Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

References

• Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003; 33:Suppl 245 - 54; http://dx.doi.org/10.1038/ng1089; PMID: 12610534
   PubMed Web of Science ®Google Scholar
• Hermann A, Gowher H, Jeltsch A. Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 2004; 61:2571 - 87; http://dx.doi.org/10.1007/s00018-004-4201-1; PMID: 15526163
   PubMed Web of Science ®Google Scholar
• Kangaspeska S, Stride B, Métivier R, Polycarpou-Schwarz M, Ibberson D, Carmouche RP, et al. Transient cyclical methylation of promoter DNA. Nature 2008; 452:112 - 5; http://dx.doi.org/10.1038/nature06640; PMID: 18322535
   PubMed Web of Science ®Google Scholar
• Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet 2006; 7:21 - 33; http://dx.doi.org/10.1038/nrg1748; PMID: 16369569
   PubMed Web of Science ®Google Scholar
• Ross JP, Rand KN, Molloy PL. Hypomethylation of repeated DNA sequences in cancer. Epigenomics 2010; 2:245 - 69; http://dx.doi.org/10.2217/epi.10.2; PMID: 22121873
   PubMed Web of Science ®Google Scholar
• Ting AH, McGarvey KM, Baylin SB. The cancer epigenome--components and functional correlates. Genes Dev 2006; 20:3215 - 31; http://dx.doi.org/10.1101/gad.1464906; PMID: 17158741
   PubMed Web of Science ®Google Scholar
• Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011; 43:768 - 75; http://dx.doi.org/10.1038/ng.865; PMID: 21706001
   PubMed Web of Science ®Google Scholar
• Baylin SB. DNA methylation and gene silencing in cancer. Nat Clin Pract Oncol 2005; 2:Suppl 1 S4 - 11; http://dx.doi.org/10.1038/ncponc0354; PMID: 16341240
   PubMedGoogle Scholar
• Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 2005; 33:5868 - 77; http://dx.doi.org/10.1093/nar/gki901; PMID: 16224102
   PubMed Web of Science ®Google Scholar
• Hu M, Yao J, Polyak K. Methylation-specific digital karyotyping. Nat Protoc 2006; 1:1621 - 36; http://dx.doi.org/10.1038/nprot.2006.278; PMID: 17406428
   PubMed Web of Science ®Google Scholar
• Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 2006; 16:1046 - 55; http://dx.doi.org/10.1101/gr.5273806; PMID: 16809668
   PubMed Web of Science ®Google Scholar
• Yamada Y, Watanabe H, Miura F, Soejima H, Uchiyama M, Iwasaka T, et al. A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res 2004; 14:247 - 66; http://dx.doi.org/10.1101/gr.1351604; PMID: 14762061
   PubMed Web of Science ®Google Scholar
• Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008; 26:779 - 85; http://dx.doi.org/10.1038/nbt1414; PMID: 18612301
   PubMed Web of Science ®Google Scholar
• Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005; 37:853 - 62; http://dx.doi.org/10.1038/ng1598; PMID: 16007088
   PubMed Web of Science ®Google Scholar
• Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG. Whole-genome DNA methylation profiling using MethylCap-seq. Methods 2010; 52:232 - 6; http://dx.doi.org/10.1016/j.ymeth.2010.06.012; PMID: 20542119
   PubMed Web of Science ®Google Scholar
• Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 2010; 38:391 - 9; http://dx.doi.org/10.1093/nar/gkp992; PMID: 19906696
   PubMed Web of Science ®Google Scholar
• Rauch T, Pfeifer GP. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 2005; 85:1172 - 80; http://dx.doi.org/10.1038/labinvest.3700311; PMID: 16025148
   PubMed Web of Science ®Google Scholar
• Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG. Whole-genome DNA methylation profiling using MethylCap-seq. Methods 2010; 52:232 - 6; http://dx.doi.org/10.1016/j.ymeth.2010.06.012; PMID: 20542119
   PubMed Web of Science ®Google Scholar
• Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu HC, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010; 28:1106 - 14; http://dx.doi.org/10.1038/nbt.1681; PMID: 20852634
   PubMed Web of Science ®Google Scholar
• Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, et al. Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 2011; 6:34 - 44; http://dx.doi.org/10.4161/epi.6.1.13313; PMID: 20818161
   PubMed Web of Science ®Google Scholar
• Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010; 11:191 - 203; http://dx.doi.org/10.1038/nrg2732; PMID: 20125086
   PubMed Web of Science ®Google Scholar
• Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong CB, Downey SL, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010; 28:1097 - 105; http://dx.doi.org/10.1038/nbt.1682; PMID: 20852635
   PubMed Web of Science ®Google Scholar
• Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 2008; 18:780 - 90; http://dx.doi.org/10.1101/gr.7301508; PMID: 18316654
   PubMed Web of Science ®Google Scholar
• Jin S-G, Kadam S, Pfeifer GP. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 2010; 38:e125; http://dx.doi.org/10.1093/nar/gkq223; PMID: 20371518
   PubMed Web of Science ®Google Scholar
• Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 2009; 5:e1000386; http://dx.doi.org/10.1371/journal.pcbi.1000386; PMID: 19461883
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26:139 - 40; http://dx.doi.org/10.1093/bioinformatics/btp616; PMID: 19910308
   PubMed Web of Science ®Google Scholar
• Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res 2009; 19:1639 - 45; http://dx.doi.org/10.1101/gr.092759.109; PMID: 19541911
   PubMed Web of Science ®Google Scholar
• Clark SJ. Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis. Hum Mol Genet 2007; 16:Spec No 1 R88 - 95; http://dx.doi.org/10.1093/hmg/ddm051; PMID: 17613553
   PubMedGoogle Scholar
• de Bustros A, Nelkin BD, Silverman A, Ehrlich G, Poiesz B, Baylin SB. The short arm of chromosome 11 is a “hot spot” for hypermethylation in human neoplasia. Proc Natl Acad Sci U S A 1988; 85:5693 - 7; http://dx.doi.org/10.1073/pnas.85.15.5693; PMID: 2840671
   PubMed Web of Science ®Google Scholar
• Makos M, Nelkin BD, Lerman MI, Latif F, Zbar B, Baylin SB. Distinct hypermethylation patterns occur at altered chromosome loci in human lung and colon cancer. Proc Natl Acad Sci U S A 1992; 89:1929 - 33; http://dx.doi.org/10.1073/pnas.89.5.1929; PMID: 1347428
   PubMed Web of Science ®Google Scholar
• Ribieras S, Song-Wang XG, Martin V, Lointier P, Frappart L, Dante R. Human breast and colon cancers exhibit alterations of DNA methylation patterns at several DNA segments on chromosomes 11p and 17p. J Cell Biochem 1994; 56:86 - 96; http://dx.doi.org/10.1002/jcb.240560113; PMID: 7806594
   PubMed Web of Science ®Google Scholar
• Haerian MS, Baum L, Haerian BS. Association of 8q24.21 loci with the risk of colorectal cancer: a systematic review and meta-analysis. J Gastroenterol Hepatol 2011; 26:1475 - 84; http://dx.doi.org/10.1111/j.1440-1746.2011.06831.x; PMID: 21722176
   PubMed Web of Science ®Google Scholar
• Migliore L, Migheli F, Spisni R, Coppedè F. Genetics, cytogenetics, and epigenetics of colorectal cancer. J Biomed Biotechnol 2011; 2011:792362; http://dx.doi.org/10.1155/2011/792362; PMID: 21490705
   PubMed Web of Science ®Google Scholar
• Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 2011; 12:R10; http://dx.doi.org/10.1186/gb-2011-12-1-r10; PMID: 21251332
   PubMed Web of Science ®Google Scholar
• Javierre BM, Rodriguez-Ubreva J, Al-Shahrour F, Corominas M, Graña O, Ciudad L, et al. Long-range epigenetic silencing associates with deregulation of Ikaros targets in colorectal cancer cells. Mol Cancer Res 2011; 9:1139 - 51; http://dx.doi.org/10.1158/1541-7786.MCR-10-0515; PMID: 21737484
   PubMed Web of Science ®Google Scholar
• Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 2011; 6:692 - 702; http://dx.doi.org/10.4161/epi.6.6.16196; PMID: 21593595
   PubMed Web of Science ®Google Scholar
• Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 2010; 11:587; http://dx.doi.org/10.1186/1471-2105-11-587; PMID: 21118553
   PubMed Web of Science ®Google Scholar
• Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 2010; 7:133 - 6; http://dx.doi.org/10.1038/nmeth.1414; PMID: 20062050
   PubMed Web of Science ®Google Scholar
• Kibriya MG, Raza M, Jasmine F, Roy S, Paul-Brutus R, Rahaman R, et al. A genome-wide DNA methylation study in colorectal carcinoma. BMC Med Genomics 2011; 4:50; http://dx.doi.org/10.1186/1755-8794-4-50; PMID: 21699707
   PubMed Web of Science ®Google Scholar
• Oster B, Thorsen K, Lamy P, Wojdacz TK, Hansen LL, Birkenkamp-Demtröder K, et al. Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas. Int J Cancer 2011; 129:2855 - 66; http://dx.doi.org/10.1002/ijc.25951; PMID: 21400501
   PubMed Web of Science ®Google Scholar
• Kim YH, Lee HC, Kim SY, Yeom YI, Ryu KJ, Min BH, et al. Epigenomic analysis of aberrantly methylated genes in colorectal cancer identifies genes commonly affected by epigenetic alterations. Ann Surg Oncol 2011; 18:2338 - 47; http://dx.doi.org/10.1245/s10434-011-1573-y; PMID: 21298349
   PubMed Web of Science ®Google Scholar
• Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487:330 - 7; http://dx.doi.org/10.1038/nature11252; PMID: 22810696
   PubMed Web of Science ®Google Scholar
• Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004; 3:e3; http://dx.doi.org/10.2202/1544-6115.1027; PMID: 16646809
   PubMedGoogle Scholar
• Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, et al. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res 2010; 38:Database issue D626 - 32; http://dx.doi.org/10.1093/nar/gkp1020; PMID: 19933760
   PubMedGoogle Scholar