Affiliation: National Institute for Medical Research
- Pedigree disequilibrium tests for multilocus haplotypesFrank 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...
- Rank truncated product of P-values, with application to genomewide association scansFrank 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...
- A survey of current software for linkage analysisFrank 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...
- Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotypePhilippa 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...
- Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factorMaria Ban
Department of Clinical Neuroscience, Addenbrooke s, Hospital, University of Cambridge, Cambridge, UK
Eur J Hum Genet 17:1309-13. 2009....
- Unbiased estimation of odds ratios: combining genomewide association scans with replication studiesJack 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...
- Two novel pathway analysis methods based on a hierarchical modelMarina Evangelou
Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, CB2 0SR, UK, JDRF Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, CB2 0XY, UK and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
Bioinformatics 30:690-7. 2014..Hierarchical models have been advocated as a way to integrate SNP and pathway effects in the same model, but their computational complexity has prevented them being applied on a genome-wide scale to date...
- 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?..
- Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype dataFrank 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...
- A general framework for two-stage analysis of genome-wide association studies and its application to case-control studiesJames 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...
- The use of edge-betweenness clustering to investigate biological function in protein interaction networksRuth 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...
- Application of the optimal discovery procedure to genetic case-control studies: comparison with p values and asymptotic Bayes factorsIoanna 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)...
- Candidate genes for obesity-susceptibility show enriched association within a large genome-wide association study for BMIKarani 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...
- Detecting multiple associations in genome-wide studiesFrank Dudbridge
MRC Biostatistics Unit, Cambridge, UK
Hum Genomics 2:310-7. 2006....
- Pelican: pedigree editor for linkage computer analysisFrank 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...
- Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteinsIain 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...
- Maximizing association statistics over genetic modelsJuan 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...
- Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studiesFrank 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...
- Linkage and potential association of obesity-related phenotypes with two genes on chromosome 12q24 in a female dizygous twin cohortScott 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...
- Identification of a role for the ARHGEF3 gene in postmenopausal osteoporosisBen 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...
- Evaluation of Nyholt's procedure for multiple testing correctionDaria 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...
- Estimation of significance thresholds for genomewide association scansFrank Dudbridge
MRC Biostatistics Unit, Institute for Public Health, Cambridge, United Kingdom
Genet Epidemiol 32:227-34. 2008....
- Improving the power to detect differentially expressed genes in comparative microarray experiments by including information from self-self hybridizationsArief 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...
- An investigation of the neurotrophic factor genes GDNF, NGF, and NT3 in susceptibility to ADHDZahoor 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...
- Polymorphism in HSD17B6 is associated with key features of polycystic ovary syndromeMichelle R Jones
Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
Fertil Steril 86:1438-46. 2006....
- A note on permutation tests in multistage association scansFrank Dudbridge
Am J Hum Genet 78:1094-5; author reply 1096. 2006
- Linkage and association mapping of the LRP5 locus on chromosome 11q13 in type 1 diabetesRebecca 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...