MBD-seq - realities of a misunderstood method for high-quality methylome-wide association studies

References

• Aberg KA, Xie L, Chan RF, et al. Evaluation of methyl-binding domain based enrichment approaches revisited. PLoS One. 2015;10(7):e0132205.
   PubMed Web of Science ®Google Scholar
• Chan RF, Shabalin AA, Xie LY, et al. Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome. Nucleic Acids Res. 2017 Jun 20;45(11):e97.
   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 Jan;38(2):391–399.
   PubMed Web of Science ®Google Scholar
• Fraga MF, Ballestar E, Montoya G, et al. The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties. Nucleic Acids Res. 2003 Mar 15;31(6):1765–1774.
   PubMed Web of Science ®Google Scholar
• Aberg KA, Chan RF, Shabalin AA, et al. A MBD-seq protocol for large-scale methylome-wide studies with (very) low amounts of DNA. Epigenetics. 2017 Sep;12(9):743–750.
   PubMed Web of Science ®Google Scholar
• Weber M, Davies JJ, Wittig D, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet. 2005 Aug;37(8):853–862.
   PubMed Web of Science ®Google Scholar
• Bock C, Tomazou EM, Brinkman AB, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol. 2010 Oct;28(10):1106–1114.
   PubMed Web of Science ®Google Scholar
• Nair SS, Coolen MW, Stirzaker C, 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 Jan;6(1):34–44.
   PubMed Web of Science ®Google Scholar
• Moreland B, Oman K, Curfman J, et al. Methyl-CpG/MBD2 interaction requires minimum separation and exhibits minimal sequence specificity. Biophys J. 2016 Dec 20;111(12):2551–2561.
   PubMed Web of Science ®Google Scholar
• Lentini A, Lagerwall C, Vikingsson S, et al. A reassessment of DNA-immunoprecipitation-based genomic profiling. Nat Methods. 2018 Jul;15(7):499–504.
   PubMed Web of Science ®Google Scholar
• van Den Oord EJ, Bukszar J, Rudolf G, et al. Estimation of CpG coverage in whole methylome next-generation sequencing studies. BMC Bioinformatics. 2013 Feb 12;14(1):50.
   PubMedGoogle Scholar
• Shabalin AA, Hattab MW, Clark SL, et al. RaMWAS: fast methylome-wide association study pipeline for enrichment platforms. Bioinformatics. 2018Feb;34(13):2283–2285.
   PubMed Web of Science ®Google Scholar
• Lee JH, Park SJ, Nakai K. Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s. Sci Rep. 2017 Sep 12;7(1):11295.
   PubMedGoogle Scholar
• Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462(7271):315.
   PubMed Web of Science ®Google Scholar
• Lister R, Mukamel EA, Nery JR, et al. Global epigenomic reconfiguration during mammalian brain development. Science (New York, NY). 2013;341(6146):1237905.
   Google Scholar
• Song C-X, Szulwach KE, Fu Y, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol. 2010;29:68.
   PubMed Web of Science ®Google Scholar
• Aberg KA, McClay JL, Nerella S, et al. MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case-control samples. Epigenomics. 2012 Dec;4(6):605–621.
   PubMed Web of Science ®Google Scholar
• Down TA, Rakyan VK, Turner DJ, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol. 2008 Jul;26(7):779–785.
   PubMed Web of Science ®Google Scholar
• Lienhard M, Grasse S, Rolff J, et al. QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments. Nucleic Acids Res. 2017 Apr 7;45(6):e44.
   PubMed Web of Science ®Google Scholar
• Aberg KA, Dean B, Shabalin AA, et al. Methylome-wide association findings for major depressive disorder overlap in blood and brain and replicate in independent brain samples. Mol Psychiatry. 2018 Sep;21. [Epub ahead of print].
   Google Scholar
• Harper KN, Peters BA, Gamble MV. Batch effects and pathway analysis: two potential perils in cancer studies involving DNA methylation array analysis. Cancer Epidemiol Biomarkers Prev. 2013 Jun;22(6):1052–1060.
   PubMed Web of Science ®Google Scholar
• Buhule OD, Minster RL, Hawley NL, et al. Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale. Front Genet. 2014;5:354.
   PubMed Web of Science ®Google Scholar
• Nygaard V, Rodland EA, Hovig E. Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses. Biostatistics. 2016 Jan;17(1):29–39.
   PubMed Web of Science ®Google Scholar
• Price EM, Robinson WP. Adjusting for batch effects in DNA methylation microarray data, a lesson learned. Front Genet. 2018;9:83.
   PubMed Web of Science ®Google Scholar
• Nagy C, Suderman M, Yang J, et al. Astrocytic abnormalities and global DNA methylation patterns in depression and suicide. Mol Psychiatry. 2015 Mar;20(3):320–328.
   PubMed Web of Science ®Google Scholar
• Aberg KA, McClay JL, Nerella S, et al. Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. JAMA Psychiatry. 2014 Mar;71(3):255–264.
   PubMed Web of Science ®Google Scholar
• Han LKM, Aghajani M, Clark SL, et al. Epigenetic aging in major depressive disorder. Am J Psychiatry. 2018 Aug 1;175(8):774–782.
   PubMed Web of Science ®Google Scholar