: None |
| Course Start |
Semester 2 |
Timetable |
Timetable |
| 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 )
|
| Assessment (Further Info) |
Written Exam
60 %,
Coursework
40 %,
Practical Exam
0 %
|
| Additional Information (Assessment) |
Two in-course assessments (data analysis reports) (each 20%), two centrally arranged exams (problem solving and essay) (each 30%). |
| Feedback |
Not entered |
| Exam Information |
| Exam Diet |
Paper Name |
Hours & Minutes |
|
| Main Exam Diet S2 (April/May) | Linkage & Association in Genome Analysis 1 (Open Book) | 1:30 | | | Main Exam Diet S2 (April/May) | Linkage & Association in Genome Analysis 2 (Closed book) | 1:30 | |
Learning Outcomes
On completion of this course, the student will be able to:
- 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.
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Additional Information
| Graduate Attributes and Skills |
Not entered |
| Keywords | LAGA |
Contacts
| Course organiser | Dr Sara Knott
Tel: (0131 6)50 5444
Email: |
Course secretary | Mrs Jennifer Morris
Tel: (0131 6)50 5513
Email: |
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