module specification

 This module applies in silico approaches to explore the relationship between genotype and phenotype in the context of human disease and health. It includes an analysis of the influence of genetic variation in human populations to the penetrance of disease phenotype and to responses to environment, lifestyle and therapy.  It runs in the Spring semester and is assessed by two pieces of coursework and a presentation.  There are no pre-requisites other than satisfaction of general entry requirements.

Standard entry requirement: Lower second (2.2) first degree, or equivalent, in Biomedical Sciences or a related subject, containing components of human genetics. 

The module aims to give an understanding of the structure and variation of the human genome, and methods of gene mapping; to give an understanding of the databases and software that can be used to address problems in genetic research. It will also enable students to apply knowledge of genetic variation and populations genetics to analysis of complex traits; review the use of functional genomics to further our understanding of the molecular basis of disease and the impact of environment on human health; and to identify and evaluate emerging approaches to analysing population genomics. 

Genome structure; physical and molecular approaches to gene mapping;
Genome databases and software;
Genome diversity, single nucleotide polymorphisms, haplotype mapping, functional analysis of polymorphisms using relevant databases and software;
Linkage analysis; mapping of complex traits;
Functional genomics – expression profiling, proteomics, metabolomics; databases and software;
Interaction between genome and environment – pharmacogenomics, foetal programming and nutrition, behaviour. 

Students will be directed in their learning through a programme of lectures (20 hrs), and tutorials / IT sessions focussing on real-world case studies and problems (20 hrs), and an oral presentation (4 hrs).  In addition there will be directed learning in preparation for and / or reflection on, lectures (10 hrs), tutorials (10 hrs) and an oral presentation (4 hrs); directed learning for preparation for two pieces of coursework (20 hrs); and self-directed learning (112 hrs).   Students will develop their knowledge and understanding of the subject, IT skills and their ability to apply their knowledge to real-world problems.

PDP:  on completion of this module students will write an evaluation of how the module allowed them to develop skills in information technology, organisation and planning, communication, time management; they will also be asked to reflect on their ability to research literature effectively.

On successful completion of this module students will be able to:
1. Show a thorough understanding of the structure of the human genome and genome variation between individuals;
2. Demonstrate a comprehensive ability to extract, analyse and accurately interpret data on gene and genome variation from primary databases;
3. Demonstrate a thorough understanding of methodology for mapping genes to complex traits;
4. Demonstrate a high level of competency in the utilisation of selected genomic and related databases and software to extract, analyse and present data that explores the relationship between genotype and phenotype in health and disease;
5. Orally present a critical review of a topic based on research of up-to-date primary literature. 

The module will be summatively assessed by two pieces of coursework that will test the ability of students to extract data and knowledge applied to a contemporary problem, and include the use of IT skills acquired through the module (30% and 50%); and an oral presentation on a seen topic of contemporary relevance (20%)

To pass the module students must achieve a minimum aggregate mark of 50%

Component   Learning outcomes
Data analysis report 1  1, 2, 3, 4
presentation                 1, 2, 3, 4, 5
data anlaysis report 2   1, 2, 3, 4 

Books
Barnes M.R. (ed) (2007).  Bioinformatics for Geneticists.  A bioinformatics primer for the analysis of genetic data (2nd edition). John Wiley and Sons Ltd.
Brown S.M. (2009). Essentials of medical genomics. Wiley-Blackwell.
Campbell A.M. and Heyer L.J. (2007)  Discovering Genomics, Proteomics and Bioinformatics (2nd edition).  Benjamin Cummings.
Dziuda D.M. (2010). Data mining for genomics and proteomics: analysis of gene and protein expression data. Wiley.
Hodgman C., French A. and Westhead D.R. (2010). Bioinformatics.  Taylor & Francis.
Kalow W., Meyer U.A. and Tyndale R.F. (eds) (2005). Pharmacogenomics (2nd edition). Taylor & Francis.
Korf B.R. (2007). Human genetics and genomics. Blackwell.
Lesk A. (2007). Introduction to Genomics.  Oxford University Press.
Lucock M. (2007). Molecular nutrition and genomics : nutrition and the ascent of humankind. Wiley-Liss.
Pevsner J. (2009). Bioinformatics and functional genomics. Wiley-Blackwell.
Scherer S. (2008). A short guide to the human genome. Cold Spring Harbour Press.
Strachan T. and Read A. (2011).  Human Molecular Genetics (4th edition). Garland
Science.