Vincent Plagnol

Summary

Affiliation: University College London
Country: UK

Publications

  1. pmc A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
    Vincent Plagnol
    UCL Genetics Institute, UCL, London, UK
    Bioinformatics 28:2747-54. 2012
  2. pmc Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases
    Vincent Plagnol
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
    PLoS Genet 7:e1002216. 2011
  3. pmc Shared and distinct genetic variants in type 1 diabetes and celiac disease
    Deborah J Smyth
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, United Kingdom
    N Engl J Med 359:2767-77. 2008
  4. pmc Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci
    Jason D Cooper
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Nat Genet 40:1399-401. 2008
  5. ncbi request reprint RP1L1 variants are associated with a spectrum of inherited retinal diseases including retinitis pigmentosa and occult macular dystrophy
    Alice E Davidson
    University College London Institute of Ophthalmology, London, UK
    Hum Mutat 34:506-14. 2013
  6. doi request reprint PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes
    Deborah J Smyth
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Diabetes 57:1730-7. 2008
  7. pmc Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource
    Calliope A Dendrou
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Hills Road, Cambridge, UK
    Nat Genet 41:1011-5. 2009
  8. pmc Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
    Jeffrey C Barrett
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Nat Genet 41:703-7. 2009
  9. pmc Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
    John A Todd
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, University of Cambridge, Addenbrooke s Hospital, Cambridge CB2 0XY, UK
    Nat Genet 39:857-64. 2007
  10. pmc Statistical independence of the colocalized association signals for type 1 diabetes and RPS26 gene expression on chromosome 12q13
    Vincent Plagnol
    Juveniles Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
    Biostatistics 10:327-34. 2009

Detail Information

Publications41

  1. pmc A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
    Vincent Plagnol
    UCL Genetics Institute, UCL, London, UK
    Bioinformatics 28:2747-54. 2012
    ..However, technical variability between samples complicates the analysis and can create spurious CNV calls...
  2. pmc Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases
    Vincent Plagnol
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
    PLoS Genet 7:e1002216. 2011
    ..Analysis of the TPOA-associated loci in 2,477 cases with Graves' disease identified two new AITD loci (BACH2 and UBASH3A)...
  3. pmc Shared and distinct genetic variants in type 1 diabetes and celiac disease
    Deborah J Smyth
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, United Kingdom
    N Engl J Med 359:2767-77. 2008
    ..Since both diseases are associated with the HLA class II genes on chromosome 6p21, we tested whether non-HLA loci are shared...
  4. pmc Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci
    Jason D Cooper
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Nat Genet 40:1399-401. 2008
    ..7 x 10(-12)), 10p15 (PRKCQ, P = 3.7 x 10(-9)), 15q24 (CTSH, P = 3.2 x 10(-15)) and 22q13 (C1QTNF6, P = 2.0 x 10(-8))...
  5. ncbi request reprint RP1L1 variants are associated with a spectrum of inherited retinal diseases including retinitis pigmentosa and occult macular dystrophy
    Alice E Davidson
    University College London Institute of Ophthalmology, London, UK
    Hum Mutat 34:506-14. 2013
    ..These findings imply an important and diverse role for RP1L1 in human retinal physiology and disease...
  6. doi request reprint PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes
    Deborah J Smyth
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Diabetes 57:1730-7. 2008
    ....
  7. pmc Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource
    Calliope A Dendrou
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Hills Road, Cambridge, UK
    Nat Genet 41:1011-5. 2009
    ....
  8. pmc Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
    Jeffrey C Barrett
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Nat Genet 41:703-7. 2009
    ..01; overall P < 5 × 10(-8)) and 4 additional regions provided nominal evidence of replication (P < 0.05). The many new candidate genes suggested by these results include IL10, IL19, IL20, GLIS3, CD69 and IL27...
  9. pmc Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
    John A Todd
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, University of Cambridge, Addenbrooke s Hospital, Cambridge CB2 0XY, UK
    Nat Genet 39:857-64. 2007
    ..Several regions, including 18q22 and 18p11, showed association with autoimmune thyroid disease. This study increases the number of T1D loci with compelling evidence from six to at least ten...
  10. pmc Statistical independence of the colocalized association signals for type 1 diabetes and RPS26 gene expression on chromosome 12q13
    Vincent Plagnol
    Juveniles Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
    Biostatistics 10:327-34. 2009
    ..Here, we derive and apply a statistical test of this hypothesis. We conclude that RPS26 expression is unlikely to be the molecular trait responsible for T1D susceptibility at this locus, at least not in a direct, linear connection...
  11. ncbi request reprint Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes
    Christopher E Lowe
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, UK
    Nat Genet 39:1074-82. 2007
    ..635). Furthermore, we have associated IL2RA T1D susceptibility genotypes with lower circulating levels of the biomarker, soluble IL-2RA (P = 6.28 x 10(-28)), suggesting that an inherited lower immune responsiveness predisposes to T1D...
  12. ncbi request reprint Autosomal-recessive cerebellar ataxia caused by a novel ADCK3 mutation that elongates the protein: clinical, genetic and biochemical characterisation
    Yo Tsen Liu
    MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
    J Neurol Neurosurg Psychiatry 85:493-8. 2014
    ..ADCK3 encodes a mitochondrial protein which functions as an electron-transfer membrane protein complex in the mitochondrial respiratory chain (MRC)...
  13. pmc Extreme clonality in lymphoblastoid cell lines with implications for allele specific expression analyses
    Vincent Plagnol
    JDRF WT Diabetes and Inflammation Laboratory, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 3:e2966. 2008
    ..Consequently, we recommend where possible the use of bulk, non cell line, ex vivo cells for allele specific expression assays...
  14. pmc Exome sequencing identifies autosomal-dominant SRP72 mutations associated with familial aplasia and myelodysplasia
    Michael Kirwan
    Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
    Am J Hum Genet 90:888-92. 2012
    ..These results suggest that inherited mutations in a component of the SRP have a role in the pathophysiology of AA/MDS, identifying a third pathway for developing these disorders alongside transcription factor and telomerase mutations...
  15. ncbi request reprint Novel C12orf65 mutations in patients with axonal neuropathy and optic atrophy
    Arianna Tucci
    Department of Molecular Neuroscience and Reta Lila Weston Research Laboratories, UCL Institute of Neurology and the National Hospital for Neurology and Neurosurgery, London, UK
    J Neurol Neurosurg Psychiatry 85:486-92. 2014
    ..Mutations in Mitofusin 2 have been found to cause dominant forms of CMT6. Phosphoribosylpyrophosphate synthetase-I mutations cause X-linked CMT6, but until now, mutations in the recessive forms of disease have never been identified...
  16. pmc Clinical characteristics of early retinal disease due to CDHR1 mutation
    Rola Ba-Abbad
    UCL Institute of Ophthalmology, University College London, London, UK Moorfields Eye Hospital, London, UK Ophthalmology Department, King Abdulaziz University Hospital, Riyadh, Saudi Arabia
    Mol Vis 19:2250-9. 2013
    ..To describe the early clinical and electrophysiological features of cone-rod dystrophy due to a mutation of cadherin-related family member 1 (CDHR1)...
  17. ncbi request reprint Mutations in the autoregulatory domain of β-tubulin 4a cause hereditary dystonia
    Joshua Hersheson
    Department of Molecular Neuroscience, University College London Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, United Kingdom
    Ann Neurol 73:546-53. 2013
    ....
  18. doi request reprint Cryptogenic multifocal ulcerating stenosing enteritis associated with homozygous deletion mutations in cytosolic phospholipase A2-α
    Matthew A Brooke
    Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
    Gut 63:96-104. 2014
    ..We investigated the genetic basis of this autosomal recessive condition in a pair of affected siblings who have 40-year histories of catastrophic gastrointestinal and extraintestinal disease...
  19. pmc Constitutional mutations in RTEL1 cause severe dyskeratosis congenita
    Amanda J Walne
    Centre for Paediatrics, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Barts and The London Children s Hospital, London, UK
    Am J Hum Genet 92:448-53. 2013
    ..They also demonstrate the severe multisystem consequences of its dysfunction...
  20. doi request reprint Kohlschütter-Tönz syndrome: mutations in ROGDI and evidence of genetic heterogeneity
    Arianna Tucci
    Department of Molecular Neuroscience, Reta Lila Weston Research Laboratories and MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, UK
    Hum Mutat 34:296-300. 2013
    ..The other families, mostly presenting with additional atypical features, were negative for ROGDI mutations, suggesting genetic heterogeneity of atypical forms of the disease...
  21. ncbi request reprint Interactions between Idd5.1/Ctla4 and other type 1 diabetes genes
    Kara Hunter
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    J Immunol 179:8341-9. 2007
    ..This masking of CTLA-4 alleles by different genetic backgrounds provides an explanation for our observation that the human CTLA-4 gene is only associated with T1D in the subgroup of human T1D patients with anti-thyroid autoimmunity...
  22. pmc A robust statistical method for case-control association testing with copy number variation
    Chris Barnes
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 40:1245-52. 2008
    ..We illustrate the power of these methods for testing for association with binary and quantitative traits, and have made this software available as the R package CNVtools...
  23. ncbi request reprint Phosphoinositide 3-kinase δ gene mutation predisposes to respiratory infection and airway damage
    Ivan Angulo
    Department of Medicine, University of Cambridge, Cambridge, UK
    Science 342:866-71. 2013
    ..Selective p110δ inhibitors IC87114 and GS-1101 reduced the activity of the mutant enzyme in vitro, which suggested a therapeutic approach for patients with APDS. ..
  24. pmc Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing
    Graham A Heap
    Centre for Digestive Diseases, Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
    Hum Mol Genet 19:122-34. 2010
    ....
  25. ncbi request reprint A genome-wide assessment of the role of untagged copy number variants in type 1 diabetes
    Manuela Zanda
    University College London UCL Genetics Institute UGI, London, United Kingdom Wellcome Trust Sanger Institute, Hinxton, United Kingdom
    PLoS Genet 10:e1004367. 2014
    ..2, 7q34 and 14q32.33, respectively. However, our data did not identify novel T1D loci. Our results do not support a major role of untagged CNVs in T1D heritability...
  26. ncbi request reprint A Homozygous Mutation in the TUB Gene Associated with Retinal Dystrophy and Obesity
    Arundhati Dev Borman
    Moorfield s Eye Hospital, London, EC1C 2PD, UK Institute of Ophthalmology, London, EC1V 9EL, UK
    Hum Mutat 35:289-93. 2014
    ....
  27. pmc Exome sequencing identifies MPL as a causative gene in familial aplastic anemia
    Amanda J Walne
    Centre for Paediatrics, Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, UK
    Haematologica 97:524-8. 2012
    ..This study shows for the first time a link between homozygous MPL mutations and familial aplastic anemia. It also highlights the important role of MPL in trilineage hematopoiesis...
  28. ncbi request reprint Bayesian test for colocalisation between pairs of genetic association studies using summary statistics
    Claudia Giambartolomei
    UCL Genetics Institute, University College London UCL, London, United Kingdom
    PLoS Genet 10:e1004383. 2014
    ..ucl.ac.uk/coloc/). Our methodology provides information about candidate causal genes in associated intervals and has direct implications for the understanding of complex diseases as well as the design of drugs to target disease pathways. ..
  29. pmc Fine-mapping, gene expression and splicing analysis of the disease associated LRRK2 locus
    Daniah Trabzuni
    Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, United Kingdom
    PLoS ONE 8:e70724. 2013
    ..Our results characterize the LRRK2 locus, and highlight the importance and difficulties of fine-mapping and integration of multiple datasets to delineate pathogenic variants and thus develop an understanding of disease mechanisms. ..
  30. pmc Association tests and software for copy number variant data
    Vincent Plagnol
    JDRF WT Diabetes and Inflammation Laboratory, Addenbrooke s Hospital, Cambridge, UK
    Hum Genomics 3:191-4. 2009
    ..Here, the programs available for CNV association testing for case control or family data are reviewed, using either discrete calls or raw continuous data...
  31. pmc Exome sequencing in an SCA14 family demonstrates its utility in diagnosing heterogeneous diseases
    Anna Sailer
    Department of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, University College London, London, UK
    Neurology 79:127-31. 2012
    ..Here we describe the use of exome sequencing to investigate a large, 5-generational British kindred with an autosomal dominant, progressive cerebellar ataxia in which conventional genetic testing had not revealed a causal etiology...
  32. pmc Fine-scale survey of X chromosome copy number variants and indels underlying intellectual disability
    Annabel C Whibley
    Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK
    Am J Hum Genet 87:173-88. 2010
    ....
  33. doi request reprint Graphical modelling of molecular networks underlying sporadic inclusion body myositis
    Thomas Thorne
    Centre for Bioinformatics and Systems Biology, Imperial College London, London, UK
    Mol Biosyst 9:1736-42. 2013
    ....
  34. doi request reprint Inflammatory skin and bowel disease linked to ADAM17 deletion
    Diana C Blaydon
    Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
    N Engl J Med 365:1502-8. 2011
    ..Despite repeated skin infections, this young man has led a relatively normal life. (Funded by Barts and the London Charity and the European Commission Seventh Framework Programme.)...
  35. pmc Copy number of FCGR3B, which is associated with systemic lupus erythematosus, correlates with protein expression and immune complex uptake
    Lisa C Willcocks
    Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, CB2 0XY, England, UK
    J Exp Med 205:1573-82. 2008
    ..This is the first report of an association between disease-related gene CNV and variation in protein expression and function that may contribute to autoimmune disease susceptibility...
  36. ncbi request reprint Profilin1 E117G is a moderate risk factor for amyotrophic lateral sclerosis
    Pietro Fratta
    MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, UK
    J Neurol Neurosurg Psychiatry 85:506-8. 2014
    ..The PFN1 E117G missense variant has been described in familial and sporadic cases, and also found in controls, casting doubt on its pathogenicity. Interpretation of such variants represents a significant clinical-genetics challenge...
  37. pmc Population genomics of cardiometabolic traits: design of the University College London-London School of Hygiene and Tropical Medicine-Edinburgh-Bristol (UCLEB) Consortium
    Tina 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
    ....
  38. pmc CNV analysis in Tourette syndrome implicates large genomic rearrangements in COL8A1 and NRXN1
    Abhishek Nag
    UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
    PLoS ONE 8:e59061. 2013
    ..Our results are consistent with the proposal that rare CNVs play a role in TS aetiology and suggest a possible role for rearrangements in the COL8A1 and NRXN1 gene regions...
  39. doi request reprint A common single-nucleotide variant in T is strongly associated with chordoma
    Nischalan Pillay
    Cancer Institute, University College London, UK
    Nat Genet 44:1185-7. 2012
    ..1, 95% confidence interval (CI) = 3.1-12.1; P = 4.4 × 10(-9)), a finding that is exceptional in cancers with a non-Mendelian mode of inheritance...
  40. pmc Biallelic mutations in PLA2G5, encoding group V phospholipase A2, cause benign fleck retina
    Panagiotis I Sergouniotis
    Institute of Ophthalmology, University College London, London, UK
    Am J Hum Genet 89:782-91. 2011
    ..Surprisingly, immunohistochemical staining of human retinal tissue revealed localization of the protein predominantly in the inner and outer plexiform layers...