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Epigenetics Volume 8, 2013 - Issue 2
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Research Paper

Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray

Yi-an Chen Genetics and Genome Biology Program; Hospital for Sick Children; Toronto, ON Canada; Institute of Medical Science; University of Toronto; Toronto, ON Canada
,
Mathieu Lemire Ontario Institute for Cancer Research; Toronto, ON Canada
,
Sanaa Choufani Genetics and Genome Biology Program; Hospital for Sick Children; Toronto, ON Canada
,
Darci T. Butcher Genetics and Genome Biology Program; Hospital for Sick Children; Toronto, ON Canada
,
Daria Grafodatskaya Genetics and Genome Biology Program; Hospital for Sick Children; Toronto, ON Canada
,
Brent W. Zanke Ontario Institute for Cancer Research; Toronto, ON Canada; Clinical Epidemiology Program; Ottawa Hospital Research Institute; Ottawa, ON Canada
,
Steven Gallinger Department of Surgery; Toronto General Hospital; University Health Network; Toronto, ON Canada
,
Thomas J. Hudson Ontario Institute for Cancer Research; Toronto, ON Canada; Department of Medical Biophysics; University of Toronto; Toronto, ON Canada
&
Rosanna Weksberg Genetics and Genome Biology Program; Hospital for Sick Children; Toronto, ON Canada; Institute of Medical Science; University of Toronto; Toronto, ON Canada; Department of Molecular Genetics; University of Toronto; Toronto, ON Canada; Department of Paediatrics; University of Toronto; Toronto, ON CanadaCorrespondence[email protected]
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Pages 203-209 | Received 08 Nov 2012, Accepted 02 Jan 2013, Published online: 11 Jan 2013

References

  • Borghol N, Suderman M, McArdle W, Racine A, Hallett M, Pembrey M, et al. Associations with early-life socio-economic position in adult DNA methylation. Int J Epidemiol 2012; 41:62 - 74; http://dx.doi.org/10.1093/ije/dyr147; PMID: 22422449
  • Shen L, Toyota M, Kondo Y, Obata T, Daniel S, Pierce S, et al. Aberrant DNA methylation of p57KIP2 identifies a cell-cycle regulatory pathway with prognostic impact in adult acute lymphocytic leukemia. Blood 2003; 101:4131 - 6; http://dx.doi.org/10.1182/blood-2002-08-2466; PMID: 12586619
  • Jones PA, Laird PW. Cancer epigenetics comes of age. Nat Genet 1999; 21:163 - 7; http://dx.doi.org/10.1038/5947; PMID: 9988266
  • 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
  • Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, et al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 2009; 1:177 - 200; http://dx.doi.org/10.2217/epi.09.14; PMID: 22122642
  • Maksimovic J, Gordon L, Oshlack A. SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol 2012; 13:R44; http://dx.doi.org/10.1186/gb-2012-13-6-r44; PMID: 22703947
  • Chen YA, Choufani S, Ferreira JC, Grafodatskaya D, Butcher DT, Weksberg R. Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray. Genomics 2011; 97:214 - 22; http://dx.doi.org/10.1016/j.ygeno.2010.12.004; PMID: 21211562
  • Liu J, Morgan M, Hutchison K, Calhoun VD. A study of the influence of sex on genome wide methylation. PLoS One 2010; 5:e10028; http://dx.doi.org/10.1371/journal.pone.0010028; PMID: 20386599
  • Adkins RM, Thomas F, Tylavsky FA, Krushkal J. Parental ages and levels of DNA methylation in the newborn are correlated. BMC Med Genet 2011; 12:47; http://dx.doi.org/10.1186/1471-2350-12-47; PMID: 21453505
  • Adkins RM, Krushkal J, Tylavsky FA, Thomas F. Racial differences in gene-specific DNA methylation levels are present at birth. Birth Defects Res A Clin Mol Teratol 2011; 91:728 - 36; http://dx.doi.org/10.1002/bdra.20770; PMID: 21308978
  • Numata S, Ye T, Hyde TM, Guitart-Navarro X, Tao R, Wininger M, et al. DNA methylation signatures in development and aging of the human prefrontal cortex. Am J Hum Genet 2012; 90:260 - 72; http://dx.doi.org/10.1016/j.ajhg.2011.12.020; PMID: 22305529
  • Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F. Evaluation of the Infinium Methylation 450K technology. Epigenomics 2011; 3:771 - 84; http://dx.doi.org/10.2217/epi.11.105; PMID: 22126295
  • Touleimat N, Tost J. Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics 2012; 4:325 - 41; http://dx.doi.org/10.2217/epi.12.21; PMID: 22690668
  • Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, Farrington SM, et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet 2007; 39:989 - 94; http://dx.doi.org/10.1038/ng2089; PMID: 17618283
  • Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res 2002; 12:656 - 64; PMID: 11932250
  • Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, et al, 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 2010; 467:1061 - 73; http://dx.doi.org/10.1038/nature09534; PMID: 20981092

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