Genomes and Genes
Affiliation: University of Cambridge
- 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...
- Detecting multiple associations in genome-wide studiesFrank Dudbridge
MRC Biostatistics Unit, Cambridge, UK
Hum Genomics 2:310-7. 2006....
- 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...
- 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...
- Family-based association studiesFrank 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...
- 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....
- Genetic prediction of quantitative lipid traits: comparing shrinkage models to gene scoresHelen 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. ..
- 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...
- 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...
- Estimating causal effects of genetic risk variants for breast cancer using marker data from bilateral and familial casesFrank 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...
- 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...
- 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....
- Early and current socio-economic position and cardiometabolic risk factors in the Indian Migration StudyUlla 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)...
- Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteinsMarie 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...
- 9q31.2-rs865686 as a susceptibility locus for estrogen receptor-positive breast cancer: evidence from the Breast Cancer Association ConsortiumHelen 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)...
- 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 HaemAtlas: characterizing gene expression in differentiated human blood cellsNicholas 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...
- Comparison of methods for competitive tests of pathway analysisMarina 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...
- 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?..
- Genetic variation at CYP3A is associated with age at menarche and breast cancer risk: a case-control studyNichola Johnson
Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
Breast Cancer Res 16:R51. 2014..1), was associated with a reduction in premenopausal urinary estrone glucuronide levels and a modest reduction in risk of breast cancer in women age ≤50 years...
- 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...
- Genetic variants at chromosomes 2q35, 5p12, 6q25.1, 10q26.13, and 16q12.1 influence the risk of breast cancer in menNick 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...
- Comparison of multimarker logistic regression models, with application to a genomewide scan of schizophreniaJames 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...
- 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)...
- 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...
- 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...
- Polymorphisms in BDNF (Val66Met) and 5-HTTLPR, morning cortisol and subsequent depression in at-risk adolescentsIan 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...
- 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...
- 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...
- 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...
- 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...
- Genetic association studies in pre-eclampsia: systematic meta-analyses and field synopsisEleonora 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...
- Alzheimer's disease and age-related macular degeneration have different genetic models for complement gene variationPetroula 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...
- A flexible model for association analysis in sibships with missing genotype dataFrank 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...
- Candidate gene-environment interactions in breast cancerOlivia Fletcher
Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
BMC Med 12:195. 2014..Before we can make this assessment we will need to replicate (or refute) the reported interactions, identify the causal variants that underlie tag-SNP associations and validate the next generation of epidemiological risk models. ..
- Testing for non-linear causal effects using a binary genotype in a Mendelian randomization study: application to alcohol and cardiovascular traitsRichard J Silverwood
Faculty of Epidemiology and Population Health, Centre for Statistical Methodology and Bloomsbury Centre for Genetic Epidemiology and Statistics, London School of Hygiene and Tropical Medicine, London, UK, Department of Epidemiology and Public Health, University College London, London, UK, MRC Integrative Epidemiology Unit and School of Social and Community Medicine, University of Bristol, Bristol, UK, Genetics, R and D, GlaxoSmithKline, Stevenage, UK, Division of Health Sciences, University of Warwick, Warwick, Coventry, UK, Center for Applied Genomics, Abramson Research Center, Children s Hospital of Philadelphia, Philadelphia, PA, USA and Institute of Cardiovascular Science, University College London, London, UK Faculty of Epidemiology and Population Health, Centre for Statistical Methodology and Bloomsbury Centre for Genetic Epidemiology and Statistics, London School of Hygiene and Tropical Medicine, London, UK, Department of Epidemiology and Public Health, University College London, London, UK, MRC Integrative Epidemiology Unit and School of Social and Community Medicine, University of Bristol, Bristol, UK, Genetics, R and D, GlaxoSmithKline, Stevenage, UK, Division of Health Sciences, University of Warwick, Warwick, Coventry, UK
Int J Epidemiol 43:1781-90. 2014..In principle, Mendelian randomization could address concerns that the apparent protective effect of light-to-moderate drinking might reflect 'sick-quitters' and confounding...
- Population genomics of cardiometabolic traits: design of the University College London-London School of Hygiene and Tropical Medicine-Edinburgh-Bristol (UCLEB) ConsortiumTina Shah
Department of Epidemiology and Public Health, UCL Institute of Epidemiology and Health Care, University College London, London, United Kingdom
PLoS ONE 8:e71345. 2013....
- 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...
- Power and predictive accuracy of polygenic risk scoresFrank 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...
- Evaluation of seven common lipid associated loci in a large Indian sib pair studySajjad 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...
- 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 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...
- 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...
- 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...
- 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...
- 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...
- A note on permutation tests in multistage association scansFrank Dudbridge
Am J Hum Genet 78:1094-5; author reply 1096. 2006