Intraindividual variation and short-term temporal trend in DNA methylation of human blood

Cancer Epidemiology Biomarkers and Prevention

Volumn 24, Issue 3, 2015, Pages 490-497

  Shvetsov, Yurii B ^a   Song, Min Ae ^b   Cai, Qiuyin ^c,d   Tiirikainen, Maarit ^a   Xiang, Yong Bing ^e   Shu, Xiao Ou ^c,d   Yu, Herbert ^a  

^a UNIVERSITY OF HAWAII   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^d VANDERBILT INGRAM CANCER CENTER   (United States)

^e SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; BLOOD SAMPLING; CHINESE; CPG ISLAND; DNA METHYLATION; FEMALE; GENE LOCATION; GENE LOCUS; GENETIC VARIABILITY; GENOMICS; HUMAN; LEUKOCYTE; MEASUREMENT; NORMAL HUMAN; PRIORITY JOURNAL; RELIABILITY; X CHROMOSOME INACTIVATION; BLOOD; BLOOD ANALYSIS; COHORT ANALYSIS; EPIGENETICS; GENETICS; HUMAN GENOME; MIDDLE AGED; PROCEDURES; PROSPECTIVE STUDY;

DNA;

ADULT; AGED; BLOOD CHEMICAL ANALYSIS; COHORT STUDIES; CPG ISLANDS; DNA; DNA METHYLATION; EPIGENOMICS; FEMALE; GENOME, HUMAN; HUMANS; MIDDLE AGED; PROSPECTIVE STUDIES;

EID: 84927760099     PISSN: 10559965     EISSN: None     Source Type: Journal    
DOI: 10.1158/1055-9965.EPI-14-0853     Document Type: Article

References (34)

1. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Gayther SA, Apostolidou S, et al. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS ONE 2009;4:e8274.
2. Marsit CJ, Koestler DC, Christensen BC, Karagas MR, Houseman EA, Kelsey KT. DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer. J Clin Oncol 2011;29: 1133-9.
3. Yang R, Pfutze K, Zucknick M, Sutter C, Wappenschmidt B, Marme F, et al. DNA methylation array analyses identified breast cancer-associated HYAL2 methylationinperipheral blood. Int J Cancer. 2014 Sep 12. [Epub ahead of print].
4. Terry MB, Delgado-Cruzata L, Vin-Raviv N, Wu HC, Santella RM. DNA methylation in white blood cells: association with risk factors in epidemiologic studies. Epigenetics 2011;6:828-37.
5. Marsit C, Christensen B. Blood-derived DNA methylation markers of cancer risk. Adv Exp Med Biol 2013;754:233-52.
6. Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 2010;20:434-9.
7. van Otterdijk SD, Mathers JC, Strathdee G. Do age-related changes in DNA methylation play a role in the development of age-related diseases? Biochem Soc Trans 2013;41:803-7.
8. Block G, Dietrich M, Norkus E, Jensen C, Benowitz NL, Morrow JD, et al. Intraindividual variability of plasma antioxidants, markers of oxidative stress, C-reactive protein, cotinine, and other biomarkers. Epidemiology 2006;17:404-12.
9. Tangney CC, Shekelle RB, Raynor W, Gale M, Betz EP. Intra- and interin-dividual variation in measurements of beta-carotene, retinol, and tocopherols in diet and plasma. Am J Clin Nutr 1987;45:764-9.
10. Shvetsov YB, Hernandez BY, Wong SH, Wilkens LR, Franke AA, Goodman MT. Intraindividual variability in serum micronutrients: effects on reliability of estimated parameters. Epidemiology 2009;20:36-43.
11. Sampson JN, Boca SM, Shu XO, Stolzenberg-Solomon RZ, Matthews CE, Hsing AW, et al. Metabolomics in epidemiology: sources of variability in metabolite measurements and implications. Cancer Epidemiol Biomarkers Prev 2013;22:631-40.
12. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods 2013;10:949-55.
13. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, et al. High density DNA methylation array with single CpG site resolution. Genomics 2011; 98:288-95.
14. Dedeurwaerder S, Defrance M, Bizet M, Calonne E, Bontempi G, Fuks F. A comprehensive overview of Infinium HumanMethylation450 data processing. Brief Bioinform 2014;15:929-41.
15. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012;13:484-92.
16. Zheng W, Chow WH, Yang G, Jin F, Rothman N, Blair A, et al. The Shanghai Women's Health Study: rationale, study design, and baseline characteristics. Am J Epidemiol 2005;162:1123-31.
17. Peters TM, Moore SC, Xiang YB, Yang G, Shu XO, Ekelund U, et al. Accelerometer-measured physical activity in Chinese adults. Am J Prev Med 2010;38:583-91.
18. Song MA, Tiirikainen M, Kwee S, Okimoto G, Yu H, Wong LL. Elucidating the landscape of aberrant DNA methylation in hepatocellular carcinoma. PLoS ONE 2013;8:e55761.
19. Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 2010;11:587.
20. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 2012;13:86.
21. Ferrari SLP, Pinheiro EC. Improved likelihood inference in beta regression. J Stat Comput Simul 2012;81:431-43.
22. Sharp AJ, Stathaki E, Migliavacca E, Brahmachary M, Montgomery SB, Dupre Y, et al. DNA methylation profiles of human active and inactive X chromosomes. Genome Res 2011;21:1592-600.
23. Johansson A, Enroth S, Gyllensten U. Continuous aging of the human DNA methylome throughout the human lifespan. PLoS ONE 2013;8:e67378.
24. Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, et al. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A 2012;109:10522-7.
25. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010;20: 440-6.
26. Martino D, Loke YJ, Gordon L, Ollikainen M, Cruickshank MN, Saffery R, 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:R42.
27. Martino DJ, Tulic MK, Gordon L, Hodder M, Richman TR, Metcalfe J, et al. Evidence for age-related and individual-specific changes in DNA methylation profile of mononuclear cells during early immune development in humans. Epigenetics 2011;6:1085-94.
28. Reinius LE, Acevedo N, Joerink M, Pershagen G, Dahlen SE, Greco D, et al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLoS ONE 2012;7: e41361.
29. Jacoby M, Gohrbandt S, Clausse V, Brons NH, Muller CP. Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics 2012;7:1421-34.
30. Koestler DC, Christensen B, Karagas MR, Marsit CJ, Langevin SM, Kelsey KT, et al. Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis. Epigenetics 2013;8: 816-26.
31. Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol 2014;15:R31.
32. Sun Z, Chai HS, Wu Y, White WM, Donkena KV, Klein CJ, et al. Batch effect correction for genome-wide methylation data with Illumina Infinium platform. BMC Med Genomics 2011;4:84.
33. Lam LL, Emberly E, Fraser HB, Neumann SM, Chen E, Miller GE, et al. Factors underlying variable DNA methylation in a human community cohort. Proc Natl Acad Sci U S A 2012;109 Suppl 2:17253-60.
34. Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, et al. Genomewide methylation profiles reveal quantitative views of human aging rates. Mol Cell 2013;49:359-67.