Professor Chris Haley (FRSE)

Group Leader

Biography

Background

I  hold joint appointments as a Group Leader in the MRC Human Genetics Unit in the Institute of Genetics and Cancer and as a Principal Investigator in the Roslin Institute, both these organisations being part of the University of Edinburgh. My research interests lie 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 (often referred to as quantitative trait loci or QTL), 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) in humans, livestock and other species and underlies responses to selection, both artificial selection in livestock and natural selection in all species. 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 both on developing approaches to dissect complex traits and in applications of these approaches to specific biological models. My group has developed the most widely used approaches for linkage mapping of QTLs livestock. We have further developed and applied methods for the analysis of the high density of markers that are available in human populations and which are becoming available in various livestock breeds and developed, disseminated and applied analysis methods for detection of gene interactions (epistasis). I have has led and collaborated in a large number of projects focusing on the dissection of complex traits in a range of species. These have included the first genome-wide scan of QTLs in livestock and many subsequent studies as well as studies in humans, fish, model vertebrates and plant species. Current research includes focus on the use of genomic information to predict individual’s complex trait phenotypes and health outcomes, the development and application of statistical approaches to capture rare variants, epistatic variation and other genetic variation that escapes standard genome-wide association analysis and understanding and utilizing the genomic causes of complex trait variation.

Qualifications

1980 Doctor of Philosophy (PhD), University of Birmingham Selection in drosophila melanogaster

1976 Bachelor of Science, University of Birmingham

 

Undergraduate teaching

None

Postgraduate teaching

I teach and supervise projects on the MSc on Quantitative Genetics and Genome Analysis (http://qgen.bio.ed.ac.uk/)

Open to PhD supervision enquiries?

Yes

Areas of interest for supervision

I welcome students with an interest PhD projects in the area of complex trait genetics. Our group is active in the anaysis of both quantitative traits and diseases and the analysis of data from our own cohorts as well as cohorts such as UK Biobank. Current student projects and recent publications give an idea of the sort of problems we are interested in, and we are happy to receive proposals for these and related areas working with real or simulated data from humans and other species. Current projects with funding are advertised on Findaphd.com but we also welcome approaches from potential students with there own funding and project ideas.

Current PhD students supervised

Andrew Bretherick, ECAT Fellow. PhD project: “Establishing causal relationships from phenotypic, genotypic, and proteomic data”. (Principal supervisor).

Melisa Chuong, PhD Student. PhD project: “Estimating the contribution of gene by environment interactions to depression”. (Principal supervisor).

David Clark, Precision Medicine DTP PhD Student. PhD project: “The effects of autozygosity on human complex trait”. (Assistant supervisor)

Bailey Harrington, PhD project: “The role of rare variants in phenotypic variance”. (Principal supervisor).

Panagiotis Kokkinias, BBSRC CASE PhD Student. PhD project: “Optimising within and between population genomic prediction in aquaculture breeding”. (Principal supervisor).

Melissa Lewins, Precision Medicine DTP PhD Student. PhD project: “Identifying genomic and phenotypic risk factors for the clinical progression of depressive symptoms”. (Assistant Supervisor)

Erin McDonald-Dunlop, Precision Medicine DTP PhD Student. PhD project: “Omics measures of aging and application to risk stratification”. (Assistant supervisor).

Richard Oppong, Darwin Trust PhD Student. PhD project: “Investigating the genetic control of complex traits”. (Assistant supervisor).

Linda Repetto, PhD Student. PhD project: “The Omics Basis of Human Health: Novel multivariate big data analysis linking omics discoveries to complex disease”. (Assistant supervisor).

Past PhD students supervised

Atia Basheer. PhD (2014) “Genetic studies of Mendelian traits and incubation behaviour in chickens”. (Assistant supervisor). https://www.researchgate.net/profile/Atia_Basheer2

Rebecca Baxter. PhD (2011) “The role of the Major Histocompatibility Complex in immune responsiveness in a Holstein Charolais cattle cross population”. (Assistant supervisor).

Sarah Blott. PhD (1997) “Genetic variation within and between European cattle breeds”. (Principal supervisor). https://www.nottingham.ac.uk/vet/people/sarah.blott

Claudia Cabrera Cardenas. PhD (2009) “Bioinformatics tools for the genetic dissection of complex traits in chickens”. (Assistant supervisor).  http://experts.webapps.qmul.ac.uk/expert.php?id=906

Dimitrios Chatziplis. PhD (1998) “Use of selective genotyping in the detection of quantitative trait loci (QTL) by sib pair analysis” (Principal supervisor). https://www.researchgate.net/profile/Dimitrios_Chatziplis

Ronald Crump. PhD (1992) “Quantitative genetic analysis of a commercial pig population undergoing selection” (Assistant supervisor). https://warwick.ac.uk/fac/sci/maths/people/staff/crump/

James Floyd. PhD (2010) “Analysis of high-density SNP data from complex populations”. (Assistant supervisor). https://www.genomicsplc.com/team/james-floyd/

Dominic Glodzik. PhD (2013) “Recent identity by descent in human genetic data - methods and applications”. (Assistant supervisor). https://www.sanger.ac.uk/people/directory/glodzik-dominik

Youping Gu. M.Phil (1988) “Estimates of genetic parameters and prediction of responses to selection in commercial pigs”. (Principal supervisor). https://www.linkedin.com/in/youping-gu-4abb0a88

Lynsey Hall. PhD (2017) “Identifying endophenotypes for depression in Generation Scotland: a Scottish family health study”. (Assistant Supervisor). https://www.cardiff.ac.uk/people/view/1047760-hall-lynsey

Gibran Hemani. PhD (2012)  “Dissecting genetic interactions in complex traits”. (Principal supervisor). http://www.bristol.ac.uk/social-community-medicine/people/gibran-hemani/index.html

Silvia Hernandez. PhD (2012) “Genetics of litter size and prenatal survival in pigs”. (Assistant supervisor).

Jules Hernandez Sanchez. PhD (2002) “ Gene mapping using linkage disequilibrium” . (Principal supervisor). https://www.researchgate.net/profile/Jules_Hernandez-Sanchez2

Peter Joshi. PhD (2015) “Exploring the inheritance of complex traits in humans”. (Assistant Supervisor). https://www.ed.ac.uk/profile/peter-joshi

Lucija Klaric. PhD (2018) “Genetic analysis of IgG N-glycosylation in health and disease” (Assistant supervisor). https://hr.linkedin.com/in/lucija-klaric-43877856

Alida Kindt. PhD (2014) “The genomic signature of trait associated variants”. (Principal supervisor). https://www.helmholtz-muenchen.de/icb/institute/staff/staff/ma/3734/Dr.-Kindt/index.html

Sara Knott. PhD (1990) “Statistical methods for the detection of major genes in farm animal populations”. (Principal Supervisor). https://www.ed.ac.uk/profile/sara-knott

Alex Lam. PhD (2009) “Design and analysis of genetical genomics studies and their potential applications in livestock research”. (Assistant supervisor).

Andrew Macleod, PhD (2005) “Detecting ancestral junctions in inbred populations”. (Assistant supervisor).

Reka Nagy. PhD (2018) “Genetic analysis using family-based populations”. (Assistant supervisor). https://www.genomicsplc.com/team/reka-nagy/

Pau Navarro Martinez. PhD (2003) “Genetic studies of ascites in broiler populations”. (Principal supervisor). https://www.ed.ac.uk/profile/pau-navarro

Carolina Peñaloza. PhD (2018) “Characterization of genome-wide deviations from Mendelian inheritance in bivalve species ”. (Assistant supervisor). https://www.research.ed.ac.uk/portal/en/persons/carolina-penaloza(fef56b74-3772-4ac9-b044-50b4c4da2046).html

Baitsi Podisi. PhD (2011) “Quantitative trait loci mapping applied to chicken breeding”. (Assistant supervisor). https://www.linkedin.com/in/baitsi-podisi-136400112

Joseph Powell. PhD (2009) “Influence of genomic architecture on the performance of association mapping: application to ascites syndrome in broiler chickens  ” (Principal supervisor). https://www.garvan.org.au/people/jospow

Suzanne Rowe. PhD (2008) “QTL mapping technology using variance components in general pedigrees applied to the poultry industry” (Assistant supervisor). https://www.researchgate.net/profile/Suzanne_Rowe/info

Amy Rowlatt. PhD (2015) “Inheritance of DNA Methylation Level in Healthy Human Tissues”. (Assistant supervisor).

Michael Schouten. PhD (2008) “Modelling dependencies in genetic-marker data and its application to haplotype analysis”  (Principal supervisor). https://www.linkedin.com/in/michael-schouten-85594043

John Stainton. PhD (2015) “Detection of signatures of selection in commercial chicken lines  ”. (Assistant supervisor). https://www.sruc.ac.uk/directory_record/35490/stainton_john

Anna Maria van Heelsum. PhD (1997) “Selection strategies in marker assisted introgression with special reference to pig breeding”. (Assistant supervisor). https://uk.linkedin.com/in/annemarie-van-heelsum-53310722

Grant Walling. PhD (1999) “” (Principal supervisor). https://uk.linkedin.com/in/walling-grant-97683227

Samantha Wilkinson. PhD (2012) “Genetic diversity and structure of livestock breeds ”. (Assistant Supervisor). https://www.research.ed.ac.uk/portal/en/persons/samantha-wilkinson(64023bc9-5e82-4e57-8647-2ac69c51c222).html

Charley Xia (Xiachi Xin). PhD (2018) “Architecture of human complex trait variation ”. (Principal supervisor). https://www.researchgate.net/profile/Charley_Xia2

Yanni Zeng. PhD (2017) “Identification of risk factors for major depressive disorder”. (Assistant Supervisor). https://www.researchgate.net/profile/Yanni_Zeng

Research summary

Understanding complex trait variation in humans and other species.

 

Current research interests

Current research includes focus on the use of genomic information to predict individual’s complex trait phenotypes and health outcomes, the development and application of statistical approaches to capture rare variants, epistatic variation and other genetic variation that escapes standard genome-wide association analysis and understanding and utilizing the genomic and environmental causes of complex trait variation together with the interactions between these effects. My research focuses both on developing approaches to dissect complex traits and in applications of these approaches to specific biological models. My group has developed the most widely used approaches for linkage mapping of QTLs livestock. We have further developed and applied methods for the analysis of the high density of markers that are available in human populations and which are becoming available in various livestock breeds and developed, disseminated and applied analysis methods for detection of gene interactions (epistasis). I have has led and collaborated in a large number of projects focusing on the dissection of complex traits in a range of species. These have included the first genome-wide scan of QTLs in livestock and many subsequent studies as well as studies in humans, fish, model vertebrates and plant species.

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