David Clayton

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. ncbi request reprint An R package for analysis of whole-genome association studies
    David Clayton
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
    Hum Hered 64:45-51. 2007
  2. pmc Linkage analysis of a derived glucose phenotype in the Genetic Analysis Workshop 13 simulated data using a variety of Haseman-Elston based regression methods
    Heather J Cordell
    University of Cambridge, Department of Medical Genetics, JDRF WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrookes Hospital, United Kingdom
    BMC Genet 4:S6. 2003
  3. pmc On inferring presence of an individual in a mixture: a Bayesian approach
    David Clayton
    Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
    Biostatistics 11:661-73. 2010
  4. ncbi request reprint Epidemiological methods for studying genes and environmental factors in complex diseases
    D Clayton
    Department of Medical Genetics, Cambridge University, Level 4, Cambridge Institute for Medical Research, Addenbrooke s Hospital, Hills Road, CB2 2QQ, Cambridge, UK
    Lancet 358:1356-60. 2001
  5. pmc Testing for association on the X chromosome
    David Clayton
    Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust MRC Building, Addenbrookes s Hospital, Cambridge, UK
    Biostatistics 9:593-600. 2008
  6. ncbi request reprint Use of unphased multilocus genotype data in indirect association studies
    David Clayton
    Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK
    Genet Epidemiol 27:415-28. 2004
  7. pmc A robust statistical method for case-control association testing with copy number variation
    Chris Barnes
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 40:1245-52. 2008
  8. pmc Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
    Jeffrey C Barrett
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Nat Genet 41:703-7. 2009
  9. pmc Haplotype structure, LD blocks, and uneven recombination within the LRP5 gene
    Rebecca C J Twells
    JDRF WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK
    Genome Res 13:845-55. 2003
  10. pmc Confirmation of HLA class II independent type 1 diabetes associations in the major histocompatibility complex including HLA-B and HLA-A
    J M M Howson
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Diabetes Obes Metab 11:31-45. 2009

Detail Information

Publications37

  1. ncbi request reprint An R package for analysis of whole-genome association studies
    David Clayton
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
    Hum Hered 64:45-51. 2007
    ..To provide data classes and methods to facilitate the analysis of whole genome association studies in the R language for statistical computing...
  2. pmc Linkage analysis of a derived glucose phenotype in the Genetic Analysis Workshop 13 simulated data using a variety of Haseman-Elston based regression methods
    Heather J Cordell
    University of Cambridge, Department of Medical Genetics, JDRF WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrookes Hospital, United Kingdom
    BMC Genet 4:S6. 2003
    ..All methods performed well, however, when applied to new simulated data in which the true genetic effects were allowed to explain a greater proportion of the overall variance...
  3. pmc On inferring presence of an individual in a mixture: a Bayesian approach
    David Clayton
    Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
    Biostatistics 11:661-73. 2010
    ..This paper sets out a Bayesian analysis of this problem which clarifies the role of the reference frequencies and allows incorporation of prior probabilities of the individual's membership in the sample...
  4. ncbi request reprint Epidemiological methods for studying genes and environmental factors in complex diseases
    D Clayton
    Department of Medical Genetics, Cambridge University, Level 4, Cambridge Institute for Medical Research, Addenbrooke s Hospital, Hills Road, CB2 2QQ, Cambridge, UK
    Lancet 358:1356-60. 2001
    ..For adequate statistical power to detect such modest risk ratios, the case-control design is more feasible than the cohort design...
  5. pmc Testing for association on the X chromosome
    David Clayton
    Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust MRC Building, Addenbrookes s Hospital, Cambridge, UK
    Biostatistics 9:593-600. 2008
    ..The proposed method remains valid when phenotype varies between sexes, provided the allele frequency does not, and avoids the loss of power resulting from stratification by sex in such circumstances...
  6. ncbi request reprint Use of unphased multilocus genotype data in indirect association studies
    David Clayton
    Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK
    Genet Epidemiol 27:415-28. 2004
    ..We also relate these analyses to alternative approaches to haplotype analysis, namely those based on haplotype similarity and those inspired by cladistics...
  7. pmc A robust statistical method for case-control association testing with copy number variation
    Chris Barnes
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 40:1245-52. 2008
    ..We illustrate the power of these methods for testing for association with binary and quantitative traits, and have made this software available as the R package CNVtools...
  8. pmc Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
    Jeffrey C Barrett
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Nat Genet 41:703-7. 2009
    ..01; overall P < 5 × 10(-8)) and 4 additional regions provided nominal evidence of replication (P < 0.05). The many new candidate genes suggested by these results include IL10, IL19, IL20, GLIS3, CD69 and IL27...
  9. pmc Haplotype structure, LD blocks, and uneven recombination within the LRP5 gene
    Rebecca C J Twells
    JDRF WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK
    Genome Res 13:845-55. 2003
    ..The identification of hot spots in between these LD blocks provides additional evidence that LD blocks are separated by areas of higher recombination...
  10. pmc Confirmation of HLA class II independent type 1 diabetes associations in the major histocompatibility complex including HLA-B and HLA-A
    J M M Howson
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Diabetes Obes Metab 11:31-45. 2009
    ..Here we test for HLA class II-independent associations in the MHC using fine mapping data generated by the Type 1 Diabetes Genetics Consortium (T1DGC)...
  11. pmc A generalization of the transmission/disequilibrium test for uncertain-haplotype transmission
    D Clayton
    MRC Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
    Am J Hum Genet 65:1170-7. 1999
    ..The proposed test is a score test based on a partial score function that omits the terms most influenced by hidden population stratification...
  12. pmc Transmission/disequilibrium tests for extended marker haplotypes
    D Clayton
    MRC Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
    Am J Hum Genet 65:1161-9. 1999
    ....
  13. pmc Link functions in multi-locus genetic models: implications for testing, prediction, and interpretation
    David Clayton
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge, Institute for Medical Research, Cambridge University, United Kingdom
    Genet Epidemiol 36:409-18. 2012
    ..These issues are reviewed, and a new association test proposed...
  14. pmc Extreme clonality in lymphoblastoid cell lines with implications for allele specific expression analyses
    Vincent Plagnol
    JDRF WT Diabetes and Inflammation Laboratory, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 3:e2966. 2008
    ..Consequently, we recommend where possible the use of bulk, non cell line, ex vivo cells for allele specific expression assays...
  15. ncbi request reprint A genome screen in multiple sclerosis reveals susceptibility loci on chromosome 6p21 and 17q22
    S Sawcer
    University of Cambridge Neurology Unit, Addenbrooke s Hospital, UK
    Nat Genet 13:464-8. 1996
    ..Two principal regions of linkage are identified, chromosomes 17q22 and 6p21 (MHC). Our results are compatible with genetic models involving epistatic interaction between these and several additional genes...
  16. ncbi request reprint Positive association of tyrosine hydroxylase microsatellite marker to essential hypertension
    P Sharma
    Clinical Pharmacology Unit, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Hypertension 32:676-82. 1998
    ..An ASP linkage model was negative, presumably because of lack of power. This study suggests that the TH gene, or a nearby gene, may be involved in the etiology of essential hypertension...
  17. ncbi request reprint Common BRCA1 variants and susceptibility to breast and ovarian cancer in the general population
    A M Dunning
    CRC Human Cancer Genetics Research Group, Addenbrooke s Hospital, Cambridge, UK
    Hum Mol Genet 6:285-9. 1997
    ..01), indicating that it may be protective against breast cancer. If this finding can be confirmed, it may provide an insight into the structural features of the BRCA1 protein that are important for its function...
  18. pmc Extra-binomial variation approach for analysis of pooled DNA sequencing data
    Xin Yang
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust MRC Building, Addenbrooke s Hospital, Cambridge CB2 0XY, UK
    Bioinformatics 28:2898-904. 2012
    ..Statistical analysis of pooled sequencing data needs to appropriately model this additional variance to avoid inflating the false-positive rate...
  19. pmc Quantification of homozygosity in consanguineous individuals with autosomal recessive disease
    C Geoffrey Woods
    Department of Medical Genetics, Cambridge Institute of Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, CB2 2XY, UK
    Am J Hum Genet 78:889-96. 2006
    ..This has important clinical and research implications...
  20. ncbi request reprint A genome-wide search for susceptibility loci to human essential hypertension
    P Sharma
    Clinical Pharmacology Unit, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Hypertension 35:1291-6. 2000
    ....
  21. ncbi request reprint A whole genome screen for linkage disequilibrium in multiple sclerosis confirms disease associations with regions previously linked to susceptibility
    Stephen Sawcer
    University of Cambridge Neurology Unit, Addenbrooke s Hospital, Cambridge, UK
    Brain 125:1337-47. 2002
    ....
  22. pmc No association between multiple sclerosis and the Notch3 gene responsible for cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL)
    S A Broadley
    University of Cambridge Neurology Unit, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 2QQ, UK
    J Neurol Neurosurg Psychiatry 71:97-9. 2001
    ..No evidence for association was found in any of the three markers and none of the commoner mutations causing CADASIL were found in the sequenced patients...
  23. ncbi request reprint No linkage between multiple sclerosis and the T cell receptor alpha chain locus
    M Eoli
    University of Cambridge Neurology Unit, Addenbrooke s Hospital, Cambridge, UK
    J Neurol Sci 124:32-7. 1994
    ..We conclude that the T cell receptor alpha locus is not linked to susceptibility in patients with MS from the United Kingdom...
  24. ncbi request reprint The heritability of plasma homocysteine, and the influence of genetic variation in the homocysteine methylation pathway
    A Siva
    Clinical Pharmacology Unit, University of Cambridge, UK
    QJM 100:495-9. 2007
    ..Many association studies have investigated common polymorphisms and their role in hyperhomocysteinaemia, but only the thermolabile variant of methylene tetrahydrofolate reductase (MTHFR) has shown an association (small but robust)...
  25. pmc Multiple sclerosis in sibling pairs: an analysis of 250 families
    J Chataway
    University of Cambridge Neurology Unit, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 2QQ, UK
    J Neurol Neurosurg Psychiatry 71:757-61. 2001
    ..These results are consistent with the hypothesis that genes influence both disease susceptibility and evolution in multiple sclerosis...
  26. ncbi request reprint One degree of freedom for dominance in indirect association studies
    Juliet Chapman
    London School of Hygiene and Tropical Medicine, London, UK
    Genet Epidemiol 31:261-71. 2007
    ..Assuming this scenario of a strong dominance effect, we present an appropriate test statistic and investigate how much power, if any, we gain by adding this single degree of freedom for dominance...
  27. pmc Genetic association analysis of inositol polyphosphate phosphatase-like 1 (INPPL1, SHIP2) variants with essential hypertension
    Ana Carolina Braga Marçano
    J Med Genet 44:603-5. 2007
    ..In particular, a haplotype of three genetic polymorphisms (rs2276047, rs9886 and an insertion/deletion polymorphism in intron 1) was found to be strongly associated with increased susceptibility to hypertension...
  28. ncbi request reprint Polymorphic variation in the 11beta-hydroxylase gene associates with reduced 11-hydroxylase efficiency
    Marianne Barr
    British Heart Foundation Glasgow Cardiovascular Research Centre, University of Glasgow, UK
    Hypertension 49:113-9. 2007
    ..This study strongly suggests that the impaired 11beta-hydroxylase efficiency associated previously with the CYP11B2 -344 and intron conversion variants is because of linkage with these newly identified polymorphisms in CYP11B1...
  29. ncbi request reprint Increased support for linkage of a novel locus on chromosome 5q13 for essential hypertension in the British Genetics of Hypertension Study
    Patricia B Munroe
    Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute Barts and the London School of Medicine, Charterhouse Square, London, United Kingdom
    Hypertension 48:105-11. 2006
    ..07). We found increased evidence for linkage and borderline-significant evidence for association for a hypertension susceptibility locus on chromosome 5q13 that is worthy of detailed fine mapping and assessment of candidate genes...
  30. ncbi request reprint Genome-wide mapping of human loci for essential hypertension
    Mark Caulfield
    Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London, Queen Mary s School of Medicine, London, UK
    Lancet 361:2118-23. 2003
    ..We describe the results of a genome scan for hypertension in a large white European population...
  31. ncbi request reprint Estimating the relative recurrence risk ratio using a global cross-ratio model
    Chris Wallace
    London School of Hygiene and Tropical Medicine, IDEU, London, UK
    Genet Epidemiol 25:293-302. 2003
    ..We apply the model to leprosy among sibling pairs from the Karonga district, Malawi. If risk factors are ignored, the apparent lambdaS in this population is over 3. Accounting for known nongenetic risk factors reduces it to just under 2...
  32. ncbi request reprint Haplotypes of the WNK1 gene associate with blood pressure variation in a severely hypertensive population from the British Genetics of Hypertension study
    Stephen J Newhouse
    Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and the London School of Medicine, London, UK
    Hum Mol Genet 14:1805-14. 2005
    ....
  33. ncbi request reprint Chromosome 2p shows significant linkage to antihypertensive response in the British Genetics of Hypertension Study
    Sandosh Padmanabhan
    BHF Glasgow Cardiovascular Research Centre, University of Glasgow, United Kingdom
    Hypertension 47:603-8. 2006
    ..We have demonstrated for the first time identification of a significant locus by partitioning different pathways of hypertension using drug response...
  34. ncbi request reprint Detecting association using epistatic information
    Juliet Chapman
    London School of Hygiene and Tropical Medicine, London, United Kingdom
    Genet Epidemiol 31:894-909. 2007
    ..In passing, the derivation of the indirect omnibus test statistic leads to a novel "indirect case-only test for interaction"...
  35. ncbi request reprint Two-dimensional genome-scan identifies novel epistatic loci for essential hypertension
    Jordana Tzenova Bell
    Department of Cardiovascular Medicine and Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Hum Mol Genet 15:1365-74. 2006
    ..This approach has discovered novel loci for hypertension and offers a unique potential to use existing data to uncover novel regions involved in complex human diseases...