Research Topics
Genomes and Genes
| Eleftheria ZegginiSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
| Collaborators
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Detail Information
Publications
Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritisJohn Bowes
Arthritis Research UK, Epidemiology Unit, University of Manchester, Manchester, UK
Hum Genet 128:627-33. 2010....- Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants?L Southam
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Diabetologia 52:1846-51. 2009.... - Large-scale association analysis of TNF/LTA gene region polymorphisms in type 2 diabetesVesna Boraska
Department of Medical Biology, University of Split School of Medicine, Split, Croatia
BMC Med Genet 11:69. 2010..The purpose of this study is to examine T2D association of tag SNPs in the TNF/LTA region capturing the majority of common variation in a large-scale sample set of UK/Irish origin... - CCRaVAT and QuTie-enabling analysis of rare variants in large-scale case control and quantitative trait association studiesRobert Lawrence
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
BMC Bioinformatics 11:527. 2010.... - Next-generation association studies for complex traitsEleftheria Zeggini
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Nat Genet 43:287-8. 2011..This strategy is poised to help elucidate the role of variants at the low end of the allele frequency spectrum in the genetic architecture of complex traits... 
Significant linkage of BMI to chromosome 10p in the U.K. population and evaluation of GAD2 as a positional candidateChristopher J Groves
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
Diabetes 55:1884-9. 2006....- The variable number of tandem repeats upstream of the insulin gene is a susceptibility locus for latent autoimmune diabetes in adultsMinal Desai
Diabetes Research Laboratories, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
Diabetes 55:1890-4. 2006..In conclusion, differences in VNTR-encoded susceptibility do not explain the differences in clinical presentation that distinguish classical type 1 diabetes and LADA... - Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association dataNicholas J Timpson
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Diabetes 58:505-10. 2009..This study examined how differences in the BMI distribution of type 2 diabetic case subjects affected genome-wide patterns of type 2 diabetes association and considered the implications for the etiological heterogeneity of type 2 diabetes... - A powerful approach to sub-phenotype analysis in population-based genetic association studiesAndrew P Morris
The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
Genet Epidemiol 34:335-43. 2010.... - Re-evaluation of putative rheumatoid arthritis susceptibility genes in the post-genome wide association study era and hypothesis of a key pathway underlying susceptibilityAnne Barton
ARC Epidemiology Unit, Stopford Building, The University of Manchester, Manchester, UK
Hum Mol Genet 17:2274-9. 2008..The effect sizes are less than those reported previously but are likely to be a more accurate reflection of the true effect size given the larger size of the cohort investigated in the current study... - Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetesEleftheria Zeggini
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Nat Genet 40:638-45. 2008..1 x 10(-9)), ADAMTS9 (P = 1.2 x 10(-8)) and NOTCH2 (P = 4.1 x 10(-8)) gene regions. Our results illustrate the value of large discovery and follow-up samples for gaining further insights into the inherited basis of T2D... - A functional promoter haplotype of macrophage migration inhibitory factor is linked and associated with juvenile idiopathic arthritisRachelle Donn
Arthritis Research Campaign Epidemiology Unit, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
Arthritis Rheum 50:1604-10. 2004..To establish linkage and replicate the association of macrophage migration inhibitory factor (MIF) with juvenile idiopathic arthritis (JIA)... - Linkage disequilibrium mapping of the replicated type 2 diabetes linkage signal on chromosome 1qInga Prokopenko
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Diabetes 58:1704-9. 2009..We performed common variant fine-mapping across a 23-Mb interval in a multiethnic sample to search for variants responsible for this linkage signal... - Evidence for a novel rheumatoid arthritis susceptibility locus on chromosome 6pWilliam Brintnell
University of Manchester, Manchester, UK
Arthritis Rheum 50:3823-30. 2004..To investigate whether the large linkage peak on chromosome 6p harbors rheumatoid arthritis (RA) susceptibility loci in addition to the well-characterized HLA-DRB1 gene... - Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definitionEleftheria Zeggini
Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
BMC Genet 6:21. 2005..5 kb, we constructed haplotype block maps using published methods and additional methods we have developed. Haplotype tagging SNPs (htSNPs) were identified for each map... - Examining the statistical properties of fine-scale mapping in large-scale association studiesSteven Wiltshire
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
Genet Epidemiol 32:204-14. 2008..Our findings help inform the interpretation and design of dense SNP-mapping follow-up studies, thus facilitating discrimination between a genuine genetic effect and chance fluctuation (false positive)... - An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data setsEleftheria Zeggini
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Nat Genet 37:1320-2. 2005.... - MCP-1 gene haplotype association in biopsy proven giant cell arteritisMahsa M Amoli
Centre for Integrated Genomic Medical Research, School of Epidemiology and Health Sciences, The University of Manchester, Manchester, UK
J Rheumatol 32:507-10. 2005..To investigate the clinical implication of MCP-1 polymorphisms in GCA, we examined the association of 3 single nucleotide polymorphisms (SNP) in a series of patients with GCA from Northwest Spain... - An evaluation of statistical approaches to rare variant analysis in genetic association studiesAndrew P Morris
Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
Genet Epidemiol 34:188-93. 2010.... - Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellitesSally John
University of Manchester, Manchester, United Kingdom
Am J Hum Genet 75:54-64. 2004..The high SNP density allows loci to be defined more precisely and provides a partial scaffold for association studies, substantially reducing the resource requirement for gene-mapping studies... - Mutation screening of the macrophage migration inhibitory factor gene: positive association of a functional polymorphism of macrophage migration inhibitory factor with juvenile idiopathic arthritisRachelle Donn
Epidemiology Unit, Arthritis Research Campaign, University of Manchester, Manchester, UK
Arthritis Rheum 46:2402-9. 2002..To determine if polymorphisms of the macrophage migration inhibitory factor (MIF) gene are associated with juvenile idiopathic arthritis (JIA)... - Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13Anne Barton
Arthritis Research Campaign, Epidemiology Unit, The University of Manchester, Manchester, UK
Nat Genet 40:1156-9. 2008.... - Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetesEleftheria Zeggini
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
Science 316:1336-41. 2007..The regions identified underscore the importance of pathways influencing pancreatic beta cell development and function in the etiology of type 2 diabetes... - Relationship between E23K (an established type II diabetes-susceptibility variant within KCNJ11), polycystic ovary syndrome and androgen levelsThomas M Barber
Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Old Road, Headington, Oxford, UK
Eur J Hum Genet 15:679-84. 2007..08). In conclusion, these data (involving >4600 subjects) provide no evidence that common variants of the KCNJ11 E23K polymorphism have a major influence on PCOS susceptibility, though modest effect sizes (OR<1.25) cannot be excluded... - Variation within the gene encoding the upstream stimulatory factor 1 does not influence susceptibility to type 2 diabetes in samples from populations with replicated evidence of linkage to chromosome 1qEleftheria Zeggini
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
Diabetes 55:2541-8. 2006..These data exclude USF1 as a major contributor to type 2 diabetes susceptibility and the basis for the chromosome 1q linkage. They reveal only limited evidence for replication of USF1 effects on continuous metabolic traits... - GLIDERS--a web-based search engine for genome-wide linkage disequilibrium between HapMap SNPsRobert Lawrence
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
BMC Bioinformatics 10:367. 2009..3 across the human genome for any SNP genotyped within HapMap phase 2 and 3, regardless of distance between the markers... - Genome-wide association scan allowing for epistasis in type 2 diabetesJordana T Bell
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Ann Hum Genet 75:10-9. 2011..Our results demonstrate the feasibility of systematic scans in GWA data, but confirm that single-locus association can underlie and obscure multilocus findings... - Defining the power limits of genome-wide association scan meta-analysesKay Chapman
Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
Genet Epidemiol 35:781-9. 2011.... - Epistatic interactions between HLA-DRB1 and interleukin 4, but not interferon-gamma, increase susceptibility to giant cell arteritisMahsa M Amoli
Centre for Integrated Genomic Medical Research, School of Epidemiology and Health Sciences, University of Manchester, Manchester, United Kingdom
J Rheumatol 31:2413-7. 2004..To assess the roles of the interleukin 4 (IL-4) and interferon-g (IFN-g) gene polymorphisms in a series of patients with biopsy-proven giant cell arteritis (GCA)... - Will the real disease gene please stand up?Neil Shephard
Epidemiology Unit, University of Manchester, Manchester, UK
BMC Genet 6:S66. 2005..Performing a comprehensive assay of all markers in a large, well-powered dataset appears to be the most effective strategy for complex disease gene identification... - Variants in MTNR1B influence fasting glucose levelsInga Prokopenko
1 Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK 2 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK 3 These authors contributed equally to this work
Nat Genet 41:77-81. 2009..Our analyses also confirm previous associations of fasting glucose with variants at the G6PC2 (rs560887, P = 1.1 x 10(-57)) and GCK (rs4607517, P = 1.0 x 10(-25)) loci... - A variant in MCF2L is associated with osteoarthritisAaron G Day-Williams
Wellcome Trust Sanger Institute, Hinxton, UK
Am J Hum Genet 89:446-50. 2011..MCF2L regulates a nerve growth factor (NGF), and treatment with a humanized monoclonal antibody against NGF is associated with reduction in pain and improvement in function for knee OA patients... - Genome-wide association study to identify common variants associated with brachial circumference: a meta-analysis of 14 cohortsVesna Boraska
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
PLoS ONE 7:e31369. 2012..Large-scale collaborations will be necessary to achieve higher power to detect loci underlying BC... - Evaluation of association of HNF1B variants with diverse cancers: collaborative analysis of data from 19 genome-wide association studiesKatherine S Elliott
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
PLoS ONE 5:e10858. 2010..We aimed to identify whether these variants may have an effect on cancer risk in general versus a specific effect on prostate cancer only... - Linkage and association studies of single-nucleotide polymorphism-tagged tumor necrosis factor haplotypes in juvenile oligoarthritisEleftheria Zeggini
Arthritis Research Campaign Epidemiology Unit, University of Manchester, Manchester, UK
Arthritis Rheum 46:3304-11. 2002..The aim of this study was to examine the association of multiple TNF SNPs with juvenile oligoarthritis and to construct and analyze SNP-tagged TNF haplotypes... - Identifying susceptibility variants for type 2 diabetesEleftheria Zeggini
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, UK
Methods Mol Biol 376:235-50. 2007.... - Evidence for linkage of HLA loci in juvenile idiopathic oligoarthritis: independent effects of HLA-A and HLA-DRB1Eleftheria Zeggini
Arthritis Research Campaign Epidemiology Unit, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
Arthritis Rheum 46:2716-20. 2002..The aim of this study was to investigate linkage of HLA-A, B, and DRB1 in UK Caucasian JIA patients with oligoarthritis... - Genome-wide association scans for Type 2 diabetes: new insights into biology and therapyMark I McCarthy
Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Old Road, Headington, Oxford, UK
Trends Pharmacol Sci 28:598-601. 2007..Here, we provide an overview of the main recent findings and discuss their significance in providing biological insights and their translational implications... - An evaluation of different meta-analysis approaches in the presence of allelic heterogeneityJennifer Asimit
Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
Eur J Hum Genet 20:709-12. 2012..We conclude that current strategies for the combination of genetic association data in the presence of allelic heterogeneity are insufficiently powered... - ARIEL and AMELIA: testing for an accumulation of rare variants using next-generation sequencing dataJennifer L Asimit
Wellcome Trust Sanger Institute, Hinxton, UK
Hum Hered 73:84-94. 2012..Here, we propose two locus-based methods that incorporate variant quality scores: a regression-based collapsing approach and an allele-matching method... - Linkage analysis of cross-sectional and longitudinally derived phenotypic measures to identify loci influencing blood pressureNeil Shephard
ARC Epidemiology Unit, University of Manchester, Manchester, United Kingdom
BMC Genet 4:S26. 2003.... 
Do genome-wide association scans have potential for translation?Margarida C Lopes
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Clin Chem Lab Med 50:255-60. 2012..The biological insights afforded by newly-identified robust associations represent the largest, albeit indirect, translational contribution of GWAS...- 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.... - An evaluation of different target enrichment methods in pooled sequencing designs for complex disease association studiesAaron G Day-Williams
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
PLoS ONE 6:e26279. 2011.... - The effect of genome-wide association scan quality control on imputation outcome for common variantsLorraine Southam
Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
Eur J Hum Genet 19:610-4. 2011..A minority of common-frequency SNPs with particular properties cannot be accurately imputed regardless of QC stringency. These findings may not generalise to the imputation of low frequency and rare variants... - Analysis of multiple data sets reveals no association between the insulin gene variable number tandem repeat element and polycystic ovary syndrome or related traitsBrenda L Powell
Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
J Clin Endocrinol Metab 90:2988-93. 2005..Variation at the insulin gene VNTR (variable number tandem repeat) minisatellite has been reported to be associated with polycystic ovary syndrome (PCOS), but findings have been inconsistent and all studies have featured small sample sizes... - Lack of association between juvenile idiopathic arthritis and fas gene polymorphismRachelle Donn
ARC Epidemiology Unit, University of Manchester, UK
J Rheumatol 29:166-8. 2002..We investigated whether a polymorphism in the Fas promoter region (-670) confers susceptibility to JIA... - Association studies of insulin receptor substrate 1 gene (IRS1) variants in type 2 diabetes samples enriched for family history and early age of onsetEleftheria Zeggini
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
Diabetes 53:3319-22. 2004.... - Genome-wide association studies in type 2 diabetesMark I McCarthy
Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Old Road, Headington, Oxford, OX3 7LJ, UK
Curr Diab Rep 9:164-71. 2009.... - Genome-wide meta-analysis of common variant differences between men and womenVesna Boraska
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Hum Mol Genet 21:4805-15. 2012..The absence of sex-specific differences is useful in guiding genetic association study design, for example when using mixed controls for sex-biased traits... - Finding common susceptibility variants for complex disease: past, present and futureKalliope Panoutsopoulou
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Brief Funct Genomic Proteomic 8:345-52. 2009..In this review, we summarize insights gained from the past, highlight practical issues relating to the design and analysis of current state-of-the-art GWA studies and look into future trends in the field of human complex trait genetics... - Genetics of type 2 diabetesMark I McCarthy
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital Campus, Old Road, Oxford OX3 7LJ, UK
Curr Diab Rep 6:147-54. 2006..The advent of genuinely genome-wide association scans and the prospects for combining genetics with high-throughput genomics are additional sources of optimism for the future... - Synthetic associations in the context of genome-wide association scan signalsGisela Orozco
Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester, UK
Hum Mol Genet 19:R137-44. 2010..In this review, we draw from empirical and theoretical data to summarize evidence showing that synthetic associations do not underlie many reported GWAS associations... - Synthetic associations are unlikely to account for many common disease genome-wide association signalsCarl A Anderson
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
PLoS Biol 9:e1000580. 2011..Synthetic associations have been posited as a possible explanation for missing heritability in complex disease. We show several lines of evidence which suggest that, while possible, these synthetic associations are not common... - Identification of novel putative rheumatoid arthritis susceptibility genes via analysis of rare variantsAndrew P Morris
Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
BMC Proc 3:S131. 2009..We apply our method to WGA SNP genotype data obtained from 868 RA cases and 1194 controls. Our results highlight novel putative RA susceptibility genes that have not previously been identified in large-scale WGA studies... - Testing for rare variant associations in complex diseasesJennifer Asimit
Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
Genome Med 1:24. 2009..have presented an approach with the theoretical capacity to detect risk and protective variants. The identification of rare risk variants could have major implications in understanding complex disease etiopathogenesis... - Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosisGeorge F Mells
Academic Department of Medical Genetics, Cambridge University, Cambridge, UK Department of Hepatology, Cambridge University Hospitals National Health Service NHS Foundation Trust, Cambridge, UK
Nat Genet 43:329-32. 2011..New candidate genes include STAT4, DENND1B, CD80, IL7R, CXCR5, TNFRSF1A, CLEC16A and NFKB1. This study has considerably expanded our knowledge of the genetic architecture of PBC... - Population-specific risk of type 2 diabetes conferred by HNF4A P2 promoter variants: a lesson for replication studiesInes Barroso
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Diabetes 57:3161-5. 2008..We aimed to investigate whether data from a large-scale mapping approach would replicate this association in novel Ashkenazi samples and in U.K. populations and whether these data would allow us to refine the association signal... - A combined functional annotation score for non-synonymous variantsMargarida C Lopes
Wellcome Trust Sanger Institute, Hinxton, Hinxton, UK
Hum Hered 73:47-51. 2012.... - The effect of next-generation sequencing technology on complex trait researchAaron G Day-Williams
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Eur J Clin Invest 41:561-7. 2011..Advances in the understanding of complex trait genetics have always been enabled by advances in genomic technology. Next-generation sequencing (NGS) is set to revolutionize the way complex trait genetics research is carried out... - Meta-analysis in genome-wide association studiesEleftheria Zeggini
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Pharmacogenomics 10:191-201. 2009..Finally, we discuss the prospects and caveats for future application of meta-analysis methods in the genome-wide setting...