Stephan Beck

Summary

Affiliation: University College London
Country: UK

Publications

  1. ncbi request reprint Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia
    Aparna Raval
    Department of Molecular Virology, Immunology, and Medical Genetics, Human Cancer Genetics Program, The Comprehensive Cancer Center at The Ohio State University, Columbus, OH 43214, USA
    Cell 129:879-90. 2007
  2. doi request reprint The methylome: approaches for global DNA methylation profiling
    Stephan Beck
    UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Trends Genet 24:231-7. 2008
  3. pmc Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
    Eleni M Tomazou
    UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
    BMC Med Genomics 1:19. 2008
  4. pmc Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project
    Roger Horton
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Immunogenetics 60:1-18. 2008
  5. pmc Advances in the identification and analysis of allele-specific expression
    Christopher G Bell
    Medical Genomics, University College London Cancer Institute, Huntley Street, London WC1E 6BT, UK
    Genome Med 1:56. 2009
  6. pmc MHC-linked and un-linked class I genes in the wallaby
    Hannah V Siddle
    Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
    BMC Genomics 10:310. 2009
  7. doi request reprint Taking the measure of the methylome
    Stephan Beck
    UCL Cancer Institute, University College London, London, UK
    Nat Biotechnol 28:1026-8. 2010
  8. pmc Identification of the ancestral killer immunoglobulin-like receptor gene in primates
    Jennifer G Sambrook
    Immunogenomics Laboratory, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 ISA, UK
    BMC Genomics 7:209. 2006
  9. pmc A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish
    Jennifer G Sambrook
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 ISA, UK
    BMC Genomics 6:152. 2005
  10. pmc Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
    Andrew Feber
    Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    Genome Res 21:515-24. 2011

Detail Information

Publications53

  1. ncbi request reprint Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia
    Aparna Raval
    Department of Molecular Virology, Immunology, and Medical Genetics, Human Cancer Genetics Program, The Comprehensive Cancer Center at The Ohio State University, Columbus, OH 43214, USA
    Cell 129:879-90. 2007
    ..Thus, reduced expression of DAPK1 can result from germline predisposition, as well as epigenetic or somatic events causing or contributing to the CLL phenotype...
  2. doi request reprint The methylome: approaches for global DNA methylation profiling
    Stephan Beck
    UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Trends Genet 24:231-7. 2008
    ....
  3. pmc Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
    Eleni M Tomazou
    UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
    BMC Med Genomics 1:19. 2008
    ..Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics...
  4. pmc Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project
    Roger Horton
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Immunogenetics 60:1-18. 2008
    ....
  5. pmc Advances in the identification and analysis of allele-specific expression
    Christopher G Bell
    Medical Genomics, University College London Cancer Institute, Huntley Street, London WC1E 6BT, UK
    Genome Med 1:56. 2009
    ....
  6. pmc MHC-linked and un-linked class I genes in the wallaby
    Hannah V Siddle
    Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
    BMC Genomics 10:310. 2009
    ..We investigated this hypothesis by characterizing the class I genes of the tammar wallaby, a model marsupial that has a novel MHC organization, with class I genes located within the MHC and 10 other chromosomal locations...
  7. doi request reprint Taking the measure of the methylome
    Stephan Beck
    UCL Cancer Institute, University College London, London, UK
    Nat Biotechnol 28:1026-8. 2010
    ..Two comparative studies from the International Human Epigenome Project find high concordance between different methods for measuring genomic methylation...
  8. pmc Identification of the ancestral killer immunoglobulin-like receptor gene in primates
    Jennifer G Sambrook
    Immunogenomics Laboratory, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 ISA, UK
    BMC Genomics 7:209. 2006
    ..Since few KIR remain orthologous between species, with only one of them, KIR2DL4, shown to be common to human, apes and monkeys, the evolution of the KIR gene family in primates remains unclear...
  9. pmc A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish
    Jennifer G Sambrook
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 ISA, UK
    BMC Genomics 6:152. 2005
    ..Here we report a survey of MHC genes and their paralogues in the zebrafish genome...
  10. pmc Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
    Andrew Feber
    Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    Genome Res 21:515-24. 2011
    ..This study establishes MeDIP-seq as an effective method to analyze cancer methylomes...
  11. ncbi request reprint From genome to epigenome
    Adele Murrell
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Hum Mol Genet 14:R3-R10. 2005
    ..Here, we review the current thinking and progress on how to get from the genome to the epigenome(s) and discuss some potential applications...
  12. doi request reprint Cancer epigenome
    Matthias Lechner
    UCL Cancer Institute, University College London, London, UK
    Adv Genet 70:247-76. 2010
    ....
  13. pmc Epigenome-wide association studies for common human diseases
    Vardhman K Rakyan
    Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
    Nat Rev Genet 12:529-41. 2011
    ..We also discuss how integration of EWASs with GWASs can help to dissect complex GWAS haplotypes for functional analysis...
  14. pmc A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
    Andrew E Teschendorff
    Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Bioinformatics 29:189-96. 2013
    ..A key statistical issue is therefore how best to adjust for the two different probe designs...
  15. pmc Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus
    Christopher G Bell
    Medical Genomics, UCL Cancer Institute, University College London, London, UK
    BMC Med Genomics 3:33. 2010
    ..Cases had T1D and nephropathy whereas controls had T1D but no evidence of renal disease...
  16. pmc Complete MHC haplotype sequencing for common disease gene mapping
    C Andrew Stewart
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 14:1176-87. 2004
    ....
  17. pmc Comments on: Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed paraffin-embedded paired tumor and normal tissue
    Christina Thirlwell
    Medical Genomics Laboratory, UCL Cancer Institute, 72, Huntley Street, London WC1E 6BT, UK
    BMC Res Notes 5:631. 2012
    ..Moreover, we continue to analyse genome-wide methylation data from DNA extracted from FFPE tissue successfully on both the HumMeth27 and 450 K arrays...
  18. pmc Human-specific CpG "beacons" identify loci associated with human-specific traits and disease
    Christopher G Bell
    Medical Genomics, UCL Cancer Institute, University College London, London, UK
    Epigenetics 7:1188-99. 2012
    ..Taken together, our data support a model for CpG beacons to contribute to CGI evolution from genesis to tissue-specific to constitutively active CGIs...
  19. pmc Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus
    Christopher G Bell
    Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    PLoS ONE 5:e14040. 2010
    ....
  20. pmc An epigenetic signature in peripheral blood predicts active ovarian cancer
    Andrew E Teschendorff
    Medical Genomics Group, University College London Cancer Institute, University College London, London, United Kingdom
    PLoS ONE 4:e8274. 2009
    ..However, to date no study has evaluated the diagnostic and predictive potential of such markers in a large case control cohort and on a genome-wide basis...
  21. ncbi request reprint Gene map of the extended human MHC
    Roger Horton
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Rev Genet 5:889-99. 2004
    ..Here, we present this map and review its content in relation to paralogy, polymorphism, immune function and disease...
  22. ncbi request reprint Identification of a single killer immunoglobulin-like receptor (KIR) gene in the porcine leukocyte receptor complex on chromosome 6q
    Jennifer G Sambrook
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, England, UK
    Immunogenetics 58:481-6. 2006
    ..Both the porcine KIR and LILR genes have diverged sufficiently to no longer be clearly orthologous with known human LRC family members...
  23. pmc Immunogenomics: molecular hide and seek
    Marcos M Miretti
    Immunogenomics Laboratory, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Hum Genomics 2:244-51. 2006
    ..The discussion will focus on data available for the major histocompatibility complex and the leukocyte receptor complex, the two most polymorphic regions of the human immune sub-genome...
  24. doi request reprint Methylome analysis using MeDIP-seq with low DNA concentrations
    Oluwatosin Taiwo
    University College London UCL Cancer Institute, University College London, London, UK
    Nat Protoc 7:617-36. 2012
    ..The protocol described here, i.e., DNA extraction to generation of MeDIP-seq library, can be completed within 3-5 d...
  25. pmc The epigenomic interface between genome and environment in common complex diseases
    Christopher G Bell
    University College London Cancer Institute, UK
    Brief Funct Genomics 9:477-85. 2010
    ..Due to the reversibility of these marks, the potential for sequence-specific targeted therapeutics exists. This review surveys recent epigenomic advances and their current and prospective application to the study of common diseases...
  26. pmc The DNA sequence of the human X chromosome
    Mark T Ross
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 434:325-37. 2005
    ..Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence...
  27. pmc Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates
    Jennifer G Sambrook
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kindgom
    Genome Res 15:25-35. 2005
    ..An analysis of the intronic regions of the two non-human primates reveals the presence of ancient repeat elements, which are indicative of the duplication events that have taken place since the last common ancestor...
  28. ncbi request reprint Immunogenomics: towards a digital immune system
    Stephan Beck
    Wellcome Trust Sanger Institute, Hinxton Genome Campus, Cambridge CB10 1SA, UK
    Novartis Found Symp 254:223-30; discussion 230-3, 250-2. 2003
    ....
  29. doi request reprint Future impact of integrated high-throughput methylome analyses on human health and disease
    Lee M Butcher
    UCL Cancer Institute, Paul O Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK
    J Genet Genomics 35:391-401. 2008
    ....
  30. ncbi request reprint Evolutionary vignettes of natural killer cell receptors
    Jennifer G Sambrook
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Curr Opin Immunol 19:553-60. 2007
    ..Here, we review recent progress with respect to two such families of NK receptors, the killer immunoglobulin-like receptors (KIRs) and the killer cell lectin-like receptors (KLRs), and attempt to trace their evolution across vertebrates...
  31. pmc DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project
    Vardhman K Rakyan
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    PLoS Biol 2:e405. 2004
    ..e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data...
  32. doi request reprint Inflammatory signalling as mediator of epigenetic modulation in tissue-specific chronic inflammation
    Liselotte Bäckdahl
    Medical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Int J Biochem Cell Biol 41:176-84. 2009
    ..Here, we review recent progress and discuss key factors driving epigenetic modulation in chronic inflammation...
  33. pmc A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms
    Marcos M Miretti
    Wellcome Trust Sanger Institute, Hinxton, United Kingdom
    Am J Hum Genet 76:634-46. 2005
    ..This LD map allowed us to give coordinates for the extremely variable LD structure underlying the MHC...
  34. pmc Germline rates of de novo meiotic deletions and duplications causing several genomic disorders
    Daniel J Turner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Nat Genet 40:90-5. 2008
    ....
  35. ncbi request reprint Gene body methylation of the dimethylarginine dimethylamino-hydrolase 2 (Ddah2) gene is an epigenetic biomarker for neural stem cell differentiation
    Liselotte Bäckdahl
    UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Epigenetics 4:248-54. 2009
    ..Here, we have identified differential DNA methylation in the gene body of the nitric oxide inhibitor Ddah2 that discriminates embryonic stem cells from neural stem cells and is positively correlated with differential gene expression...
  36. pmc Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers
    Gareth A Wilson
    Medical Genomics, UCL Cancer Institute, University College London, London, UK
    Gigascience 1:3. 2012
    ..However, quality control and analysis of MeDIP-seq data have remained to be a challenge...
  37. pmc Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2
    Paul Guilhamon
    Medical Genomics, UCL Cancer Institute, University College London, London, UK
    Nat Commun 4:2166. 2013
    ....
  38. pmc Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner
    Stefan H Stricker
    Department of Cancer Biology, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
    Genes Dev 27:654-69. 2013
    ..However, in the context of the neural lineage, widespread resetting of GBM-associated epigenetic abnormalities is not sufficient to override the cancer genome...
  39. doi request reprint Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip
    Christina Thirlwell
    Medical Genomics Group, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    Methods 52:248-54. 2010
    ..Here, we describe a protocol for the analysis of FFPE samples using the Infinium HumanMethylation27 BeadChip...
  40. ncbi request reprint Epigenetic variation and inheritance in mammals
    Vardhman K Rakyan
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
    Curr Opin Genet Dev 16:573-7. 2006
    ..Recent work from mouse models, human monozygotic twin studies, and large-scale epigenetic profiling suggests that epigenetically determined phenotypes and epigenetic inheritance are more common than previously appreciated...
  41. ncbi request reprint Sequences encoded in the class II region of the MHC related to the 'ABC' superfamily of transporters. 1990
    John Trowsdale
    Imperial Cancer Research Fund, Lincolns Inn Fields, London, UK
    J Immunol 180:2733-6. 2008
  42. pmc The good, the bad and the ugly: epigenetic mechanisms in glioblastoma
    Helena Caren
    UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
    Mol Aspects Med 34:849-62. 2013
    ..3/H3F3A. These constitute the 'good, the bad and the ugly' of epigenetic mechanisms in cancer...
  43. pmc An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways
    James West
    Statistical Cancer Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    Sci Rep 3:1630. 2013
    ..The proposed algorithm will be useful to any study seeking to identify interactome hotspots associated with common phenotypes...
  44. pmc AutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assay
    Lee M Butcher
    UCL Cancer Institute, Paul O Gorman Building, University College London, 72 Huntley Street, London WC1E 6BT, UK
    Methods 52:223-31. 2010
    ..86), and that it is highly specific (>99%). AutoMeDIP-seq offers a competitive approach to high-throughput methylome analysis of medium to large cohorts...
  45. pmc Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer
    Andrew E Teschendorff
    University College London, London WC1E 6BT, UK
    Genome Res 20:440-6. 2010
    ..These findings shed substantial novel insights into the epigenetic effects of aging and support the view that age may predispose to malignant transformation by irreversibly stabilizing stem cell features...
  46. ncbi request reprint Replication timing profile reflects the distinct functional and genomic features of the MHC class II region
    Petros Takousis
    Human Cytogenetics Laboratory, Cancer Research, UK London Research Institute, London, UK
    Cell Cycle 6:2393-8. 2007
    ..These data suggest that despite AT-richness, an early-to-middle replication time in the class II region is defined by an open chromatin conformation that allows rapid transcriptional activation as a defence against pathogens...
  47. pmc An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    Vardhman K Rakyan
    Institute of Cell and Molecular Science, Barts and The London, London E1 2AT, United Kingdom
    Genome Res 18:1518-29. 2008
    ....
  48. ncbi request reprint Future potential of the Human Epigenome Project
    Florian Eckhardt
    Epigenomics AG, Kleine Präsidentenstrasse 1, 10178 Berlin, Germany
    Expert Rev Mol Diagn 4:609-18. 2004
    ..Like single nucleotide polymorphisms, methylation variable positions will greatly advance our ability to elucidate and diagnose the molecular basis of human diseases...
  49. pmc A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    Thomas A Down
    Wellcome Trust Cancer Research UK Gurdon Institute, and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nat Biotechnol 26:779-85. 2008
    ....
  50. ncbi request reprint The Human Genome Project: what we have learnt about the MHC region on chromosome 6 and its potential to Behçet's disease
    Stephan Beck
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
    Adv Exp Med Biol 528:207-11. 2003
  51. pmc DNA methylation profiling of human chromosomes 6, 20 and 22
    Florian Eckhardt
    Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
    Nat Genet 38:1378-85. 2006
    ..Our data suggest DNA methylation to be ontogenetically more stable than previously thought...
  52. pmc Somatically acquired hypomethylation of IGF2 in breast and colorectal cancer
    Yoko Ito
    Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Hum Mol Genet 17:2633-43. 2008
    ..These results indicate that IGF2 DMR0 hypomethylation has diagnostic potential for colon cancer rather than value as a surrogate biomarker for constitutive LOI...
  53. ncbi request reprint Physical and transcript map of the region between D6S264 and D6S149 on chromosome 6q27, the minimal region of allele loss in sporadic epithelial ovarian cancer
    Ying Liu
    ICRF Molecular Oncology Laboratories, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
    Oncogene 21:387-99. 2002
    ..Clonogenic assays were performed by transfecting the full-length gene in to ovarian cancer cell lines and no suppression of growth was observed...