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

Research output: Contribution to journalArticle

12 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 - 01-01-2016

Fingerprint

DNA methylation
DNA Methylation
Blood
DNA
blood
Chemical analysis
cells
storage conditions
Cold storage
blood cells
Genetic Markers
cold storage
volunteers
Volunteers
Blood Cells
Statistical methods
storage time
statistical analysis
Cells
Association reactions

All Science Journal Classification (ASJC) codes

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

Cite this

Shiwa, Yuh ; Hachiya, Tsuyoshi ; Furukawa, Ryohei ; Ohmomo, Hideki ; Ono, Kanako ; Kudo, Hisaaki ; Hata, Jun ; Hozawa, Atsushi ; Iwasaki, Motoki ; Matsuda, Koichi ; Minegishi, Naoko ; Satoh, Mamoru ; Tanno, Kozo ; Yamaji, Taiki ; Wakai, Kenji ; Hitomi, Jiro ; Kiyohara, Yutaka ; Kubo, Michiaki ; Tanaka, Hideo ; Tsugane, Shoichiro ; Yamamoto, Masayuki ; Sobue, Kenji ; Shimizu, Atsushi. / Adjustment of cell-type composition minimizes systematic bias in blood DNA methylation profiles derived by DNA collection protocols. In: PloS one. 2016 ; Vol. 11, No. 1.
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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.",
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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, Tsugane, S, Yamamoto, M, Sobue, K & Shimizu, A 2016, 'Adjustment of cell-type composition minimizes systematic bias in blood DNA methylation profiles derived by DNA collection protocols', PloS one, vol. 11, no. 1, e0147519. https://doi.org/10.1371/journal.pone.0147519

Adjustment of cell-type composition minimizes systematic bias in blood DNA methylation profiles derived by DNA collection protocols. / Shiwa, Yuh; Hachiya, Tsuyoshi; Furukawa, Ryohei; Ohmomo, Hideki; Ono, Kanako; Kudo, Hisaaki; Hata, Jun; Hozawa, Atsushi; Iwasaki, Motoki; Matsuda, Koichi; Minegishi, Naoko; Satoh, Mamoru; Tanno, Kozo; Yamaji, Taiki; Wakai, Kenji; Hitomi, Jiro; Kiyohara, Yutaka; Kubo, Michiaki; Tanaka, Hideo; Tsugane, Shoichiro; Yamamoto, Masayuki; Sobue, Kenji; Shimizu, Atsushi.

In: PloS one, Vol. 11, No. 1, e0147519, 01.01.2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Adjustment of cell-type composition minimizes systematic bias in blood DNA methylation profiles derived by DNA collection protocols

AU - Shiwa, Yuh

AU - Hachiya, Tsuyoshi

AU - Furukawa, Ryohei

AU - Ohmomo, Hideki

AU - Ono, Kanako

AU - Kudo, Hisaaki

AU - Hata, Jun

AU - Hozawa, Atsushi

AU - Iwasaki, Motoki

AU - Matsuda, Koichi

AU - Minegishi, Naoko

AU - Satoh, Mamoru

AU - Tanno, Kozo

AU - Yamaji, Taiki

AU - Wakai, Kenji

AU - Hitomi, Jiro

AU - Kiyohara, Yutaka

AU - Kubo, Michiaki

AU - Tanaka, Hideo

AU - Tsugane, Shoichiro

AU - Yamamoto, Masayuki

AU - Sobue, Kenji

AU - Shimizu, Atsushi

PY - 2016/1/1

Y1 - 2016/1/1

N2 - 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.

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