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Series GSE123914 Query DataSets for GSE123914
Status Public on Dec 18, 2018
Title Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Assessing DNA methylation profiles in human blood has become a major focus of epidemiologic inquiry. Understanding variability in CpG-specific DNA methylation over moderate periods of time is a critical first step in identifying CpG sites that are candidates for DNA methylation-based etiologic, diagnostic and prognostic predictors of pathogenesis. Using the Illumina MethylationEPIC [850K] BeadArray, DNA methylation was profiled in paired whole blood samples collected approximately 1 year apart from 35 healthy women enrolled in the Nurses Study II cohort. The median intraclass correlation coefficient (ICC) across all CpG loci was 0.19 [Interquartile Range (IQR) 0.00–0.50]; 74.8% of ICCs were in the low range (0–0.5), 16.9% in the mid-range of ICCs (0.5–0.8), and 8.3% in the high-range of ICCs (0.8–1). ICCs were similar for CpG probes on the 450K Illumina array (median 0.17) and the new probes added to the 850K array (median 0.21). ICCs for CpG loci on the sex chromosomes and known metastable epialleles were high (median 0.71, 0.97, respectively), and ICCs among methylation quantitative trait loci (mQTL) CpGs were significantly higher as compared to non-mQTL CpGs (median 0.73, 0.16, respectively, P < 2 × 10–16). We observed wide variation in DNA methylation stability over a 1-year period. Probes considered non-stable, due to substantial variation over a moderate period of time and with minimal variability across individuals could be removed in large epidemiological studies. Moreover, adjusting for technical variation that arises from using high-dimensional arrays is critical.
 
Overall design Peripheral blood samples collected from 35 healthy women enrolled in the Nurses Study II cohort at two time-points, spaced approximately 1 year from one another, were profiled for DNA methylation using the Illumina Infinium HumanMethylationEPIC Beadchip. One of the study samples was excluded due to poor quality DNA methylation data, leaving 69 total samples with 34 individuals having DNA methylation measurements at both time-points.
 
Contributor(s) Zaimi I, Pei D, Koestler DC, Marsit CJ, De Vivo I, Tworoger SS, Shields AE, Kelsey KT, Michaud DS
Citation(s) 30270718
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 CA207110 Prospective immune profiling using methylation markers and pancreatic cancer risk TUFTS UNIVERSITY BOSTON Dominique S Michaud
R01 CA163451 Psychological stress, associate biologic mediators, and ovarian cancer risk BRIGHAM AND WOMEN'S HOSPITAL Shelley S Tworoger
P30 CA168524 Cancer Center Support Grant UNIVERSITY OF KANSAS MEDICAL CENTER RESEARCH INSTITUTE INC ROY A. JENSEN
UM1 CA176726 Life Course Cancer Epidemiology Cohort in Women HARVARD SCHOOL OF PUBLIC HEALTH Walter C. Willett
P20 GM103418 Kansas IDeA Network of Biomedical Research Excellence UNIVERSITY OF KANSAS MEDICAL CENTER RESEARCH INSTITUTE INC Douglas E Wright
Submission date Dec 17, 2018
Last update date Jan 20, 2019
Contact name Devin Charles Koestler
E-mail(s) [email protected]
Organization name The University of Kansas Cancer Center
Department Biostatistics
Lab the Koestler Lab
Street address 3901 Rainbow Boulevard
City Kansas City
State/province KS
ZIP/Postal code 66160
Country USA
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (69)
GSM3516780 Genomic DNA from adult human whole blood [C480312460]
GSM3516781 Genomic DNA from adult human whole blood [C480338863]
GSM3516782 Genomic DNA from adult human whole blood [C480313014]
Relations
BioProject PRJNA510310

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Supplementary file Size Download File type/resource
GSE123914_RAW.tar 1.1 Gb (http)(custom) TAR (of IDAT)
Processed data included within Sample table
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