Publications

For a full list of my personal publications visit my PI page.

I have been centrally involved in many genome-wide association studies. Please click for links to paper. Most papers include new, often Bayesian, methodology detailed in supplementary material. Bold indicates first or last authorship:

    
Malaria  Africa MalariaGEN  Bayesian locus and effect heterogeneity
Visceral leishmaniasis  India & Brazil WTCCC2  HLA haplotype association
Bactereamia Kenya WTCCC2  Bayesian sub-type analysis 
       
Iscemic stroke UK & Europe WTCCC2  Effect heterogeneity with shared controls
Type 2 diabetes  UK WTCCC1  *
Coronary heart disease  UK WTCCC1  *
Glucoma Australia WTCCC2  1000 genomes imputation 
Hypertension UK WTCCC1  *
Pre-eclampsia Columbia WTCCC2  
Bipolar disorder UK WTCCC1  *
Schizophrenia  Ireland WTCCC2  HLA conditional analysis
Psychosis Europe WTCCC2  Replication in related phenotypes 
Parkinson's disease UK and France WTCCC2  Haplotype association with secondary hits
       
Statins & Metformin response Scotland WTCCC2  Treatment-response association analysis
Reading & maths ability  UK WTCCC2  Bi-variate variance components
       
Barrett's esophagus  UK & Europe WTCCC2  Deep replication and HLA association
Ankylosing spondylitis UK WTCCC2  Tree-based interactions and meta-analysis 
Crohn's disease UK WTCCC1  *
Rheumatoid arthritis UK WTCCC1  *
Multiple sclerosis Worldwide WTCCC2  Mixed models, meta-analysis and pleiotropy 
Type1 diabetes UK WTCCC1  *
Ulcerative colitis UK WTCCC1  *
Psoriasis  UK & Europe WTCCC2  Intereaction and secondary hits

*The Wellcome Trust Control Consortium paper introduced many new methods for genotype calling, quality control, population structure, Bayesian association analysis, model comparision and intepretation.

Recent technical publications include:

Pirinen M., Donnelly P., and Spencer C. (2013) Efficient computation with a linear mixed model on large-scale data sets with applications to genetic studies. Ann Appl Stat, Volume 7, Number 1, 369-390.

Pirinen, M., Donnelly, P., & Spencer, C. C. (2012). Including known covariates can reduce power to detect genetic effects in case-control studies.. Nat Genet44(8), 848-851. doi:10.1038/ng.2346

Bellenguez, C., Strange, A., Freeman, C., Wellcome Trust Case Control Consortium., Donnelly, P., & Spencer, C. C. (2012). A robust clustering algorithm for identifying problematic samples in genome-wide association studies.. Bioinformatics28(1), 134-135. doi:10.1093/bioinformatics/btr599

Vukcevic, D., Hechter, E., Spencer, C., & Donnelly, P. (2011). Disease model distortion in association studies.. Genet Epidemiol. doi:10.1002/gepi.20576

Spencer, C., Hechter, E., Vukcevic, D., & Donnelly, P. (2011). Quantifying the underestimation of relative risks from genome-wide association studies.. PLoS Genet7(3), e1001337. doi:10.1371/journal.pgen.1001337