Frank Dudbridge

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    Ruth Dunn
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Bioinformatics 6:39. 2005
  2. pmc Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data
    Frank Dudbridge
    MRC Biostatistics Unit, Cambridge, UK
    Hum Hered 66:87-98. 2008
  3. pmc Detecting multiple associations in genome-wide studies
    Frank Dudbridge
    MRC Biostatistics Unit, Cambridge, UK
    Hum Genomics 2:310-7. 2006
  4. pmc Estimation of significance thresholds for genomewide association scans
    Frank Dudbridge
    MRC Biostatistics Unit, Institute for Public Health, Cambridge, United Kingdom
    Genet Epidemiol 32:227-34. 2008
  5. pmc Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studies
    Frank Dudbridge
    MRC Rosalind Franklin Centre for Genomics Research, and MRC Biostatistics Unit, Cambridge, United Kingdom
    Am J Hum Genet 75:424-35. 2004
  6. doi request reprint Family-based association studies
    Frank Dudbridge
    Department Non communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
    Methods Mol Biol 713:119-27. 2011
  7. doi request reprint Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype
    Philippa Burns
    Department of Haematology, University of Cambridge and National Health Service Blood and Transplant, Cambridge, UK
    Platelets 19:258-67. 2008
  8. pmc Estimating causal effects of genetic risk variants for breast cancer using marker data from bilateral and familial cases
    Frank Dudbridge
    Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
    Cancer Epidemiol Biomarkers Prev 21:262-72. 2012
  9. pmc Unbiased estimation of odds ratios: combining genomewide association scans with replication studies
    Jack Bowden
    Institute of Public Health, Cambridge, UK
    Genet Epidemiol 33:406-18. 2009
  10. pmc Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor
    Maria Ban
    Department of Clinical Neuroscience, Addenbrooke s, Hospital, University of Cambridge, Cambridge, UK
    Eur J Hum Genet 17:1309-13. 2009

Detail Information

Publications42

  1. pmc The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    Ruth Dunn
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Bioinformatics 6:39. 2005
    ..This paper describes an automated method for finding clusters of interconnected proteins in protein interaction networks and retrieving protein annotations associated with these clusters...
  2. pmc Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data
    Frank Dudbridge
    MRC Biostatistics Unit, Cambridge, UK
    Hum Hered 66:87-98. 2008
    ..In comparison to APL and MITDT, the model is more robust to stratification and can accommodate sibships of any size. The methods are implemented for binary and continuous traits in software, UNPHASED, available from the author...
  3. pmc Detecting multiple associations in genome-wide studies
    Frank Dudbridge
    MRC Biostatistics Unit, Cambridge, UK
    Hum Genomics 2:310-7. 2006
    ....
  4. pmc Estimation of significance thresholds for genomewide association scans
    Frank Dudbridge
    MRC Biostatistics Unit, Institute for Public Health, Cambridge, United Kingdom
    Genet Epidemiol 32:227-34. 2008
    ....
  5. pmc Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studies
    Frank Dudbridge
    MRC Rosalind Franklin Centre for Genomics Research, and MRC Biostatistics Unit, Cambridge, United Kingdom
    Am J Hum Genet 75:424-35. 2004
    ..The estimation of analytic distributions for combined evidence will allow these powerful methods to be applied more widely in large exploratory studies...
  6. doi request reprint Family-based association studies
    Frank Dudbridge
    Department Non communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
    Methods Mol Biol 713:119-27. 2011
    ..The problem of testing association in general pedigrees is discussed, with particular reference to sib pairs without parents...
  7. doi request reprint Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype
    Philippa Burns
    Department of Haematology, University of Cambridge and National Health Service Blood and Transplant, Cambridge, UK
    Platelets 19:258-67. 2008
    ..The identification of DE genes may identify critical pathways and nodes not previously known to be involved in platelet development and function...
  8. pmc Estimating causal effects of genetic risk variants for breast cancer using marker data from bilateral and familial cases
    Frank Dudbridge
    Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
    Cancer Epidemiol Biomarkers Prev 21:262-72. 2012
    ..This can be explained by incomplete linkage disequilibrium between the tested marker and the underlying causal variant...
  9. pmc Unbiased estimation of odds ratios: combining genomewide association scans with replication studies
    Jack Bowden
    Institute of Public Health, Cambridge, UK
    Genet Epidemiol 33:406-18. 2009
    ..We illustrate our approach on some recently completed scans and explore its efficiency by simulation...
  10. pmc Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor
    Maria Ban
    Department of Clinical Neuroscience, Addenbrooke s, Hospital, University of Cambridge, Cambridge, UK
    Eur J Hum Genet 17:1309-13. 2009
    ....
  11. pmc Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins
    Marie N O'Connor
    Department of Haematology, University of Cambridge, Cambridge, United Kingdom
    Blood 113:4754-62. 2009
    ..We conclude that phenotypic analysis of MO-injected zebrafish is a fast and powerful method for initial screening of novel platelet proteins for function in thrombosis...
  12. pmc 9q31.2-rs865686 as a susceptibility locus for estrogen receptor-positive breast cancer: evidence from the Breast Cancer Association Consortium
    Helen Warren
    Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
    Cancer Epidemiol Biomarkers Prev 21:1783-91. 2012
    ..Our recent genome-wide association study identified a novel breast cancer susceptibility locus at 9q31.2 (rs865686)...
  13. ncbi request reprint Rank truncated product of P-values, with application to genomewide association scans
    Frank Dudbridge
    MRC Human Genome Mapping Project Resource Centre, Cambridge, UK
    Genet Epidemiol 25:360-6. 2003
    ..We show that, under realistic scenarios, it provides increased power to detect genomewide association, while identifying a candidate set of good quality and fixed size for follow-up studies...
  14. pmc A HaemAtlas: characterizing gene expression in differentiated human blood cells
    Nicholas A Watkins
    Department of Haematology, University of Cambridge, National Health Service Blood and Transplant, Cambridge, United Kingdom
    Blood 113:e1-9. 2009
    ..The data, which are freely accessible, will be invaluable for future studies on hematopoiesis and the role of specific genes and will also aid the understanding of the recent genome-wide association studies...
  15. pmc Comparison of methods for competitive tests of pathway analysis
    Marina Evangelou
    Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
    PLoS ONE 7:e41018. 2012
    ..The simulation and data application results are in agreement with previous work on association tests and suggests that the ARTP should be preferred for both enrichment and association testing...
  16. pmc What role for genetics in the prediction of multiple sclerosis?
    Stephen Sawcer
    Department of Clinical Neurosciences, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Ann Neurol 67:3-10. 2010
    ..There is an inevitable feeling that the same should be true in complex disease, but is it?..
  17. pmc A general framework for two-stage analysis of genome-wide association studies and its application to case-control studies
    James M S Wason
    Medical Research Council Biostatistics Unit, Institute for Public Health, Cambridge, UK
    Am J Hum Genet 90:760-73. 2012
    ..We give some analytic properties of the methods and discuss some underlying principles...
  18. pmc Genetic variants at chromosomes 2q35, 5p12, 6q25.1, 10q26.13, and 16q12.1 influence the risk of breast cancer in men
    Nick Orr
    The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
    PLoS Genet 7:e1002290. 2011
    ..Additional studies of well-defined patient subgroups could provide further insight into the biological basis of breast cancer development...
  19. doi request reprint Application of the optimal discovery procedure to genetic case-control studies: comparison with p values and asymptotic Bayes factors
    Ioanna Tachmazidou
    Medical Research Council, Biostatistics Unit, Institute of Public Health, Cambridge, UK
    Hum Hered 71:37-49. 2011
    ..We aimed to adapt the ODP to genetic case-control studies and to compare its power to p values and asymptotic BFs (ABFs)...
  20. pmc Comparison of multimarker logistic regression models, with application to a genomewide scan of schizophrenia
    James M S Wason
    MRC Biostatistics Unit, Institute of Public Health, Cambridge CB2 0SR, UK
    BMC Genet 11:80. 2010
    ..This is compared to two other commonly used multimarker GLMs: one with a main-effect parameter for each SNP; one with a parameter for each haplotype...
  21. ncbi request reprint Pelican: pedigree editor for linkage computer analysis
    Frank Dudbridge
    MRC Rosalind Franklin Centre for Genomics Research, Hinxton, Cambridge CB10 1SB, UK
    Bioinformatics 20:2327-8. 2004
    ..This is currently only available in commercial packages that include much greater functionality. We have therefore developed Pelican, a lightweight graphical pedigree editor for rapid construction of linkage pedigree files and diagrams...
  22. ncbi request reprint Pedigree disequilibrium tests for multilocus haplotypes
    Frank Dudbridge
    MRC Human Genome Mapping Project Resource Centre, Hinxton, Cambridge, UK
    Genet Epidemiol 25:115-21. 2003
    ..Exact permutation tests are difficult to construct in small samples, but an approximate procedure is appropriate in large samples, and can be used to account for dependencies between tests of multiple haplotypes and loci...
  23. ncbi request reprint Linkage and association mapping of the LRP5 locus on chromosome 11q13 in type 1 diabetes
    Rebecca C J Twells
    Department of Medical Genetics, JDRF WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust MRC Building, Addenbrooke s Hospital, Cambridge CB2 2XY, UK
    Hum Genet 113:99-105. 2003
    ..The continued search for the variants of the putative IDDM4 locus will greatly benefit from the future development of a haplotype map of the genome...
  24. pmc Polymorphisms in BDNF (Val66Met) and 5-HTTLPR, morning cortisol and subsequent depression in at-risk adolescents
    Ian M Goodyer
    Developmental Psychiatry Section, Department of Psychiatry, University of Cambridge, Douglas House, 18b Trumpington Road, Cambridge CB2 8AH, UK
    Br J Psychiatry 197:365-71. 2010
    ..There is increasing evidence for genetic effects on the hypothalamic-pituitary axis system. More than one gene is likely to moderate corticoid-mediated activity...
  25. ncbi request reprint Improving the power to detect differentially expressed genes in comparative microarray experiments by including information from self-self hybridizations
    Arief Gusnanto
    Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge CB2 2SR, UK
    Comput Biol Chem 31:178-85. 2007
    ..The largest increase in sensitivity occurs when the amount of information in the comparative hybridization is limited...
  26. pmc Candidate genes for obesity-susceptibility show enriched association within a large genome-wide association study for BMI
    Karani S Vimaleswaran
    MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke s Hospital, Cambridge, UK
    Hum Mol Genet 21:4537-42. 2012
    ..Studies that focus on candidate genes have only slightly increased chances of detecting associations, and are likely to miss many true effects in non-candidate genes, at least for obesity-related traits...
  27. ncbi request reprint An investigation of the neurotrophic factor genes GDNF, NGF, and NT3 in susceptibility to ADHD
    Zahoor Syed
    Addenbrookes Hospital, Cambridge, United Kingdom
    Am J Med Genet B Neuropsychiatr Genet 144:375-8. 2007
    ..69, odds ratio (OR) = 1.65, P = 0.05). Although this SNP is located in the 5' pro-NGF sequence and not the mature NGF protein, it may affect intracellular processing and secretion of NGF...
  28. pmc Early and current socio-economic position and cardiometabolic risk factors in the Indian Migration Study
    Ulla Sovio
    Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, UK
    Eur J Prev Cardiol 20:844-53. 2013
    ..The aim of this study is to estimate the associations of early and current socio-economic position (SEP) on adult cardiometabolic risk factors in the Indian Migration Study (N = 7,067)...
  29. doi request reprint Genetic association studies in pre-eclampsia: systematic meta-analyses and field synopsis
    Eleonora Staines-Urias
    Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, UK
    Int J Epidemiol 41:1764-75. 2012
    ..Pre-eclampsia is thought to have a polygenic basis, but the identification of susceptibility genes and the quantification of associated risks have been elusive owing to lack of replication from published genetic association studies...
  30. doi request reprint Alzheimer's disease and age-related macular degeneration have different genetic models for complement gene variation
    Petroula Proitsi
    King s College London, Institute of Psychiatry, De Crespigny Park, London, UK
    Neurobiol Aging 33:1843.e9-17. 2012
    ..Our study provides further support to the hypothesis that while activation of the alternative complement pathway is central to AMD pathogenesis, it is less involved in AD...
  31. doi request reprint A flexible model for association analysis in sibships with missing genotype data
    Frank Dudbridge
    London School of Hygiene and Tropical Medicine, London, UK
    Ann Hum Genet 75:428-38. 2011
    ..Compared to summing over all possible untransmitted alleles, we achieve similar power with considerable reductions in computation time...
  32. doi request reprint Genetic prediction of quantitative lipid traits: comparing shrinkage models to gene scores
    Helen Warren
    Department of Non communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
    Genet Epidemiol 38:72-83. 2014
    ..Instead, the most important choice for the prediction model is the number of SNPs and selection of the most predictive SNPs to include. However further comparisons, in larger samples and for other phenotypes, would still be of interest. ..
  33. ncbi request reprint Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins
    Iain C Macaulay
    Department of Haematology, University of Cambridge, Cambridge, UK
    Blood 109:3260-9. 2007
    ..The identification of the succinate receptor SUCNR1 in platelets is of particular interest, because physiologically relevant concentrations of succinate were shown to potentiate the effect of low doses of a variety of platelet agonists...
  34. pmc Evaluation of seven common lipid associated loci in a large Indian sib pair study
    Sajjad Rafiq
    Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
    Lipids Health Dis 11:155. 2012
    ..Given the rising prevalence of metabolic disorders and heart disease in the Indian sub-continent, these studies could be of future clinical relevance...
  35. pmc Power and predictive accuracy of polygenic risk scores
    Frank Dudbridge
    Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
    PLoS Genet 9:e1003348. 2013
    ..Therefore, polygenic scores currently have more utility for association testing than predicting complex traits, but prediction will become more feasible as sample sizes continue to grow...
  36. ncbi request reprint Linkage and potential association of obesity-related phenotypes with two genes on chromosome 12q24 in a female dizygous twin cohort
    Scott G Wilson
    Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
    Eur J Hum Genet 14:340-8. 2006
    ..0067) and P2RX4 (P = 0.017). These data provide replication and refinement of the 12q24 obesity locus and suggest that genes involved in phospholipase and purinoreceptor pathways may regulate fat accumulation and distribution...
  37. pmc Identification of a role for the ARHGEF3 gene in postmenopausal osteoporosis
    Ben H Mullin
    Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, 6009, Australia
    Am J Hum Genet 82:1262-9. 2008
    ..In conclusion, genetic variation in ARHGEF3 plays a role in the determination of bone density in Caucasian women. This data implicates the RhoGTPase-RhoGEF pathway in osteoporosis...
  38. ncbi request reprint Evaluation of Nyholt's procedure for multiple testing correction
    Daria Salyakina
    Max Planck Institute of Psychiatry, Munich, Germany
    Hum Hered 60:19-25; discussion 61-2. 2005
    ..We sought to carry out an empirical and theoretical evaluation of Nyholt's method...
  39. ncbi request reprint Polymorphism in HSD17B6 is associated with key features of polycystic ovary syndrome
    Michelle R Jones
    Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
    Fertil Steril 86:1438-46. 2006
    ....
  40. doi request reprint Maximizing association statistics over genetic models
    Juan R Gonzalez
    Center for research in environmental epidemiology CREAL, Barcelona, Spain
    Genet Epidemiol 32:246-54. 2008
    ..A simulation study shows that the use of the max-statistic is a powerful approach that provides safeguard against model uncertainty...
  41. pmc A survey of current software for linkage analysis
    Frank Dudbridge
    MRC Human Genome Mapping Project Resource Centre, Hinxton, Cambridge CB10 1SB, UK
    Hum Genomics 1:63-5. 2003
    ..The computational limits of current approaches can be improved with SIMWALK2 and the promising new SUPERLINK program. Directions for future work include improved user interfaces and consensus formats for data input and exchange...
  42. pmc A note on permutation tests in multistage association scans
    Frank Dudbridge
    Am J Hum Genet 78:1094-5; author reply 1096. 2006