Improved reporting of DNA methylation data derived from studies of the human placenta

Epigenetics

Volumn 9, Issue 3, 2014, Pages 333-337

  Hogg, Kirsten ^a,b   Price, E Magda ^a,b   Robinson, Wendy P ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Analysis; DNA methylation; DOHAD; Epigenetics; Guidelines; Placenta

Indexed keywords

AGE; ARTICLE; CHORION VILLUS SAMPLING; CPG ISLAND; DATA ANALYSIS; DNA METHYLATION; EPIGENETIC REPRESSION; GENE EXPRESSION; HUMAN; MOSAICISM; PLACENTA; SEX DIFFERENCE;

ANALYSIS; DNA METHYLATION; DOHAD; EPIGENETICS; GUIDELINES; PLACENTA;

CPG ISLANDS; DATA INTERPRETATION, STATISTICAL; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; HUMANS; MALE; PLACENTA; PREGNANCY; RESEARCH DESIGN; SEX FACTORS; SPECIMEN HANDLING;

EID: 84899138108     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.27648     Document Type: Article

References (42)

1. Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010; 11:191-203; PMID:20125086; http://dx.doi. org/10.1038/nrg2732
2. 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; PMID:21839163; http://dx.doi.org/10.1016/j. ygeno.2011.07.007
3. Perera F, Herbstman J. Prenatal environmental exposures, epigenetics, and disease. Reprod Toxicol 2011; 31:363-73; PMID:21256208; http://dx.doi. org/10.1016/j.reprotox.2010.12.055
4. Feil R, Fraga MF. Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet 2011; 13:97-109; PMID:22215131
5. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods 2013; 10:949-55; PMID:24076989; http://dx.doi.org/10.1038/ nmeth.2632
6. Heijmans BT, Mill J. Commentary: The seven plagues of epigenetic epidemiology. Int J Epidemiol 2012; 41:74-8; PMID:22269254; http://dx.doi. org/10.1093/ije/dyr225
7. Mill J, Heijmans BT. From promises to practical strategies in epigenetic epidemiology. Nat Rev Genet 2013; 14:585-94; PMID:23817309; http://dx.doi. org/10.1038/nrg3405
8. Koukoura O, Sifakis S, Spandidos DA. DNA methylation in the human placenta and fetal growth (review). Mol Med Rep 2012; 5:883-9; PMID:22294146
9. Hogg K, Price EM, Hanna CW, Robinson WP. Prenatal and perinatal environmental influences on the human fetal and placental epigenome. Clin Pharmacol Ther 2012; 92:716-26; PMID:23047650; http://dx.doi.org/10.1038/clpt.2012.141
10. Benediktsson R, Calder AA, Edwards CR, Seckl JR. Placental 11 beta-hydroxysteroid dehydrogenase: a key regulator of fetal glucocorticoid exposure. Clin Endocrinol (Oxf) 1997; 46:161-6; PMID:9135697; http://dx.doi. org/10.1046/j.1365-2265.1997.1230939.x
11. Nelissen EC, van Montfoort AP, Dumoulin JC, Evers JL. Epigenetics and the placenta. Hum Reprod Update 2011; 17:397-417; PMID:20959349; http:// dx.doi.org/10.1093/humupd/dmq052
12. Novakovic B, Saffery R. The ever growing complexity of placental epigenetics-role in adverse pregnancy outcomes and fetal programming. Placenta 2012; 33:959-70; PMID:23102655; http://dx.doi. org/10.1016/j.placenta.2012.10.003
13. Nelson DM, Burton GJ. A technical note to improve the reporting of studies of the human placenta. Placenta 2011; 32:195-6; PMID:21239055; http:// dx.doi.org/10.1016/j.placenta.2010.12.008
14. Bernischke K, Kaufman P. Pathology of the Human Placenta. New York: Springer, 2000.
15. Wyatt SM, Kraus FT, Roh CR, Elchalal U, Nelson DM, Sadovsky Y. The correlation between sampling site and gene expression in the term human placenta. Placenta 2005; 26:372-9; PMID:15850641; http:// dx.doi.org/10.1016/j.placenta.2004.07.003
16. Sood R, Zehnder JL, Druzin ML, Brown PO. Gene expression patterns in human placenta. Proc Natl Acad Sci U S A 2006; 103:5478-83; PMID:16567644; http://dx.doi.org/10.1073/pnas.0508035103
17. Tzschoppe AA, Struwe E, Dörr HG, Goecke TW, Beckmann MW, Schild RL, Dötsch J. Differences in gene expression dependent on sampling site in placental tissue of fetuses with intrauterine growth restriction. Placenta 2010; 31:178-85; PMID:20045557; http://dx.doi.org/10.1016/j.placenta.2009.12.002
18. Bourque DK, Peñaherrera MS, Yuen RK, Van Allen MI, McFadden DE, Robinson WP. The utility of quantitative methylation assays at imprinted genes for the diagnosis of fetal and placental disorders. Clin Genet 2011; 79:169-75; PMID:20507345; http:// dx.doi.org/10.1111/j.1399-0004.2010.01443.x
19. Avila L, Yuen RK, Diego-Alvarez D, Peñaherrera MS, Jiang R, Robinson WP. Evaluating DNA methylation and gene expression variability in the human term placenta. Placenta 2010; 31:1070-7; PMID:20947161; http://dx.doi.org/10.1016/j.placenta.2010.09.011
20. Peñaherrera MS, Jiang R, Avila L, Yuen RK, Brown CJ, Robinson WP. Patterns of placental development evaluated by X chromosome inactivation profiling provide a basis to evaluate the origin of epigenetic variation. Hum Reprod 2012; 27:1745-53; PMID:22431562; http://dx.doi.org/10.1093/ humrep/des072
21. Burton GJ, Sebire NJ, Myatt L, Tannetta D, Wang YL, Sadovsky Y, Staff AC, Redman CW. Optimising sample collection for placental research. Placenta 2014; 35:9-22; PMID:24290528; http://dx.doi. org/10.1016/j.placenta.2013.11.005
22. Grigoriu A, Ferreira JC, Choufani S, Baczyk D, Kingdom J, Weksberg R. Cell specific patterns of methylation in the human placenta. Epigenetics 2011; 6:368-79; PMID:21131778; http://dx.doi. org/10.4161/epi.6.3.14196
23. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, Kelsey KT. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 2012; 13:86; PMID:22568884; http://dx.doi.org/10.1186/1471-2105-13-86
24. Novakovic B, Yuen RK, Gordon L, Peñaherrera MS, Sharkey A, Moffett A, Craig JM, Robinson WP, Saffery R. Evidence for widespread changes in promoter methylation profile in human placenta in response to increasing gestational age and environmental/stochastic factors. BMC Genomics 2011; 12:529; PMID:22032438; http://dx.doi. org/10.1186/1471-2164-12-529
25. Yuen RK, Peñaherrera MS, von Dadelszen P, McFadden DE, Robinson WP. DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia. Eur J Hum Genet 2010; 18:1006-12; PMID:20442742; http://dx.doi.org/10.1038/ ejhg.2010.63
26. Bernischke K, Kaufman P. Pathology of the Human Placenta. New York: Springer, 2006.
27. Cotton AM, Avila L, Penaherrera MS, Affleck JG, Robinson WP, Brown CJ. Inactive X chromosome-specific reduction in placental DNA methylation. Hum Mol Genet 2009; 18:3544-52; PMID:19586922; http://dx.doi.org/10.1093/hmg/ ddp299
28. Blair JD, Price EM. Illuminating potential technical artifacts of DNA-methylation array probes. Am J Hum Genet 2012; 91:760-2; PMID:23040498; http://dx.doi.org/10.1016/j.ajhg.2012.05.028
29. 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; PMID:21211562; http://dx.doi. org/10.1016/j.ygeno.2010.12.004
30. Chen YA, Choufani S, Grafodatskaya D, Butcher DT, Ferreira JC, Weksberg R. Cross-reactive DNA microarray probes lead to false discovery of autosomal sex-associated DNA methylation. Am J Hum Genet 2012; 91:762-4; PMID:23040499; http://dx.doi. org/10.1016/j.ajhg.2012.06.020
31. Price ME, Cotton AM, Lam LL, Farré P, Emberly E, Brown CJ, Robinson WP, Kobor MS. Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin 2013; 6:4; PMID:23452981; http:// dx.doi.org/10.1186/1756-8935-6-4
32. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 2009; 27:361-8; PMID:19329998; http://dx.doi. org/10.1038/nbt.1533
33. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 2011; 12:R10; PMID:21251332; http://dx.doi. org/10.1186/gb-2011-12-1-r10
34. Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol 2012; 41:200-9; PMID:22422453; http://dx.doi.org/10.1093/ije/ dyr238
35. Sánchez BN, Budtz-Jørgensen E, Ryan LM, Hu H. Structural equation models: A review with applications to environmental epidemiology. J Am Stat Assoc 2005; 100:1443-55; http://dx.doi. org/10.1198/016214505000001005
36. Alexeeff SE, Baccarelli AA, Halonen J, Coull BA, Wright RO, Tarantini L, Bollati V, Sparrow D, Vokonas P, Schwartz J. Association between blood pressure and DNA methylation of retrotransposons and pro-inflammatory genes. Int J Epidemiol 2013; 42:270-80; PMID:23508416; http://dx.doi. org/10.1093/ije/dys220
37. Mikeska T, Felsberg J, Hewitt CA, Dobrovic A. Analysing DNA methylation using bisulphite pyrosequencing. Methods Mol Biol 2011; 791:33-53; PMID:21913070; http://dx.doi. org/10.1007/978-1-61779-316-5_4
38. Desoye G, Hauguel-de Mouzon S. The human placenta in gestational diabetes mellitus. The insulin and cytokine network. Diabetes Care 2007; 30(Suppl 2):S120-6; PMID:17596459; http://dx.doi. org/10.2337/dc07-s203
39. Cruickshank MN, Oshlack A, Theda C, Davis PG, Martino D, Sheehan P, Dai Y, Saffery R, Doyle LW, Craig JM. Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy. Genome Med 2013; 5:96; PMID:24134860; http://dx.doi. org/10.1186/gm500
40. Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res 2013; 23:1522-40; PMID:23804400; http://dx.doi. org/10.1101/gr.156539.113
41. Lam LL, Emberly E, Fraser HB, Neumann SM, Chen E, Miller GE, Kobor MS. Factors underlying variable DNA methylation in a human community cohort. Proc Natl Acad Sci U S A 2012; 109(Suppl 2):17253-60; PMID:23045638; http://dx.doi.org/10.1073/ pnas.1121249109
42. Reinius LE, Acevedo N, Joerink M, Pershagen G, Dahlén SE, Greco D, Söderhäll C, Scheynius A, Kere J. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLoS One 2012; 7:e41361; PMID:22848472; http://dx.doi.org/10.1371/journal. pone.0041361