Advanced search
Publication Cover
Epigenetics Volume 18, 2023 - Issue 1
Submit an article Journal homepage
952
Views
1
CrossRef citations to date
0
Altmetric
Brief report

A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data

Julian Heckera Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USACorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0001-7918-089XView further author information
ORCID Icon,
Sanghun Leea Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA;b Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA;c Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin-si, South KoreaView further author information
,
Priyadarshini Kachrooa Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USAView further author information
,
Dmitry Prokopenkod Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USAView further author information
,
Anna Maaser-Heckerd Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USAView further author information
,
Sharon M. Lutzb Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA;e Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care and Harvard Medical School, Boston, MA, USAView further author information
,
Georg Hahnb Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USAView further author information
,
Rafael Irizarryb Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA;f Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USAView further author information
,
Scott T. Weissa Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USAView further author information
,
Dawn L. DeMeoa Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USAView further author information
&
Christoph Langea Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA;b Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USAView further author information
 show all
Article: 2257437 | Received 18 Apr 2023, Accepted 01 Sep 2023, Published online: 20 Sep 2023

References

  • Li M, Zou D, Li Z, et al. EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. Nucleic Acids Res. 2019;47(D1):D983–9. doi: 10.1093/nar/gky1027
  • Ross JP, van Dijk S, Phang M, et al. Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data. Clin Epigenetics. 2022;14(1):58. doi: 10.1186/s13148-022-01277-9
  • Randomized Trial: Maternal Vitamin D Supplementation to Prevent Childhood Asthma (VDAART) - Full Text View - ClinicalTrials.gov [Internet]. [cited 2022 Nov 17]. Available from: https://clinicaltrials.gov/ct2/show/NCT00920621
  • Hunninghake GM, Soto-Quiros ME, Avila L, et al. Sensitization to ascaris lumbricoides and severity of childhood asthma in Costa Rica. J Allergy Clin Immunol. 2007;119(3):654–661. doi: 10.1016/j.jaci.2006.12.609
  • The Childhood Asthma Management Program (CAMP): design, rationale, and methods Childhood Asthma Management Program Research Group. Control Clin Trials. 1999;20:91–120. doi: 10.1016/S0197-2456(98)00044-0
  • McKennan C, Naughton K, Stanhope C, et al. Longitudinal data reveal strong genetic and weak non-genetic components of ethnicity-dependent blood DNA methylation levels. Epigenetics. 2021;16(6):662–676. doi: 10.1080/15592294.2020.1817290
  • Du P, Zhang X, Huang C-C, et al. Comparison of beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinf. 2010;11(1):587. doi: 10.1186/1471-2105-11-587
  • Leek JT, Johnson WE, Parker HS, et al. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28(6):882–883. doi: 10.1093/bioinformatics/bts034
  • Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14:3156. doi: 10.1186/gb-2013-14-10-r115
  • Hannum G, Guinney J, Zhao L, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013;49(2):359–367. doi: 10.1016/j.molcel.2012.10.016
  • Yang Z, Wong A, Kuh D, et al. Correlation of an epigenetic mitotic clock with cancer risk. Genome Biol. 2016;17(1):205. doi: 10.1186/s13059-016-1064-3
  • Higgins-Chen AT, Thrush KL, Wang Y, et al. A computational solution for bolstering reliability of epigenetic clocks: implications for clinical trials and longitudinal tracking. Nat Aging. 2022;2(7):644–661. doi: 10.1038/s43587-022-00248-2
  • Sugden K, Hannon EJ, Arseneault L, et al. Patterns of reliability: assessing the reproducibility and integrity of DNA methylation measurement. Patterns. 2020;1(2):100014. doi: 10.1016/j.patter.2020.100014
  • 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 Bioinf. 2014;15(1):312. doi: 10.1186/1471-2105-15-312
  • Logue MW, Smith AK, Wolf EJ, et al. The correlation of methylation levels measured using Illumina 450K and EPIC BeadChips in blood samples. Epigenomics. 2017;9(11):1363–1371. doi: 10.2217/epi-2017-0078
  • Zhou W, Laird PW, Shen H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res. 2017;45:e22. doi: 10.1093/nar/gkw967
  • Xiong Z, Yang F, Li M, et al. EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. Nucleic Acids Res. 2022;50(D1):D1004–9. doi: 10.1093/nar/gkab972
  • Novakovic B, Lewis S, Halliday J, et al. Assisted reproductive technologies are associated with limited epigenetic variation at birth that largely resolves by adulthood. Nat Commun. 2019;10(1):3922. doi: 10.1038/s41467-019-11929-9
  • McCartney DL, Zhang F, Hillary RF, et al. An epigenome-wide association study of sex-specific chronological ageing. Genome Med. 2019;12:1. doi: 10.1186/s13073-019-0693-z

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.