3,614
Views
32
CrossRef citations to date
0
Altmetric
Research Papers

Agreement in DNA methylation levels from the Illumina 450K array across batches, tissues, and time

, , , , , , , , , & show all
Pages 19-32 | Received 05 Jan 2017, Accepted 27 Nov 2017, Published online: 30 Jan 2018

References

  • Marioni RE, Shah S, McRae AF, et al. DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol. 2015;16:25. doi:10.1186/s13059-015-0584-6. PMID:25633388
  • Marioni RE, Shah S, McRae AF, et al. The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936. Int J Epidemiol. 2015;44(4):1388–1396. doi:10.1093/ije/dyu277. PMID:25617346
  • Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14(10):R115. doi:10.1186/gb-2013-14-10-r115. PMID:24138928
  • Kato N, Loh M, Takeuchi F, et al. Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Nat Genet. 2015;47(11):1282–1293. doi:10.1038/ng.3405. PMID:26390057
  • Liu Y, Aryee MJ, Padyukov L, et al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risin rheumatoid arthritis. Nat Biotechnol. 2013;31(2):142–147. doi:10.1038/nbt.2487. PMID:23334450
  • Lowe R, Gemma C, Beyan H, et al. Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies. Epigenetics. 2013;8(4):445–454. doi:10.4161/epi.24362. PMID:23538714
  • Jiang R, Jones MJ, Chen E, et al. Discordance of DNA methylation variance between two accessible human tissues. Sci Rep. 2015;5:8257. doi:10.1038/srep08257. PMID:25660083
  • Smith AK, Kilaru V, Klengel T, et al. DNA extracted from saliva for methylation studies of psychiatric traits: evidence tissue specificity and relatedness to brain. Am J Med Genet B Neuropsychiatr Genet. 2015;168B(1):36–44. doi:10.1002/ajmg.b.32278. PMID:25355443
  • Bibikova M, Barnes B, Tsan C, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98(4):288–295. doi:10.1016/j.ygeno.2011.07.007. PMID:21839163
  • Bose M, Wu C, Pankow JS, et al. Evaluation of microarray-based DNA methylation measurement using technical replicates: the Atherosclerosis Risk in Communities (ARIC) study. BMC Bioinformatics. 2014;15:312. doi:10.1186/1471-2105-15-312. PMID:25239148
  • Chen J, Just AC, Schwartz J, et al. CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. Bioinformatics. 2016;32(3):469–471. doi:10.1093/bioinformatics/btv577. PMID:26449931
  • Shvetsov YB, Song MA, Cai Q, et al. Intraindividual variation and short-term temporal trend in DNA methylation of human blood. Cancer Epidemiol Biomarkers Prev. 2015;24(3):490–497. doi:10.1158/1055-9965.EPI-14-0853. PMID:25538225
  • Dugue PA, English DR, MacInnis RJ, et al. Reliability of DNA methylation measures from dried blood spots and mononuclear cells using the HumanMethylation450k BeadArray. Sci Rep. 2016;6:30317. doi:10.1038/srep30317. PMID:27457678
  • Huang LH, Lin PH, Tsai KW, et al. The effects of storage temperature and duration of blood samples on DNA and RNA qualities. Plos One. 2017;12(9):e0184692. doi:10.1371/journal.pone.0184692 PMID:28926588
  • Joo JE, Wong EM, Baglietto L, et al. The use of DNA from archival dried blood spots with the Infinium HumanMethylation450 array. BMC Biotechnol. 2013;13:23. doi:10.1186/1472-6750-13-23 PMID:23497093
  • Bulla A, De Witt B, Ammerlaan W, et al. Blood DNA yield but not integrity or methylation is impacted after long-term storage. Biopreserv Biobank. 2016;14(1):29–38. doi:10.1089/bio.2015.0045 PMID:26812548
  • Wang Y, Zheng H, Chen J, et al. The impact of different preservation conditions and freezing-thawing cycles on quality of RNA, DNA, and proteins in cancer tissue. Biopreserv Biobank. 2015;13(5):335–347. doi:10.1089/bio.2015.0029. PMID:26484573
  • Florath I, Butterbach K, Muller H, et al. Cross-sectional and longitudinal changes in DNA methylation with age: an epigenome-wide analysis revealing over 60 novel age-associated CpG sites. Hum Mol Genet. 2014;23(5):1186–1201. doi:10.1093/hmg/ddt531. PMID:24163245
  • Martino D, Loke YJ, Gordon L, et al. Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance. Genome Biol. 2013;14(5):R42. doi:10.1186/gb-2013-14-5-r42. PMID:23697701
  • Kimmel M, Clive M, Gispen F, et al. Oxytocin receptor DNA methylation in postpartum depression. Psychoneuroendocrinology.2016;69:150–160. doi:10.1016/j.psyneuen.2016.04.008. PMID:27108164
  • Osborne L, Clive M, Kimmel M, et al. Replication of epigenetic postpartum depression biomarkers and variation with hormone levels. Neuropsychopharmacology. 2016;41(6):1648–1658. doi:10.1038/npp.2015.333. PMID:26503311
  • Groleau P, Joober R, Israel M, et al. Methylation of the dopamine D2 receptor (DRD2) gene promoter in women with a bulimia-spectrum disorder: associations with borderline personality disorder and exposure to childhood abuse. J Psychiatr Res. 2014;48(1):121–127. doi:10.1016/j.jpsychires.2013.10.003. PMID:24157248
  • Docherty SJ, Davis OS, Haworth CM, et al. A genetic association study of DNA methylation levels in the DRD4 gene region finds associations with nearby SNPs. Behav Brain Funct. 2012;8:31. doi:10.1186/1744-9081-8-31. PMID:22691691
  • Ursini G, Bollati V, Fazio L, et al. Stress-related methylation of the catechol-O-methyltransferase Val 158 allele predicts human prefrontal cognition and activity. J Neurosci. 2011;31(18):6692–6698. doi:10.1523/jneurosci.6631-10.2011. PMID:21543598
  • Ikegame T, Bundo M, Murata Y, et al. DNA methylation of the BDNF gene and its relevance to psychiatric disorders. J Hum Genet. 2013;58(7):434–438. doi:10.1038/jhg.2013.65. PMID:23739121
  • van IJzendoorn MH, Caspers K, Bakermans-Kranenburg MJ, Beach SR, et al. Methylation matters: interaction between methylation density and serotonin transporter genotype predicts unresolved loss or trauma. Biol Psychiatry.2010;68(5):405–407. doi:10.1016/j.biopsych.2010.05.008.
  • Philibert RA, Sandhu H, Hollenbeck N, et al. The relationship of 5HTT (SLC6A4) methylation and genotype on mRNA expression and liability to major depression and alcohol dependence in subjects from the Iowa Adoption Studies. Am J Med Genet B Neuropsychiatr Genet. 2008;147B(5):543–549. doi:10.1002/ajmg.b.30657. PMID:17987668
  • Reese SE, Archer KJ, Therneau TM, et al. A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. Bioinformatics. 2013;29(22):2877–2883. doi:10.1093/bioinformatics/btt480. PMID:23958724
  • Legendre P, Legendre L. Numerical ecology, 2nd ed. Amsterdam, The Netherlands: Elsevier Science; 1998.
  • Edgar RD, Jones MJ, Robinson WP, et al. An empirically driven data reduction method on the human 450K methylation array to remove tissue specific non-variable CpGs. Clin Epigenetics. 2017;9:11. doi:10.1186/s13148-017-0320-z. PMID:28184257
  • Stadler MB, Merr R, Burger L, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011;484(7378):490–495. doi:10.1038/nature10716.
  • Klengel T, Mehta D, Anacker C, et al. et al. Allele-specific FKBP5 DNA demethylation mediates gene-childhood trauma interactions. Nat Neurosci. 2013;16(1):33–41. doi:10.1038/nn.3275. PMID:23201972
  • Fortin J-P, Labbe A, Lemire M, et al. Functional normalization of 450K methylation array data improves replication in large cancer studies. Genome Biol. 2014;15:503. doi:10.1186/s13059-014-0503-2. PMID:25599564
  • Liu J, Siegmund KD. An evaluation of processing methods for HumanMethylation450 BeadChip data. BMC Genomics. 2016;17(469):1–11. doi:10.1186/s12864-016-2819-7.
  • Fejes AP, Jones MJ, Kobor MS. DaVIE: Database for the visualization and integration of epigenetic data. Front Genet. 2014;5:325. doi:10.3389/fgene.2014.00325. PMID:25278960
  • Lehne B, Drong AW, Loh M, et al. A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. Genome Biol. 2015;16:37. doi:10.1186/s13059-015-0600-x. PMID:25853392
  • Price ME, Cotton AM, Lam LL, et al. Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin. 2013;6(1):4. doi:10.1186/1756-8935-6-4. PMID:23452981
  • Soriano-Tarraga C, Jimenez-Conde J, Giralt-Steinhauer E, et al. DNA isolation method is a source of global DNA methylation variability measured with LUMA. Experimental analysis and a systematic review. PLoS One. 2013;8(4):e60750. doi:10.1371/journal.pone.0060750.
  • Oros Klein K, Grinek S, Bernatsky S, et al. funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types. Bioinformatics. 2016;32(4):593–595. doi:10.1093/bioinformatics/btv615. PMID:26500152
  • O'Donnell KA, Gaudreau H, Colalillo S, et al. The maternal adversity vulnerability and neurodevelopment (MAVAN) project: theory and methodology. Can J Psychiat. 2014;59(9):497–508. doi:10.1177/070674371405900906. PMID:25565695
  • Houseman EA, Accomando WP, Koestler DC, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012;13(1):86. doi:10.1186/1471-2105-13-86. PMID:22568884
  • McGregor K. Methods for estimating changes in DNA methylation in the presence of cell type heterogeneity [M.Sc. Thesis]. Montreal, QC, Canada: McGill University; 2015.
  • Leek JT, Scharpf RB, Bravo HC, et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010;11:733–739. doi:10.1038/nrg2825. PMID:20838408
  • Shrout PE, Fleiss JL. Intraclass correlations: uses in assessing rater reliability. Psychol Bull. 1979;86(2):420–428. doi:10.1037/0033-2909.86.2.420. PMID:18839484
  • egan Community Ecology Package. R-Forge. 2013 Jan 4; [ accessed 2016 Jan]. http://vegan.r-forge.r-project.org/.