Institution
Wellcome Trust Centre for Human Genetics
Facility•Oxford, United Kingdom•
About: Wellcome Trust Centre for Human Genetics is a facility organization based out in Oxford, United Kingdom. It is known for research contribution in the topics: Population & Genome-wide association study. The organization has 2122 authors who have published 4269 publications receiving 433899 citations.
Topics: Population, Genome-wide association study, Single-nucleotide polymorphism, Gene, Locus (genetics)
Papers published on a yearly basis
Papers
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TL;DR: Mapping of susceptibility to PCOS to the INS VNTR implies that PCOS is due, in part, to an inherited alteration in insulin production, which suggests a mechanistic link between type 2 diabetes and PCOS, which is a risk factor for diabetes later in life.
320 citations
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UCL Institute of Child Health1, University of Reading2, University of Tromsø3, German Cancer Research Center4, Boston University5, University of Oulu6, Imperial College London7, University of Groningen8, University of Helsinki9, Sahlgrenska University Hospital10, University College London11, King's College London12, George Washington University13, Wake Forest University14, University of Copenhagen15, Gentofte Hospital16, University of Exeter17, Trinity College, Dublin18, University of Edinburgh19, Ludwig Maximilian University of Munich20, University of Oxford21, Wellcome Trust Centre for Human Genetics22, Oulu University Hospital23, National Institutes of Health24, Finnish Institute of Occupational Health25, Heidelberg University26, University of Southampton27, Turku University Hospital28, University of Turku29, VU University Amsterdam30, Aarhus University Hospital31, University of Bristol32, Uppsala University33, Science for Life Laboratory34, University of Split35, Lund University36, Frederiksberg Hospital37, Harvard University38, University of Tampere39, Synlab Group40, Medical University of Graz41, Vanderbilt University42, GlaxoSmithKline43, University of South Australia44
TL;DR: In this article, the authors used a mendelian randomisation approach to test whether low plasma 25-hydroxyvitamin D (25[OH]D) concentration is causally associated with blood pressure and hypertension risk.
320 citations
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TL;DR: A new simulation algorithm based on a successful resampling method, HAPGEN, that can simulate multiple nearby disease SNPs on the same chromosome is introduced and expands the range of disease models that current simulators offer.
Abstract: Motivation: Performing experiments with simulated data is an inexpensive approach to evaluating competing experimental designs and analysis methods in genome-wide association studies. Simulation based on resampling known haplotypes is fast and efficient and can produce samples with patterns of linkage disequilibrium (LD), which mimic those in real data. However, the inability of current methods to simulate multiple nearby disease SNPs on the same chromosome can limit their application. Results: We introduce a new simulation algorithm based on a successful resampling method, HAPGEN, that can simulate multiple nearby disease SNPs on the same chromosome. The new method, HAPGEN2, retains many advantages of resampling methods and expands the range of disease models that current simulators offer. Availability: HAPGEN2 is freely available from http://www.stats.ox.ac.uk/~marchini/software/gwas/gwas.html. Contact: zhan@well.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
320 citations
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TL;DR: Trans-ethnic analyses of exome array data identify new risk loci for type 2 diabetes and fine-mapping analyses using genome-wide association data show that the index coding variants represent the likely causal variants at only a subset of these loci.
Abstract: We aggregated coding variant data for 81,412 type 2 diabetes cases and 370,832 controls of diverse ancestry, identifying 40 coding variant association signals (P < 2.2 × 10−7); of these, 16 map outside known risk-associated loci. We make two important observations. First, only five of these signals are driven by low-frequency variants: even for these, effect sizes are modest (odds ratio ≤1.29). Second, when we used large-scale genome-wide association data to fine-map the associated variants in their regional context, accounting for the global enrichment of complex trait associations in coding sequence, compelling evidence for coding variant causality was obtained for only 16 signals. At 13 others, the associated coding variants clearly represent ‘false leads’ with potential to generate erroneous mechanistic inference. Coding variant associations offer a direct route to biological insight for complex diseases and identification of validated therapeutic targets; however, appropriate mechanistic inference requires careful specification of their causal contribution to disease predisposition.
318 citations
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TL;DR: It is shown that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling, and a method for combining WGS panels to improve variant coverage and downstream imputations accuracy is presented.
Abstract: Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants.
318 citations
Authors
Showing all 2127 results
Name | H-index | Papers | Citations |
---|---|---|---|
Mark I. McCarthy | 200 | 1028 | 187898 |
John P. A. Ioannidis | 185 | 1311 | 193612 |
Gonçalo R. Abecasis | 179 | 595 | 230323 |
Simon I. Hay | 165 | 557 | 153307 |
Robert Plomin | 151 | 1104 | 88588 |
Ashok Kumar | 151 | 5654 | 164086 |
Julian Parkhill | 149 | 759 | 104736 |
James F. Wilson | 146 | 677 | 101883 |
Jeremy K. Nicholson | 141 | 773 | 80275 |
Hugh Watkins | 128 | 524 | 91317 |
Erik Ingelsson | 124 | 538 | 85407 |
Claudia Langenberg | 124 | 452 | 67326 |
Adrian V. S. Hill | 122 | 589 | 64613 |
John A. Todd | 121 | 515 | 67413 |
Elaine Holmes | 119 | 560 | 58975 |