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Epigenetics Volume 8, 2013 - Issue 11
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Research Paper

Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies

Paul Yousefi School of Public Health; University of California; Berkeley, CA USA
,
Karen Huen School of Public Health; University of California; Berkeley, CA USA
,
Raul Aguilar Schall School of Public Health; University of California; Berkeley, CA USA
,
Anna Decker School of Public Health; University of California; Berkeley, CA USA
,
Emon Elboudwarej School of Public Health; University of California; Berkeley, CA USA
,
Hong Quach School of Public Health; University of California; Berkeley, CA USA
,
Lisa Barcellos School of Public Health; University of California; Berkeley, CA USA
&
Nina Holland School of Public Health; University of California; Berkeley, CA USACorrespondence[email protected]
 show all
Pages 1141-1152 | Received 24 May 2013, Accepted 03 Aug 2013, Published online: 19 Aug 2013

References

  • Foley DL, Craig JM, Morley R, Olsson CA, Dwyer T, Smith K, Saffery R. Prospects for epigenetic epidemiology. Am J Epidemiol 2009; 169:389 - 400; http://dx.doi.org/10.1093/aje/kwn380; PMID: 19139055
  • Pennisi E. Behind the scenes of gene expression. Science 2001; 293:1064 - 7; http://dx.doi.org/10.1126/science.293.5532.1064; PMID: 11498570
  • Ho SM, Tang WY. Techniques used in studies of epigenome dysregulation due to aberrant DNA methylation: an emphasis on fetal-based adult diseases. Reprod Toxicol 2007; 23:267 - 82; http://dx.doi.org/10.1016/j.reprotox.2007.01.004; PMID: 17317097
  • Tammen SA, Friso S, Choi SW. Epigenetics: the link between nature and nurture. Mol Aspects Med 2012; 34:753 - 64; PMID: 22906839
  • 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
  • Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, et al. High density DNA methylation array with single CpG site resolution. Genomics 2011; 98:288 - 95; http://dx.doi.org/10.1016/j.ygeno.2011.07.007; PMID: 21839163
  • Roessler J, Ammerpohl O, Gutwein J, Hasemeier B, Anwar SL, Kreipe HH, Lehmann U. Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc. BMC Res Notes 2012; 5:210; http://dx.doi.org/10.1186/1756-0500-5-210; PMID: 22546179
  • Du P, Kibbe WA, Lin SM. lumi: a pipeline for processing Illumina microarray. Bioinformatics 2008; 24:1547 - 8; http://dx.doi.org/10.1093/bioinformatics/btn224; PMID: 18467348
  • 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
  • Schalkwyk L, Pidsley R, Wong C, Touleimat N, Defrance M, Teschendorff A, et al. wateRmelon: Illumina 450 methylation array normalization and metrics. R package version 0.99.16. 2013.
  • 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
  • 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
  • Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 2013; 29:189 - 96; http://dx.doi.org/10.1093/bioinformatics/bts680; PMID: 23175756
  • Marabita F, Almgren M, Lindholm ME, Ruhrmann S, Fagerström-Billai F, Jagodic M, Sundberg CJ, Ekström TJ, Teschendorff AE, Tegnér J, et al. An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics 2013; 8:333 - 46; http://dx.doi.org/10.4161/epi.24008; PMID: 23422812
  • Illumina. GenomeStudio Methylation Module v1.8 User Guide November, 2010, Accessed 5/1/2013.
  • Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M. 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
  • International HapMap Project. . www.hapmap.ncbi.nlm.nih.gov.
  • Vineis P, Garte S. Biomarker Validation. In: C. Wild, Vineis P, Garte S, eds. Molecular Epidemiology of Chronic Diseases. Chichester, UK: John Wiley & Sons, Ltd, 2008:pg72.

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