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Epigenomics Volume 1, 2009 - Issue 1
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Review

Epigenetic Biomarker Development

Christoph BockMax-Planck-Institut für Informatik, Saarbrücken, Germany. Tel.: +49 541 385 9670 Fax: +49 681 932 [email protected]View further author information
Pages 99-110 | Published online: 01 Oct 2009

Bibliography

  • Kouzarides T : Chromatin modifications and their function.Cell128 , 693–705 (2007).
  • Weber M , SchübelerD: Genomic patterns of DNA methylation: targets and function of an epigenetic mark.Curr. Opin. Cell Biol.19 , 273–280 (2007).
  • Reik W : Stability and flexibility of epigenetic gene regulation in mammalian development.Nature447 , 425–432 (2007).
  • Heijmans BT , TobiEW, SteinAD et al.: Persistent epigenetic differences associated with prenatal exposure to famine in humans.Proc. Natl Acad. Sci. USA105 , 17046–17049 (2008).
  • McGowan PO , SasakiA, D‘AlessioAC et al.: Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse.Nat. Neurosci.12 , 342–348 (2009).
  • Fraga MF , BallestarE, PazMF et al.: Epigenetic differences arise during the lifetime of monozygotic twins.Proc. Natl Acad. Sci. USA102 , 10604–10609 (2005).
  • Hirst M , MarraMA: Epigenetics and human disease.Int. J. Biochem. Cell Biol.41 , 136–146 (2009).
  • Feinberg AP : Phenotypic plasticity and the epigenetics of human disease.Nature447 , 433–440 (2007).
  • Bjornsson HT , FallinMD, FeinbergAP: An integrated epigenetic and genetic approach to common human disease.Trends Genet.20 , 350–358 (2004).
  • Richardson B : Primer: epigenetics of autoimmunity.Nat. Clin. Pract. Rheumatol.3 , 521–527 (2007).
  • Mehler MF : Epigenetics and the nervous system.Ann. Neurol.64 , 602–617 (2008).
  • Petronis A : The origin of schizophrenia: genetic thesis, epigenetic antithesis, and resolving synthesis.Biol. Psychiatry55 , 965–970 (2004).
  • Kalsi G , PrescottCA, KendlerKS, RileyBP: Unraveling the molecular mechanisms of alcohol dependence.Trends Genet.25 , 49–55 (2009).
  • Esteller M : Epigenetics in cancer.N. Engl. J. Med.358 , 1148–1159 (2008).
  • Feinberg AP , TyckoB: The history of cancer epigenetics.Nat. Rev. Cancer4 , 143–153 (2004).
  • Esteller M : Cancer epigenomics: DNA methylomes and histone-modification maps.Nat. Rev. Genet.8 , 286–298 (2007).
  • Jones PA , BaylinSB: The epigenomics of cancer.Cell128 , 683–692 (2007).
  • Feinberg AP , OhlssonR, HenikoffS: The epigenetic progenitor origin of human cancer.Nat. Rev. Genet.7 , 21–33 (2006).
  • Berger SL , KouzaridesT, ShiekhattarR, ShilatifardA: An operational definition of epigenetics.Genes Dev.23 , 781–783 (2009).
  • Bird A : Perceptions of epigenetics.Nature447 , 396–398 (2007).
  • Suzuki MM , BirdA: DNA methylation landscapes: provocative insights from epigenomics.Nat. Rev. Genet.9 , 465–476 (2008).
  • Kondo Y , ShenL, ChengAS et al.: Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation.Nat. Genet.40 , 741–750 (2008).
  • He L , ThomsonJM, HemannMT et al.: A microRNA polycistron as a potential human oncogene.Nature435 , 828–833 (2005).
  • Lu J , GetzG, MiskaEA et al.: MicroRNA expression profiles classify human cancers.Nature435 , 834–838 (2005).
  • Irizarry RA , Ladd-AcostaC, WenB et al.: The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.Nat. Genet.41 , 178–186 (2009).
  • Weisenberger DJ , SiegmundKD, CampanM et al.: CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer.Nat. Genet.38 , 787–793 (2006).
  • Laird PW : The power and the promise of DNA methylation markers.Nat. Rev. Cancer3 , 253–266 (2003).
  • Glockner SC , DhirM, YiJM et al.: Methylation of TFPI2 in stool DNA: a potential novel biomarker for the detection of colorectal cancer.Cancer Res.69 , 4691–4699 (2009).
  • Müller HM , OberwalderM, FieglH et al.: Methylation changes in faecal DNA: a marker for colorectal cancer screening.Lancet363 , 1283–1285 (2004).
  • Payne SR , SerthJ, SchostakM et al.: DNA methylation biomarkers of prostate cancer: Confirmation of candidates and evidence urine is the most sensitive body fluid for non-invasive detection.Prostate69(12) , 1257–1269 (2009).
  • Woodson K , O‘ReillyKJ, HansonJC, NelsonD, WalkEL, TangreaJA: The usefulness of the detection of GSTP1 methylation in urine as a biomarker in the diagnosis of prostate cancer.J. Urol.179 , 508–511; discussion 511–512 (2008).
  • Yu J , ZhuT, WangZ et al.: A novel set of DNA methylation markers in urine sediments for sensitive/specific detection of bladder cancer.Clin. Cancer. Res.13 , 7296–7304 (2007).
  • Friedrich MG , WeisenbergerDJ, ChengJC et al.: Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients.Clin. Cancer. Res.10 , 7457–7465 (2004).
  • Fiegl H , GattringerC, WidschwendterA et al.: Methylated DNA collected by tampons – a new tool to detect endometrial cancer.Cancer Epidemiol. Biomarkers Prev.13 , 882–888 (2004).
  • Kahn SL , RonnettBM, GravittPE, GustafsonKS: Quantitative methylation-specific PCR for the detection of aberrant DNA methylation in liquid-based Pap tests.Cancer114 , 57–64 (2008).
  • Olesen LH , AggerholmA, AndersenBL et al.: Molecular typing of adult acute myeloid leukaemia: significance of translocations, tandem duplications, methylation, and selective gene expression profiling.Br. J. Haematol.131 , 457–467 (2005).
  • Strathdee G , HolyoakeTL, SimA et al.: Inactivation of HOXA genes by hypermethylation in myeloid and lymphoid malignancy is frequent and associated with poor prognosis.Clin. Cancer. Res.13 , 5048–5055 (2007).
  • Widschwendter M , ApostolidouS, RaumE et al.: Epigenotyping in peripheral blood cell DNA and breast cancer risk: a proof of principle study.PLoS ONE3 , E2656 (2008).
  • Korshunova Y , MaloneyRK, LakeyN et al.: Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA.Genome Res.18 , 19–29 (2008).
  • Devos T , TetznerR, ModelF et al.: Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer.Clin. Chem.55(7) , 1337–1346 (2009).
  • Grutzmann R , MolnarB, PilarskyC et al.: Sensitive detection of colorectal cancer in peripheral blood by septin 9 DNA methylation assay.PLoS ONE3 , e3759 (2008).
  • Lofton-Day C , ModelF, DevosT et al.: DNA methylation biomarkers for blood-based colorectal cancer screening.Clin. Chem.54 , 414–423 (2008).
  • Issa JP : CpG island methylator phenotype in cancer.Nat. Rev. Cancer4 , 988–993 (2004).
  • Hegi ME , DiserensAC, GorliaT et al.: MGMT gene silencing and benefit from temozolomide in glioblastoma.N. Engl. J. Med.352 , 997–1003 (2005).
  • Iafrate AJ , LouisDN: “MGMT for pt mgmt”: is methylguanine-DNA methyltransferase testing ready for patient management?J. Mol. Diagn.10 , 308–310 (2008).
  • Mikeska T , BockC, El-MaarriO et al.: Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis.J. Mol. Diagn.9 , 368–381 (2007).
  • Bernstein BE , MeissnerA, LanderES: The mammalian epigenome.Cell128 , 669–681 (2007).
  • Jeddeloh JA , GreallyJM, RandoOJ: Reduced-representation methylation mapping.Genome Biol.9 , 231 (2008).
  • Meissner A , MikkelsenTS, GuH et al.: Genome-scale DNA methylation maps of pluripotent and differentiated cells.Nature454 , 766–770 (2008).
  • Down TA , RakyanVK, TurnerDJ et al.: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.Nat. Biotechnol.26 , 779–785 (2008).
  • Irizarry RA , Ladd-AcostaC, CarvalhoB et al.: Comprehensive high-throughput arrays for relative methylation (CHARM).Genome Res.18 , 780–790 (2008).
  • Oda M , GlassJL, ThompsonRF et al.: High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers.Nucleic Acids Res.37(12) , 3829–3839 (2009).
  • Ball MP , LiJB, GaoY et al.: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.Nat. Biotechnol.27 , 361–368 (2009).
  • Deng J , ShoemakerR, XieB et al.: Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming.Nat. Biotechnol.27 , 353–360 (2009).
  • Eckhardt F , LewinJ, CorteseR et al.: DNA methylation profiling of human chromosomes 6, 20 and 22.Nat. Genet.38 , 1378–1385 (2006).
  • Meng H , MurrelleEL, LiG: Identification of a small optimal subset of CpG sites as biomarkers from high-throughput DNA methylation profiles.BMC Bioinformatics9 , 457 (2008).
  • Tost J , GutIG: DNA methylation analysis by pyrosequencing.Nat. Protoc.2 , 2265–2275 (2007).
  • Gonzalgo ML , LiangG: Methylation-sensitive single-nucleotide primer extension (Ms-SNuPE) for quantitative measurement of DNA methylation.Nat. Protoc.2 , 1931–1936 (2007).
  • Brena RM , AuerH, KornackerK, PlassC: Quantification of DNA methylation in electrofluidics chips (Bio-COBRA).Nat. Protoc.1 , 52–58 (2006).
  • Ehrich M , NelsonMR, StanssensP et al.: Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry.Proc. Natl Acad. Sci. USA102 , 15785–15790 (2005).
  • Eads CA , DanenbergKD, KawakamiK et al.: MethyLight: a high-throughput assay to measure DNA methylation.Nucleic Acids Res.28 , E32 (2000).
  • Herman JG , GraffJR, MyohanenS, NelkinBD, BaylinSB: Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.Proc. Natl Acad. Sci. USA93 , 9821–9826 (1996).
  • Zhang Y , RohdeC, TierlingS et al.: DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution.PLoS Genet.5 , E1000438 (2009).
  • Bock C , WalterJ, PaulsenM, LengauerT: Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.Nucleic Acids Res.36 , e55 (2008).
  • Bock C , LengauerT: Computational epigenetics.Bioinformatics24 , 1–10 (2008).
  • Reich M , LiefeldT, GouldJ, LernerJ, TamayoP, MesirovJP: GenePattern 2.0.Nat. Genet.38 , 500–501 (2006).
  • Gentleman RC , CareyVJ, BatesDM et al.: Bioconductor: open software development for computational biology and bioinformatics.Genome Biol.5 , R80 (2004).
  • Langmead .B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol.10 , R25 (2009).
  • Li H , RuanJ, DurbinR: Mapping short DNA sequencing reads and calling variants using mapping quality scores.Genome Res.18 , 1851–1858 (2008).
  • Pelizzola M , KogaY, UrbanAE et al.: MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment.Genome Res.18 , 1652–1659 (2008).
  • Bock C , HalachevK, BüchJ, LengauerT: EpiGRAPH: User-friendly software for statistical analysis and prediction of (epi-) genomic data.Genome Biol.10 , R14 (2009).
  • Ji H , Jiang Ma WH, Johnson DS, Myers RM, Wong WH: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol.26 , 1293–1300 (2008).
  • Blankenberg D , TaylorJ, SchenckI et al.: A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.Genome Res.17 , 960–964 (2007).
  • Du P , KibbeWA, LinSM: Lumi: a pipeline for processing Illumina microarray.Bioinformatics24 , 1547–1548 (2008).
  • Dunning MJ , SmithML, RitchieME, TavaréS: Beadarray: R classes and methods for Illumina bead-based data.Bioinformatics23 , 2183–2184 (2007).
  • Frank E , HallM, TriggL, HolmesG, WittenIH: Data mining in bioinformatics using Weka.Bioinformatics20 , 2479–2481 (2004).
  • Bock C , WalterJ, PaulsenM, LengauerT: CpG island mapping by epigenome prediction.PLoS Comput. Biol.3 , e110 (2007).
  • Bock C , PaulsenM, TierlingS, MikeskaT, LengauerT, WalterJ: CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure.PLoS Genet.2 , e26 (2006).
  • Keshet I , SchlesingerY, FarkashS et al.: Evidence for an instructive mechanism of de novo methylation in cancer cells.Nat. Genet.38 , 149–153 (2006).
  • Goh L , MurphySK, MuhkerjeeS, FureyTS: Genomic sweeping for hypermethylated genes.Bioinformatics23 , 281–288 (2007).
  • McCabe MT , LeeEK, VertinoPM: A multifactorial signature of DNA sequence and polycomb binding predicts aberrant CpG island methylation.Cancer Res.69 , 282–291 (2009).
  • Rhodes DR , Kalyana-SundaramS, MahavisnoV et al.: Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.Neoplasia9 , 166–180 (2007).
  • Lauss M , VisneI, WeinhaeuselA, VierlingerK, NoehammerC, KriegnerA: MethCancerDB-aberrant DNA methylation in human cancer.Br. J. Cancer98 , 816–817 (2008).
  • Suderman M , HallettM: Tools for visually exploring biological networks.Bioinformatics23 , 2651–2659 (2007).
  • Tusnady GE , SimonI, VaradiA, AranyiT: BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes.Nucleic Acids Res.33 , e9 (2005).
  • Bock C , ReitherS, MikeskaT, PaulsenM, WalterJ, LengauerT: BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.Bioinformatics21 , 4067–4068 (2005).
  • Kumaki Y , OdaM, OkanoM: QUMA: quantification tool for methylation analysis.Nucleic Acids Res.36 , W170–5 (2008).
  • Thompson RF , SuzukiM, LauKW, GreallyJM: A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry.Bioinformatics25(17) , 2164–2170 (2009).
  • Tarca AL , CareyVJ, ChenXW, RomeroR, DraghiciS: Machine learning and its applications to biology.PLoS Comput. Biol.3 , e116 (2007).
  • Witten IH , FrankE: Data mining: practical machine learning tools and techniques with Java implementations. Morgan Kaufmann, CA, USA, 25 , 371 (2000).
  • Jurisica I , WigleD, WongB: Cancer informatics in the post genomic era: toward information-based medicine. Springer, Berlin, Germany, 19 , 180 (2007)
  • Bibikova M , FanJB: GoldenGate assay for DNA methylation profiling.Methods Mol. Biol.507 , 149–163 (2009).
  • Bibikova M , LinZ, ZhouL et al.: High-throughput DNA methylation profiling using universal bead arrays.Genome Res.16 , 383–393 (2006).
  • Ley TJ , MardisER, DingL et al.: DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.Nature456 , 66–72 (2008).
  • Wood LD , ParsonsDW, JonesS et al.: The genomic landscapes of human breast and colorectal cancers.Science318 , 1108–1113 (2007).
  • Altshuler D , DalyMJ, LanderES: Genetic mapping in human disease.Science322 , 881–888 (2008).
  • Ludwig JA , WeinsteinJN: Biomarkers in cancer staging, prognosis and treatment selection.Nat. Rev. Cancer5 , 845–856 (2005).
  • McLendon R , FriedmanA, BignerD: Comprehensive genomic characterization defines human glioblastoma genes and core pathways.Nature455 , 1061–1068 (2008).
  • Herman JG , BaylinSB: Gene silencing in cancer in association with promoter hypermethylation.N. Engl. J. Med.349 , 2042–2054 (2003).
  • Jones PA , BaylinSB: The fundamental role of epigenetic events in cancer.Nat. Rev. Genet.3 , 415–428 (2002).
  • Chan TA , GlocknerS, YiJM et al.: Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.PLoS Med.5 , e114 (2008).
  • Hong C , MoorefieldKS, JunP et al.: Epigenome scans and cancer genome sequencing converge on WNK2, a kinase-independent suppressor of cell growth.Proc. Natl Acad. Sci. USA104 , 10974–10979 (2007).
  • Schuebel KE , ChenW, CopeL et al.: Comparing the DNA hypermethylome with gene mutations in human colorectal cancer.PLoS Genet.3 , 1709–1723 (2007).
  • Pepe MS , EtzioniR, FengZ et al.: Phases of biomarker development for early detection of cancer.J. Natl. Cancer Inst.93 , 1054–1061 (2001).
  • Johannes F , ColotV, JansenRC: Epigenome dynamics: a quantitative genetics perspective.Nat. Rev. Genet.9 , 883–890 (2008).
  • Butcher LM , BeckS: Future impact of integrated high-throughput methylome analyses on human health and disease.J. Genet. Genomics35 , 391–401 (2008).
  • Foley DL , CraigJM, MorleyR et al.: Prospects for epigenetic epidemiology.Am. J. Epidemiol.169 , 389–400 (2009).
  • McCarthy MI , AbecasisGR, CardonLR et al.: Genome-wide association studies for complex traits: consensus, uncertainty and challenges.Nat. Rev. Genet.9 , 356–369 (2008).
  • Becker KG , HosackDA, DennisG Jr, et al.: PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics4 , 61 (2003).

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