Geraldine M Clarke

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. doi request reprint Aspects of observing and claiming allele flips in association studies
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
    Genet Epidemiol 34:266-74. 2010
  2. pmc A flexible approach for the analysis of rare variants allowing for a mixture of effects on binary or quantitative traits
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 9:e1003694. 2013
  3. pmc Basic statistical analysis in genetic case-control studies
    Geraldine M Clarke
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Protoc 6:121-33. 2011
  4. pmc A comparison of sample size and power in case-only association studies of gene-environment interaction
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Am J Epidemiol 171:498-505. 2010
  5. pmc A comparison of case-only designs for detecting gene x gene interaction in rheumatoid arthritis using genome-wide case-control data in Genetic Analysis Workshop 16
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
    BMC Proc 3:S73. 2009
  6. pmc Disentangling linkage disequilibrium and linkage from dense single-nucleotide polymorphism trio data
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
    Genetics 171:2085-95. 2005
  7. pmc Marker selection for genetic case-control association studies
    Fredrik H Pettersson
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Protoc 4:743-52. 2009
  8. pmc Fine mapping versus replication in whole-genome association studies
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
    Am J Hum Genet 81:995-1005. 2007
  9. pmc Data quality control in genetic case-control association studies
    Carl A Anderson
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Protoc 5:1564-73. 2010
  10. pmc Recent human effective population size estimated from linkage disequilibrium
    Albert Tenesa
    Colon Cancer Genetics Group, University of Edinburgh, Western General Hospital, Edinburgh, UK
    Genome Res 17:520-6. 2007

Detail Information

Publications10

  1. doi request reprint Aspects of observing and claiming allele flips in association studies
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
    Genet Epidemiol 34:266-74. 2010
    ..We conclude that evidence of variation in local patterns of LD, ancestral composition of study samples, and environmental exposures between study populations can provide compelling practical evidence in defense of a genuine allele flip...
  2. pmc A flexible approach for the analysis of rare variants allowing for a mixture of effects on binary or quantitative traits
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 9:e1003694. 2013
    ..We apply our method to investigate association of type-1 diabetes with imputed rare variants within genes in the major histocompatibility complex using genotype data from the Wellcome Trust Case Control Consortium. ..
  3. pmc Basic statistical analysis in genetic case-control studies
    Geraldine M Clarke
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Protoc 6:121-33. 2011
    ..Study design, marker selection and quality control of case-control studies have also been discussed in earlier protocols. The protocol should take ~1 h to complete...
  4. pmc A comparison of sample size and power in case-only association studies of gene-environment interaction
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Am J Epidemiol 171:498-505. 2010
    ..The common practice of assuming a dominant pattern of inheritance can cause serious losses of power in the presence of any recessive, or modest dominant, effects...
  5. pmc A comparison of case-only designs for detecting gene x gene interaction in rheumatoid arthritis using genome-wide case-control data in Genetic Analysis Workshop 16
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
    BMC Proc 3:S73. 2009
    ..Porportional odds and multinomial methods provide new tools for identification of G x G interactions...
  6. pmc Disentangling linkage disequilibrium and linkage from dense single-nucleotide polymorphism trio data
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
    Genetics 171:2085-95. 2005
    ..0 shows detection of the same coldspots and most hotspots: The Spearman rank correlation between the estimates from our method and those from PHASE is 0.58 (p < 2.2(-16))...
  7. pmc Marker selection for genetic case-control association studies
    Fredrik H Pettersson
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Protoc 4:743-52. 2009
    ..Publicly available web-based resources are utilized to browse and retrieve data, and software, such as Haploview and Goldsurfer2, is applied to investigate LD and to select tagSNPs...
  8. pmc Fine mapping versus replication in whole-genome association studies
    Geraldine M Clarke
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
    Am J Hum Genet 81:995-1005. 2007
    ..Our results provide a basis for the design and interpretation of GWA replication studies and point to the importance of a clear distinction between fine mapping and replication after GWA...
  9. pmc Data quality control in genetic case-control association studies
    Carl A Anderson
    Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
    Nat Protoc 5:1564-73. 2010
    ..Issues concerning study design and marker selection in case-control studies have been discussed in our earlier protocols. This protocol, which is routinely used in our labs, should take approximately 8 h to complete...
  10. pmc Recent human effective population size estimated from linkage disequilibrium
    Albert Tenesa
    Colon Cancer Genetics Group, University of Edinburgh, Western General Hospital, Edinburgh, UK
    Genome Res 17:520-6. 2007
    ..The estimates of N(e) are lower than previously published estimates based on heterozygosity, possibly because they represent one or more bottlenecks in human population size that occurred approximately 10,000 to 200,000 years ago...