Peter Donnelly

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event
    Tanya Golubchik
    Department of Statistics, University of Oxford, UK
    Nat Genet 44:352-5. 2012
  2. doi request reprint Progress and challenges in genome-wide association studies in humans
    Peter Donnelly
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Nature 456:728-31. 2008
  3. pmc A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection
    George Nicholson
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 7:e1002270. 2011
  4. pmc Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population
    Rory Bowden
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 8:e1002504. 2012
  5. pmc The fine-scale genetic structure of the British population
    Stephen Leslie
    1 Murdoch Childrens Research Institute, Royal Children s Hospital, Flemington Road, Parkville, Victoria 3052, Australia 2 University of Melbourne, Department of Mathematics and Statistics, Parkville, Victoria 3010, Australia 3 University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
    Nature 519:309-14. 2015
  6. pmc Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip
    Chris C A Spencer
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000477. 2009
  7. pmc Dissection of the genetics of Parkinson's disease identifies an additional association 5' of SNCA and multiple associated haplotypes at 17q21
    Chris C A Spencer
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Hum Mol Genet 20:345-53. 2011
  8. pmc Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke
    Celine Bellenguez
    Wellcome Trust Centre for Human Genetics, University of Oxford, UK
    Nat Genet 44:328-33. 2012
  9. pmc A fine-scale chimpanzee genetic map from population sequencing
    Adam Auton
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Science 336:193-8. 2012
  10. ncbi request reprint A fine-scale map of recombination rates and hotspots across the human genome
    Simon Myers
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Science 310:321-4. 2005

Detail Information

Publications37

  1. pmc Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event
    Tanya Golubchik
    Department of Statistics, University of Oxford, UK
    Nat Genet 44:352-5. 2012
    ....
  2. doi request reprint Progress and challenges in genome-wide association studies in humans
    Peter Donnelly
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Nature 456:728-31. 2008
    ..Genetic association data are now providing new routes to understanding the aetiology of disease, as well as new footholds on the long and difficult path to better treatment and disease prevention...
  3. pmc A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection
    George Nicholson
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 7:e1002270. 2011
    ....
  4. pmc Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population
    Rory Bowden
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 8:e1002504. 2012
    ..They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions...
  5. pmc The fine-scale genetic structure of the British population
    Stephen Leslie
    1 Murdoch Childrens Research Institute, Royal Children s Hospital, Flemington Road, Parkville, Victoria 3052, Australia 2 University of Melbourne, Department of Mathematics and Statistics, Parkville, Victoria 3010, Australia 3 University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
    Nature 519:309-14. 2015
    ....
  6. pmc Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip
    Chris C A Spencer
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000477. 2009
    ..Our results have been encapsulated into an R software package that allows users to design future association studies and our methods provide a framework with which new chip sets can be evaluated...
  7. pmc Dissection of the genetics of Parkinson's disease identifies an additional association 5' of SNCA and multiple associated haplotypes at 17q21
    Chris C A Spencer
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Hum Mol Genet 20:345-53. 2011
    ..We found no support for the previously reported SNP association in 12q12/LRRK2. We also found an association of the two SNPs in 4q22/SNCA with the age of onset of the disease...
  8. pmc Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke
    Celine Bellenguez
    Wellcome Trust Centre for Human Genetics, University of Oxford, UK
    Nat Genet 44:328-33. 2012
    ..28-1.57). All four loci exhibited evidence for heterogeneity of effect across the stroke subtypes, with some and possibly all affecting risk for only one subtype. This suggests distinct genetic architectures for different stroke subtypes...
  9. pmc A fine-scale chimpanzee genetic map from population sequencing
    Adam Auton
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Science 336:193-8. 2012
    ..The contrasting locations of hotspots provide a natural experiment, which demonstrates the impact of recombination on base composition...
  10. ncbi request reprint A fine-scale map of recombination rates and hotspots across the human genome
    Simon Myers
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Science 310:321-4. 2005
    ....
  11. pmc Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus
    Zhan Su
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Nat Genet 44:1131-6. 2012
    ..We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus...
  12. pmc Assessing association between protein truncating variants and quantitative traits
    Manuel A Rivas
    Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK, Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00290, Finland, Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, Oxford OX3 7LJ, UK, NIHR Oxford Biomedical Research Centre, OUH Trust, Oxford OX3 7LE, UK and Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Bioinformatics 29:2419-26. 2013
    ..We propose a Bayesian modelling framework for the analysis of protein truncating variants and quantitative traits...
  13. pmc Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array
    Niall Cardin
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, United Kingdom
    Genet Epidemiol 35:536-48. 2011
    ..We illustrate the methods performance using real data from the Wellcome Trust Case Control Consortium's CNV association study and using simulated data...
  14. doi request reprint A common sequence motif associated with recombination hot spots and genome instability in humans
    Simon Myers
    Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1124-9. 2008
    ....
  15. ncbi request reprint A new multipoint method for genome-wide association studies by imputation of genotypes
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 39:906-13. 2007
    ..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
  16. pmc A comparison of phasing algorithms for trios and unrelated individuals
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
    Am J Hum Genet 78:437-50. 2006
    ..Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8...
  17. ncbi request reprint Patterns of Eurasian HSV-1 molecular diversity and inferences of human migrations
    Rory Bowden
    MRC Virology Unit, Church Street, Glasgow G11 5JR, UK
    Infect Genet Evol 6:63-74. 2006
    ..A specific pattern detected amongst East Asian HSV-1 isolates is currently best explained by the two waves of migration responsible for the peopling of Japan...
  18. ncbi request reprint The fine-scale structure of recombination rate variation in the human genome
    Gilean A T McVean
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Science 304:581-4. 2004
    ..We demonstrate that recombination hotspots are a ubiquitous feature of the human genome, occurring on average every 200 kilobases or less, but recombination occurs preferentially outside genes...
  19. ncbi request reprint The effects of human population structure on large genetic association studies
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 36:512-7. 2004
    ..The results of our analysis can guide the design of large-scale association studies...
  20. pmc Disease model distortion in association studies
    Damjan Vukcevic
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    Genet Epidemiol 35:278-90. 2011
    ..Thus, it is worth explicitly testing for such deviations routinely...
  21. pmc A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1
    Amy Strange
    Wellcome Trust Centre for Human Genetics, Oxford, UK
    Nat Genet 42:985-90. 2010
    ..Our findings implicate pathways that integrate epidermal barrier dysfunction with innate and adaptive immune dysregulation in psoriasis pathogenesis...
  22. ncbi request reprint Genome-wide strategies for detecting multiple loci that influence complex diseases
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 37:413-7. 2005
    ..These results suggest that searching for interactions among genetic loci can be fruitfully incorporated into analysis strategies for genome-wide association studies...
  23. pmc Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes
    Eleftheria Zeggini
    Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
    Science 316:1336-41. 2007
    ..The regions identified underscore the importance of pathways influencing pancreatic beta cell development and function in the etiology of type 2 diabetes...
  24. pmc HAPGEN2: simulation of multiple disease SNPs
    Zhan Su
    Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
    Bioinformatics 27:2304-5. 2011
    ..However, the inability of current methods to simulate multiple nearby disease SNPs on the same chromosome can limit their application...
  25. pmc Bayesian refinement of association signals for 14 loci in 3 common diseases
    Julian B Maller
    The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Genet 44:1294-301. 2012
    ..Our results also show the value of more detailed mapping to target sequences for functional studies...
  26. doi request reprint Including known covariates can reduce power to detect genetic effects in case-control studies
    Matti Pirinen
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Genet 44:848-51. 2012
    ..When the disease is common (prevalence of >20%), the inclusion of covariates typically increases power, whereas, for rarer diseases, it can often decrease power to detect new genetic associations...
  27. pmc Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome
    Manuel A Rivas
    Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
    Science 348:666-9. 2015
    ..Furthermore, we found that robustness to heterozygous gene inactivation is not due to dosage compensation. Our results illustrate the value of transcriptome data in the functional interpretation of genetic variants. ..
  28. pmc Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination
    Simon Myers
    Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK
    Science 327:876-9. 2010
    ..The involvement of PRDM9, which causes histone H3 lysine 4 trimethylation, implies that there is a common mechanism for recombination hotspots in eukaryotes but raises questions about what forces have driven such rapid change...
  29. pmc Human metabolic profiles are stably controlled by genetic and environmental variation
    George Nicholson
    Department of Statistics, University of Oxford, Oxford, UK
    Mol Syst Biol 7:525. 2011
    ..We provide a power-calculation method which reveals that sample sizes of a few thousand should offer sufficient statistical precision to detect ¹H NMR-based biomarkers quantifying predisposition to disease...
  30. pmc People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population
    Bruce Winney
    Department of Oncology, University of Oxford, ORCRB, Headington, Oxford, UK
    Eur J Hum Genet 20:203-10. 2012
    ..Preliminary genotyping of 1057 samples demonstrates the value of these samples for investigating a fine-scale population structure within the UK, and shows how this can be enhanced by the use of surnames...
  31. pmc A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    Bryan N Howie
    Department of Statistics, University of Oxford, Oxford, UK
    PLoS Genet 5:e1000529. 2009
    ....
  32. pmc A robust clustering algorithm for identifying problematic samples in genome-wide association studies
    Celine Bellenguez
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Bioinformatics 28:134-5. 2012
    ..Its use as a semi-automated quality control tool is demonstrated using several summary statistics, selected to identify different potential problems, and it is applied to two different genotyping platforms and sample collections...
  33. pmc Quantifying the underestimation of relative risks from genome-wide association studies
    Chris Spencer
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    PLoS Genet 7:e1001337. 2011
    ....
  34. pmc Is mate choice in humans MHC-dependent?
    Raphaelle Chaix
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 4:e1000184. 2008
    ..This study thus supports the hypothesis that the MHC influences mate choice in some human populations...
  35. pmc A statistical method for predicting classical HLA alleles from SNP data
    Stephen Leslie
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Am J Hum Genet 82:48-56. 2008
    ....