Research Topics
Genomes and Genes | Stephan BeckSummaryAffiliation: University College London Country: UK Publications
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Publications
Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemiaAparna 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...
Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysisEleni 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...- Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype ProjectRoger Horton
Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Immunogenetics 60:1-18. 2008.... - Advances in the identification and analysis of allele-specific expressionChristopher G Bell
Medical Genomics, University College London Cancer Institute, Huntley Street, London WC1E 6BT, UK
Genome Med 1:56. 2009.... - MHC-linked and un-linked class I genes in the wallabyHannah 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... 
Taking the measure of the methylomeStephan 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...- The methylome: approaches for global DNA methylation profilingStephan Beck
UCL Cancer Institute, University College London, London WC1E 6BT, UK
Trends Genet 24:231-7. 2008.... - Identification of the ancestral killer immunoglobulin-like receptor gene in primatesJennifer 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... - A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafishJennifer 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... - Comparative methylome analysis of benign and malignant peripheral nerve sheath tumorsAndrew 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... - From genome to epigenomeAdele 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... - Epigenome-wide association studies for common human diseasesVardhman 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... - Cancer epigenomeMatthias Lechner
UCL Cancer Institute, University College London, London, UK
Adv Genet 70:247-76. 2010.... - Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitusChristopher 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... - Complete MHC haplotype sequencing for common disease gene mappingC Andrew Stewart
Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
Genome Res 14:1176-87. 2004.... - Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locusChristopher G Bell
Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
PLoS ONE 5:e14040. 2010.... - Gene map of the extended human MHCRoger 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... - An epigenetic signature in peripheral blood predicts active ovarian cancerAndrew 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... - Immunogenomics: molecular hide and seekMarcos 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... - Identification of a single killer immunoglobulin-like receptor (KIR) gene in the porcine leukocyte receptor complex on chromosome 6qJennifer 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... - The epigenomic interface between genome and environment in common complex diseasesChristopher 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... - Comments on: Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed paraffin-embedded paired tumor and normal tissueChristina 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... - Methylome analysis using MeDIP-seq with low DNA concentrationsOluwatosin 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... - Evolutionary vignettes of natural killer cell receptorsJennifer 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... - Immunogenomics: towards a digital immune systemStephan Beck
Wellcome Trust Sanger Institute, Hinxton Genome Campus, Cambridge CB10 1SA, UK
Novartis Found Symp 254:223-30; discussion 230-3, 250-2. 2003.... - DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome projectVardhman 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... - Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primatesJennifer 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... - Future impact of integrated high-throughput methylome analyses on human health and diseaseLee 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.... - The DNA sequence of the human X chromosomeMark 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... - Inflammatory signalling as mediator of epigenetic modulation in tissue-specific chronic inflammationLiselotte 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... - Human-specific CpG "beacons" identify loci associated with human-specific traits and diseaseChristopher 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... - Gene body methylation of the dimethylarginine dimethylamino-hydrolase 2 (Ddah2) gene is an epigenetic biomarker for neural stem cell differentiationLiselotte 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... - A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphismsMarcos 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... - Germline rates of de novo meiotic deletions and duplications causing several genomic disordersDaniel J Turner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
Nat Genet 40:90-5. 2008.... - A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation dataAndrew 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... - Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChipChristina 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... - Sequences encoded in the class II region of the MHC related to the 'ABC' superfamily of transporters. 1990John Trowsdale
Imperial Cancer Research Fund, Lincolns Inn Fields, London, UK
J Immunol 180:2733-6. 2008 - Epigenetic variation and inheritance in mammalsVardhman 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... - Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancerAndrew 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... - AutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assayLee 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... - Replication timing profile reflects the distinct functional and genomic features of the MHC class II regionPetros 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... - 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.... - DNA methylation profiling of human chromosomes 6, 20 and 22Florian Eckhardt
Epigenomics AG, , 10178 Berlin, Germany
Nat Genet 38:1378-85. 2006..Our data suggest DNA methylation to be ontogenetically more stable than previously thought... - Physical and transcript map of the region between D6S264 and D6S149 on chromosome 6q27, the minimal region of allele loss in sporadic epithelial ovarian cancerYing 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... - Somatically acquired hypomethylation of IGF2 in breast and colorectal cancerYoko 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... - The Human Genome Project: what we have learnt about the MHC region on chromosome 6 and its potential to Behçet's diseaseStephan Beck
Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
Adv Exp Med Biol 528:207-11. 2003 - A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysisThomas 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.... - Future potential of the Human Epigenome ProjectFlorian 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...