Research Biographies

PROFESSOR CHRIS HALEY

Biomedical Systems Analysis

Programme Leader

Contact Details

E-mail address:	chris.haley@igmm.ed.ac.uk
Telephone:	+44 (0)131 332 2471 (extension 4026)
Fax:	+44 (0)131 467 8456
Address:	MRC Human Genetics Unit MRC IGMM, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh EH4 2XU

 

 

Research Areas

My research interests lie in quantitative genetics. In particular in developing an understanding of the control complex traits, where inter-individual variation within and between populations is controlled by variation at a number of genes, by environmental factors and by the complex interactions of these components. Most variation between individuals within and between populations is in the form of complex traits. Consequently variation in complex traits is responsible for most inter-individual variation in susceptibility to disease (both infectious and metabolic) and underlies responses to selection, both natural and artificial. Thus understanding the genetic architecture of complex traits, both in general and for specific traits in particular populations, is essential if we are to understand why and how individuals vary. We can only be really effective in understanding and treating many diseases, in predicting individual’s risk of developing particular conditions and in dissecting the causes and consequences of natural selection if we understand the genetic control of variation in complex traits.

My research focuses on developing a general understanding of the control of complex traits illustrated by results from specific examples. It has involved the development of specific experimental studies and the resources necessary to implement these studies together with the development and application of methods and tools capable of analysing and interpreting the data generated by my group and our collaborators. In recent years research has focused on the development and application of approaches to locate loci controlling quantitative traits in the genome in order to identify some of the major determinants of variation in complex traits (gridQTL). The tools of structural and functional genomics have now reached a point where we can identify genes controlling variation with ever increasing precision, we can dissect interactions between genes and not just their direct effects and we can start piecing together the complex networks of interactions in expression and function that lie between genes and the phenotypes.

I hold a joint appointment with the Roslin Institute at the University of Edinburgh. Studies of quantitative trait variation have included a variety of traits in species from mice and fish through chickens and pigs to humans.

 

Recent Publications

• Nagamine Y, Pong-Wong R, Navarro P, Vitart V, Hayward C, Rudan I, Campbell H, Wilson J, Wild S, Hicks AA, Pramstaller PP, Hastie N, Wright AF, Haley CS: Localising Loci underlying Complex Trait Variation Using Regional Genomic Relationship Mapping. PLoS One 7:e46501, 2012.
  PubMed Abstract
• Gutierrez-Gil B, Wiener P, Williams JL, Haley CS: Investigation of the genetic architecture of a bone carcass weight QTL on BTA6. Anim Genet 43:654-661, 2012.
  PubMed Abstract
• Gyenesei A, Moody J, Laiho A, Semple CA, Haley CS, Wei WH: BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies.
  Nucleic Acids Res 40:W628-W632, 2012.
  PubMed Abstract
• Gyenesei A, Moody J, Semple CA, Haley CS, Wei WH: High-throughput analysis of epistasis in genome-wide association studies with BiForce. Bioinformatics 28:1957-1964, 2012.
  PubMed Abstract
• Cabrera CP, Dunn IC, Fell M, Wilson PW, Burt DW, Waddington D, Talbot R, Hocking PM, Law A, Knott S, Haley CS, De Koning DJ: Complex traits analysis of chicken growth using targeted genetical genomics.
  Anim Genet 43:163-171, 2012.
  PubMed Abstract
• Wei W, Hemani G, Hicks AA, Vitart V, Cabrera-Cardenas C, Navarro P, Huffman J, Hayward C, Knott SA, Rudan I, Pramstaller PP, Wild SH, Wilson JF, Campbell H, Dunlop MG, Hastie N, Wright AF, Haley CS: Characterisation of genome-wide association epistasis signals for serum uric Acid in human population isolates. PLoS One 6:e23836, 2011. PubMed Abstract
• Wilkinson S, Haley C, Alderson L, Wiener P: An empirical assessment of individual-based population genetic statistical techniques: application to British pig breeds
  Heredity 106(2):261-269, 2011. PubMed Abstract
• Wei WH, Skinner TM, Anderson JA, Southwood OI, Plastow G, Archibald AL, Haley CS: Mapping QTL in the porcine MHC region affecting fatness and growth traits in a Meishan/Large White composite population 5. Anim Genet 42:83-85, 2011. PubMed Abstract
• Wei WH, Duan Y, Haley CS, Ren J, De Koning DJ, Huang LS: High throughput analyses of epistasis for swine body dimensions and organ weights
  4. Anim Genet 42:15-21, 2011. PubMed Abstract
• Massault C, Franch R, Haley C, De Koning DJ, Bovenhuis H, Pellizzari C, Patarnello T, Bargelloni L: Quantitative trait loci for resistance to fish pasteurellosis in gilthead sea bream (Sparus aurata). Anim Genet 42(2):191-203, 2011. PubMed Abstract
• Hemani G, Theocharidis A, Wei W, Haley C: EpiGPU: Exhaustive pairwise epistasis scans parallelised on consumer level graphics cards. Bioinformatics 2011. PubMed Abstract
• Guo, Y.; Mao, H.; Ren, J.; Yan, X.; Duan, Y.; Yang, G.; Ren, D.; Zhang, Z.; Yang, B.; Ouyang, J.; Brenig, B.; Haley, C. and Huang, L. A linkage map of the porcine genome from a large-scale White Duroc x Erhualian resource population and evaluation of factors affecting recombination rates.
  Anim Genet. 40(1):47-52, 2009 PubMed Abstract
• Haley, C. Human and livestock genetics: parallel evolution and horizontal exchange. J Animal Breed Genet 126:413-414, 2009 PubMed Abstract
• Nagamine, Y.; Pong-Wong, R.; Visscher, P.M. and Haley, C.S. Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations. Genet Sel Evol 41:44, 2009
  PubMed Abstract
• Navarro, P.; Vitart, V.; Hayward, C.; Tenesa, A.; Zgaga, L.; Juricic, D.; Polasek, O.; Hastie, N.D.; Rudan, I.; Campbell, H.; Wright, A.F.; Haley, C.S. and Knott, S.A. Genetic comparison of a Croatian isolate and CEPH European founders. Genet.Epidemiol e-pub Aug 20, 2009
  PubMed Abstract
• Rowe, S.J.; Pong-Wong, R.; Haley, C.S.; Knott, S.A. and De Koning, D.J. Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology. Genet.Sel Evol. 41(1):6, 2009 PubMed Abstract