Andrew E Teschendorff

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R157. 2007
  2. pmc High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
    Suet F Chin
    Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R215. 2007
  3. pmc A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancer
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, CB2 0RE, UK
    Breast Cancer Res 10:R73. 2008
  4. pmc A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the proliferation, immune response and RNA splicing modules in breast cancer
    Fabien Reyal
    Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Breast Cancer Res 10:R93. 2008
  5. pmc Critical evaluation of HPV16 gene copy number quantification by SYBR green PCR
    Ian Roberts
    MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 0XZ, UK
    BMC Biotechnol 8:57. 2008
  6. pmc Elucidating the altered transcriptional programs in breast cancer using independent component analysis
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, United Kingdom
    PLoS Comput Biol 3:e161. 2007
  7. pmc The breast cancer somatic 'muta-ome': tackling the complexity
    Andrew E Teschendorff
    Medical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, London, UK
    Breast Cancer Res 11:301. 2009
  8. pmc A consensus prognostic gene expression classifier for ER positive breast cancer
    Andrew E Teschendorff
    Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison MRC Research Center, Hills Road, Cambridge CB2 2XZ, UK
    Genome Biol 7:R101. 2006
  9. ncbi PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
    Andrew E Teschendorff
    Cancer Genomics Program, Department of Oncology University of Cambridge, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK
    Bioinformatics 22:2269-75. 2006
  10. ncbi A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data
    Andrew E Teschendorff
    Department of Oncology, Cancer Genomics Program, Hutchison MRC Research Centre, University of Cambridge Hills Road, Cambridge CB2 2XZ, UK
    Bioinformatics 21:3025-33. 2005

Detail Information

Publications46

  1. pmc An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R157. 2007
    ..Reliable identification of ER-negative tumors that have a good prognosis is not yet possible...
  2. pmc High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
    Suet F Chin
    Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R215. 2007
    ..To date, most genome-wide array comparative genomic hybridization studies have used tumor panels of relatively large tumor size and high Nottingham Prognostic Index (NPI) that are not as representative of breast cancer demographics...
  3. pmc A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancer
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, CB2 0RE, UK
    Breast Cancer Res 10:R73. 2008
    ..However, identification of such patients with a good prognosis remains difficult and at present is only possible through examining histopathological factors...
  4. pmc A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the proliferation, immune response and RNA splicing modules in breast cancer
    Fabien Reyal
    Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Breast Cancer Res 10:R93. 2008
    ..we address the following issues: Do these signatures perform similarly? Are there (common) molecular processes reported by these signatures? Can better prognostic predictors be constructed based on these identified molecular processes?..
  5. pmc Critical evaluation of HPV16 gene copy number quantification by SYBR green PCR
    Ian Roberts
    MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 0XZ, UK
    BMC Biotechnol 8:57. 2008
    ..We assessed a modified method, in which external calibration curves were generated from a single construct containing HPV16 E2, HPV16 E6 and the host gene hydroxymethylbilane synthase in a 1:1:1 ratio...
  6. pmc Elucidating the altered transcriptional programs in breast cancer using independent component analysis
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, United Kingdom
    PLoS Comput Biol 3:e161. 2007
    ..Adopting ICA as the analysis tool of choice will help understand the phenotype-pathway relationship and thus help elucidate the molecular taxonomy of heterogeneous cancers and of other complex genetic diseases...
  7. pmc The breast cancer somatic 'muta-ome': tackling the complexity
    Andrew E Teschendorff
    Medical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, London, UK
    Breast Cancer Res 11:301. 2009
    ....
  8. pmc A consensus prognostic gene expression classifier for ER positive breast cancer
    Andrew E Teschendorff
    Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison MRC Research Center, Hills Road, Cambridge CB2 2XZ, UK
    Genome Biol 7:R101. 2006
    ..A consensus prognostic gene expression classifier is still elusive in heterogeneous diseases such as breast cancer...
  9. ncbi PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
    Andrew E Teschendorff
    Cancer Genomics Program, Department of Oncology University of Cambridge, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK
    Bioinformatics 22:2269-75. 2006
    ..Feature selection methods that can identify relevant classifiers or that can remove likely false positives prior to supervised analysis are therefore desirable...
  10. ncbi A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data
    Andrew E Teschendorff
    Department of Oncology, Cancer Genomics Program, Hutchison MRC Research Centre, University of Cambridge Hills Road, Cambridge CB2 2XZ, UK
    Bioinformatics 21:3025-33. 2005
    ..Parametric mixture modelling provides a natural setting to address this problem...
  11. 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
    ....
  12. pmc A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform
    Joanna Zhuang
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    BMC Bioinformatics 13:59. 2012
    ....
  13. 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...
  14. 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...
  15. 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...
  16. ncbi BEX2 is overexpressed in a subset of primary breast cancers and mediates nerve growth factor/nuclear factor-kappaB inhibition of apoptosis in breast cancer cell lines
    Ali Naderi
    Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison Medical Research Council Research Center, Hills Road, Cambridge, United Kingdom
    Cancer Res 67:6725-36. 2007
    ..These data suggest that a NGF/BEX2/NF-kappaB pathway is involved in regulating apoptosis in breast cancer cells and in modulating response to tamoxifen in primary tumors...
  17. doi Common germline polymorphisms in COMT, CYP19A1, ESR1, PGR, SULT1E1 and STS and survival after a diagnosis of breast cancer
    Miriam S Udler
    Strangeways Research Laboratory, Departments of Public Health and Primary Care and Oncology, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, United Kingdom
    Int J Cancer 125:2687-96. 2009
    ..These results suggest that COMT rs4818, or a variant it tags, is associated with breast cancer prognosis. Further study of COMT and its putative association with breast cancer prognosis is warranted...
  18. pmc Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer
    Kerstin B Meyer
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
    PLoS Biol 6:e108. 2008
    ..We propose a model in which the Oct-1/Runx2 and C/EBPbeta binding sites in the disease-associated allele are able to lead to an increase in FGFR2 gene expression, thereby increasing the propensity for tumour formation...
  19. pmc DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference
    Yan Jiao
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    BMC Bioinformatics 12:403. 2011
    ..g protein interaction networks) or more generally with prior knowledge pathway databases. However, it is unclear how best to use the pathway knowledge information in the context of molecular profiles of any given study...
  20. 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...
  21. pmc Differential network entropy reveals cancer system hallmarks
    James West
    Statistical Cancer Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    Sci Rep 2:802. 2012
    ..These findings may have potential implications for identifying novel drug targets...
  22. doi Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions
    Andrew E Teschendorff
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London, UK
    Bioinformatics 28:1487-94. 2012
    ....
  23. pmc Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
    Caryn S Ross-Innes
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Nature 481:389-93. 2012
    ..By establishing transcription-factor mapping in primary tumour material, we show that there is plasticity in ER-binding capacity, with distinct combinations of cis-regulatory elements linked with the different clinical outcomes...
  24. pmc MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype
    Cherie Blenkiron
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R214. 2007
    ..MicroRNAs (miRNAs), a class of short non-coding RNAs found in many plants and animals, often act post-transcriptionally to inhibit gene expression...
  25. pmc Increased entropy of signal transduction in the cancer metastasis phenotype
    Andrew E Teschendorff
    Medical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    BMC Syst Biol 4:104. 2010
    ..However, relatively little is known as to what network features differ between the cancer and normal cell physiologies, or between different cancer cell phenotypes...
  26. pmc Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Department of Oncology University of Cambridge, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    BMC Cancer 10:604. 2010
    ..However, relatively few strategies for estimating pathway activity from such model signatures exist and only few studies have used activation patterns of pathways to refine molecular classifications of cancer...
  27. ncbi Co-amplification of 8p12 and 11q13 in breast cancers is not the result of a single genomic event
    Anna L Paterson
    Hutchison MRC Research Centre, Department of Pathology, University of Cambridge, Cambridge, UK
    Genes Chromosomes Cancer 46:427-39. 2007
    ..This article contains supplementary material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat...
  28. pmc Role of DNA methylation and epigenetic silencing of HAND2 in endometrial cancer development
    Allison Jones
    Department of Women s Cancer, UCL Elizabeth Garrett Anderson Institute for Women s Health, University College London, London, United Kingdom
    PLoS Med 10:e1001551. 2013
    ..The objective of this study was to determine the functional role of epigenetic factors in endometrial cancer development...
  29. pmc The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer
    Joanna Zhuang
    Department of Women s Cancer, University College London Elizabeth Garrett Anderson Institute for Women s Health, London, UK
    PLoS Genet 8:e1002517. 2012
    ..These findings have major implications for cancer and embryonic stem cell biology and establish the importance of systemic DNA hypomethylation for predicting prognosis in a wide range of different cancers...
  30. pmc Prognostic gene network modules in breast cancer hold promise
    Andrew E Teschendorff
    Medical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Breast Cancer Res 12:317. 2010
    ..We envisage that further improvements and insights may come from integrative expression pathway analyses that dissect prognostic signatures into modules related to cancer hallmarks...
  31. doi Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies
    Andrew E Teschendorff
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, London WC1E 6BT, UK
    Bioinformatics 27:1496-505. 2011
    ..To deal with these difficulties, an algorithmic framework known as Surrogate Variable Analysis (SVA) was recently proposed...
  32. 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...
  33. doi Epigenetics makes its mark on women-specific cancers--an opportunity to redefine oncological approaches?
    Martin Widschwendter
    Department of Women s Cancer, UCL Elizabeth Garrett Anderson Institute for Women s Health, University College London, UK
    Gynecol Oncol 128:134-43. 2013
    ..This review focuses attention on DNA methylation-a core epigenetic mechanism that can be readily detected in body fluids and has the potential to substantially reform cancer screening and treatment...
  34. pmc Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation
    Andrew E Teschendorff
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    Genome Med 4:24. 2012
    ..We aimed to demonstrate that epigenetic changes in normal cells, collected years in advance of the first signs of morphological transformation, can predict the risk of such transformation...
  35. ncbi Network transfer entropy and metric space for causality inference
    Christopher R S Banerji
    Department of Computer Science, University College London, London WC1E 6BT, United Kingdom
    Phys Rev E Stat Nonlin Soft Matter Phys 87:052814. 2013
    ....
  36. pmc Cellular network entropy as the energy potential in Waddington's differentiation landscape
    Christopher R S Banerji
    1 Statistical Cancer Genomics, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom 2 Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E6BT United Kingdom
    Sci Rep 3:3039. 2013
    ..In summary, network entropy provides a quantitative measure of a cell's undifferentiated state, defining its elevation in Waddington's landscape. ..
  37. pmc Distinctive topology of age-associated epigenetic drift in the human interactome
    James West
    Statistical Cancer Genomics, University College London Cancer Institute, University College London, London WC1E 6BT, United Kingdom
    Proc Natl Acad Sci U S A 110:14138-43. 2013
    ..Thus, these results point toward a potentially distinct mechanistic and biological role of DNA methylation in dictating the complex aging and disease phenotypes. ..
  38. pmc Effects of common germline genetic variation in cell cycle control genes on breast cancer survival: results from a population-based cohort
    Elizabeth M Azzato
    Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
    Breast Cancer Res 10:R47. 2008
    ..Of particular interest are genes involved in cell cycle pathways, which regulate cell division...
  39. pmc Differential expression of selected histone modifier genes in human solid cancers
    Hilal Ozdag
    Department of Oncology, Hutchison MRC Research Centre, University of Cambridge, Cambridge CB2 2XZ, UK
    BMC Genomics 7:90. 2006
    ..Expression of each gene in 225 samples (135 primary tumours, 47 cancer cell lines, and 43 normal tissues) was analysedby QRT-PCR, normalized with 8 housekeeping genes, and given as a ratio by comparison with a universal reference RNA...
  40. 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...
  41. 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
    ....
  42. pmc Corruption of the intra-gene DNA methylation architecture is a hallmark of cancer
    Thomas E Bartlett
    CoMPLEX, University College London, London, United Kingdom
    PLoS ONE 8:e68285. 2013
    ..Our findings strongly support the view that intra-gene methylation architecture has great clinical potential for the development of DNA-based cancer biomarkers...
  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. ncbi Distribution of breakpoints on chromosome 18 in breast, colorectal, and pancreatic carcinoma cell lines
    Amber E Alsop
    Cancer Genomics Program, Hutchison MRC Research Centre, Department of Pathology and Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, United Kingdom
    Cancer Genet Cytogenet 164:97-109. 2006
    ..We show that the latter is predicted by a simple model that invokes random breakage following anchorage of some random point on the chromosome, or selection of breaks proximal to one of several tumor suppressor genes...
  45. ncbi Interferon-beta treatment of cervical keratinocytes naturally infected with human papillomavirus 16 episomes promotes rapid reduction in episome numbers and emergence of latent integrants
    M Trent Herdman
    Medical Research Council Cancer Cell Unit, Cambridge CB2 2XZ, UK
    Carcinogenesis 27:2341-53. 2006
    ..Greater emphasis should be placed on episome loss in models of HPV-related carcinogenesis. We provide the strongest evidence to date that treating HPV-16 lesions by inducing an IFN response may cause clinical progression...
  46. pmc ESR1 gene amplification in breast cancer: a common phenomenon?
    Lindsay A Brown
    Nat Genet 40:806-7; author reply 810-2. 2008