Adjustment of cell-type composition minimizes systematic bias in blood DNA methylation profiles derived by DNA collection protocols

Yuh Shiwa, Tsuyoshi Hachiya, Ryohei Furukawa, Hideki Ohmomo, Kanako Ono, Hisaaki Kudo, Jun Hata, Atsushi Hozawa, Motoki Iwasaki, Koichi Matsuda, Naoko Minegishi, Mamoru Satoh, Kozo Tanno, Taiki Yamaji, Kenji Wakai, Jiro Hitomi, Yutaka Kiyohara, Michiaki Kubo, Hideo Tanaka, Shoichiro TsuganeMasayuki Yamamoto, Kenji Sobue, Atsushi Shimizu

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13 Citations (Scopus)

Abstract

Differences in DNA collection protocols may be a potential confounder in epigenome-wide association studies (EWAS) using a large number of blood specimens from multiple biobanks and/or cohorts. Here we show that pre-analytical procedures involved in DNA collection can induce systematic bias in the DNA methylation profiles of blood cells that can be adjusted by cell-type composition variables. In Experiment 1, whole blood from 16 volunteers was collected to examine the effect of a 24 h storage period at 4°C on DNA methylation profiles as measured using the Infinium HumanMethylation450 BeadChip array. Our statistical analysis showed that the P-value distribution of more than 450,000 CpG sites was similar to the theoretical distribution (in quantile-quantile plot, λ = 1.03) when comparing two control replicates, which was remarkably deviated from the theoretical distribution (λ = 1.50) when comparing control and storage conditions.We then considered cell-type composition as a possible cause of the observed bias in DNA methylation profiles and found that the bias associated with the cold storage condition was largely decreased (λadjusted = 1.14) by taking into account a cell-type composition variable. As such, we compared four respective sample collection protocols used in large-scale Japanese biobanks or cohorts as well as two control replicates. Systematic biases in DNA methylation profiles were observed between control and three of four protocols without adjustment of cell-type composition (λ = 1.12-1.45) and no remarkable biases were seen after adjusting for cell-type composition in all four protocols (λadjusted = 1.00-1.17). These results revealed important implications for comparing DNA methylation profiles between blood specimens from different sources and may lead to discovery of disease-associated DNA methylation markers and the development of DNA methylation profile-based predictive risk models.

Original languageEnglish
Article numbere0147519
JournalPloS one
Volume11
Issue number1
DOIs
Publication statusPublished - 2016 Jan 1

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Shiwa, Y., Hachiya, T., Furukawa, R., Ohmomo, H., Ono, K., Kudo, H., Hata, J., Hozawa, A., Iwasaki, M., Matsuda, K., Minegishi, N., Satoh, M., Tanno, K., Yamaji, T., Wakai, K., Hitomi, J., Kiyohara, Y., Kubo, M., Tanaka, H., ... Shimizu, A. (2016). Adjustment of cell-type composition minimizes systematic bias in blood DNA methylation profiles derived by DNA collection protocols. PloS one, 11(1), [e0147519]. https://doi.org/10.1371/journal.pone.0147519