The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip

Sarah H Watkins; Karen M Ho; Christian Testa; Louise Falk; Patrice Soule; Linda V Nguyen; Sophie J FitzGibbon; Catherine J Slack; Jarvis Chen; George Davey Smith; Immaculata De Vivo; Andrew J Simpkin; Kate M Tilling; Pamela Waterman; Nancy Krieger; Matthew J Suderman; Caroline L Relton

doi:10.1080/15592294.2022.2123898

The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip

Sarah H Watkins^*, Karen M Ho, Christian Testa, Louise Falk, Patrice Soule, Linda V Nguyen, Sophie J FitzGibbon, Catherine J Slack, Jarvis Chen, George Davey Smith, Immaculata De Vivo, Andrew J Simpkin, Kate M Tilling, Pamela Waterman, Nancy Krieger, Matthew J Suderman, Caroline L Relton

^*Corresponding author for this work

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Abstract

DNA methylation (DNAm) is commonly assayed using the Illumina Infinium MethylationEPIC BeadChip, but there is currently little published evidence to define the lower limits of the amount of DNA that can be used whilst preserving data quality. Such evidence is valuable for analyses utilising precious or limited DNA sources. We used a single pooled sample of DNA in quadruplicate at three dilutions to define replicability and noise, and an independent population dataset of 328 individuals (from a community-based study including US-born non-Hispanic Black and white persons) to assess the impact of total DNA input on the quality of data generated using the Illumina Infinium MethylationEPIC BeadChip. We found that data are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; and that low DNA input is associated with a reduction in power to detect EWAS associations, requiring larger sample sizes. We conclude that DNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.

Original language	English
Pages (from-to)	2366-2376
Number of pages	11
Journal	Epigenetics
Volume	17
Issue number	13
Early online date	14 Oct 2022
DOIs	https://doi.org/10.1080/15592294.2022.2123898
Publication status	E-pub ahead of print - 14 Oct 2022

Bibliographical note

Funding Information:
This work was funded by the National Institutes of Health (NIH)/National Institute on Minority Health and Health Disparities (NIMHD) (5R01MD014304). The prior MBMS study was funded by the National Institutes of Health/National Institute on Aging (1 R01 AG027122). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. GDS, CR, KT, MS and SHW work within the MRC Integrative Epidemiology Unit at the University of Bristol, which is supported by the Medical Research Council (MC_UU_00011/1, 3 & 5). We are extremely grateful to all the MBMS participants who took part in this study, the staff at the four participating community health centers, and the researchers who conducted participant recruitment and interviews. We thank Elmer Freeman, Director of the Center for Community Health Education Research and Services, Inc (Northeastern University, Boston) and Brent Coull, Professor of Biostatistics and Environmental Health (Harvard TH Chan School of Public Health) for their involvement with the original MBMS study and continued engagement with this project.

Funding Information:
The MBMS study protocol, implemented in accordance with the Helsinki Declaration of 1975, as revised in 2000, was approved by the Harvard School of Public Health Office of Human Research Administration (protocol #11950–127, which covered 3 of the 4 health centers through reciprocal IRB agreements), and was also separately approved by the fourth community health center’s Institutional Review Board. All participants provided written informed consent. Additionally, the protocol for the current study, funded by the National Institutes of Health/National Institute of Minority Health and Health Disparities (R01MD014304), was approved by the Harvard T.H. Chan School of Public Health Office of Human Research Administration (Protocol # IRB19-0524).

Publisher Copyright:
© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

Structured keywords

Bristol Population Health Science Institute

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10.1080/15592294.2022.2123898Licence: CC BY

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IEU: MRC Integrative Epidemiology Unit Quinquennial renewal
Gaunt, L. F. & Davey Smith, G.
1/04/18 → 31/03/23
Project: Research

The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip
Watkins, S. H. (Creator), Ho, K. (Creator), Testa, C. (Creator), Falk, L. (Creator), Soule, P. (Creator), Nguyen, L. V. (Creator), FitzGibbon, S. (Creator), Slack, C. (Creator), Chen, J. T. (Creator), Davey Smith, G. (Creator), De Vivo, I. (Creator), Simpkin, A. J. (Creator), Tilling, K. M. (Creator), Waterman, P. D. (Creator), Krieger, N. (Creator), Suderman, M. J. (Creator) & Relton, C. (Creator), Taylor & Francis, 2022
DOI: 10.6084/m9.figshare.21333079.v1, https://tandf.figshare.com/articles/dataset/The_impact_of_low_input_DNA_on_the_reliability_of_DNA_methylation_as_measured_by_the_Illumina_Infinium_MethylationEPIC_BeadChip/21333079/1
Dataset

Research Data Storage Facility (RDSF)
Sadaf R Alam (Manager), D A G Williams (Manager), Steven A Chapman (Manager), Polly E Eccleston (Manager) & Simon H Atack (Manager)
IT Services
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Cite this

Watkins, S. H., Ho, K. M., Testa, C., Falk, L., Soule, P., Nguyen, L. V., FitzGibbon, S. J., Slack, C. J., Chen, J., Davey Smith, G., De Vivo, I., Simpkin, A. J., Tilling, K. M., Waterman, P., Krieger, N., Suderman, M. J., & Relton, C. L. (2022). The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip. Epigenetics, 17(13), 2366-2376. Advance online publication. https://doi.org/10.1080/15592294.2022.2123898

@article{a5f0115c8e8e4a49a8b9321baf94c578,

title = "The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip",

abstract = "DNA methylation (DNAm) is commonly assayed using the Illumina Infinium MethylationEPIC BeadChip, but there is currently little published evidence to define the lower limits of the amount of DNA that can be used whilst preserving data quality. Such evidence is valuable for analyses utilising precious or limited DNA sources. We used a single pooled sample of DNA in quadruplicate at three dilutions to define replicability and noise, and an independent population dataset of 328 individuals (from a community-based study including US-born non-Hispanic Black and white persons) to assess the impact of total DNA input on the quality of data generated using the Illumina Infinium MethylationEPIC BeadChip. We found that data are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; and that low DNA input is associated with a reduction in power to detect EWAS associations, requiring larger sample sizes. We conclude that DNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.",

author = "Watkins, {Sarah H} and Ho, {Karen M} and Christian Testa and Louise Falk and Patrice Soule and Nguyen, {Linda V} and FitzGibbon, {Sophie J} and Slack, {Catherine J} and Jarvis Chen and {Davey Smith}, George and {De Vivo}, Immaculata and Simpkin, {Andrew J} and Tilling, {Kate M} and Pamela Waterman and Nancy Krieger and Suderman, {Matthew J} and Relton, {Caroline L}",

note = "Funding Information: This work was funded by the National Institutes of Health (NIH)/National Institute on Minority Health and Health Disparities (NIMHD) (5R01MD014304). The prior MBMS study was funded by the National Institutes of Health/National Institute on Aging (1 R01 AG027122). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. GDS, CR, KT, MS and SHW work within the MRC Integrative Epidemiology Unit at the University of Bristol, which is supported by the Medical Research Council (MC_UU_00011/1, 3 & 5). We are extremely grateful to all the MBMS participants who took part in this study, the staff at the four participating community health centers, and the researchers who conducted participant recruitment and interviews. We thank Elmer Freeman, Director of the Center for Community Health Education Research and Services, Inc (Northeastern University, Boston) and Brent Coull, Professor of Biostatistics and Environmental Health (Harvard TH Chan School of Public Health) for their involvement with the original MBMS study and continued engagement with this project. Funding Information: The MBMS study protocol, implemented in accordance with the Helsinki Declaration of 1975, as revised in 2000, was approved by the Harvard School of Public Health Office of Human Research Administration (protocol #11950–127, which covered 3 of the 4 health centers through reciprocal IRB agreements), and was also separately approved by the fourth community health center{\textquoteright}s Institutional Review Board. All participants provided written informed consent. Additionally, the protocol for the current study, funded by the National Institutes of Health/National Institute of Minority Health and Health Disparities (R01MD014304), was approved by the Harvard T.H. Chan School of Public Health Office of Human Research Administration (Protocol # IRB19-0524). Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.",

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Watkins, SH, Ho, KM, Testa, C, Falk, L, Soule, P, Nguyen, LV, FitzGibbon, SJ, Slack, CJ, Chen, J, Davey Smith, G, De Vivo, I, Simpkin, AJ, Tilling, KM, Waterman, P, Krieger, N, Suderman, MJ & Relton, CL 2022, 'The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip', Epigenetics, vol. 17, no. 13, pp. 2366-2376. https://doi.org/10.1080/15592294.2022.2123898

TY - JOUR

T1 - The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip

AU - Watkins, Sarah H

AU - Ho, Karen M

AU - Testa, Christian

AU - Falk, Louise

AU - Soule, Patrice

AU - Nguyen, Linda V

AU - FitzGibbon, Sophie J

AU - Slack, Catherine J

AU - Chen, Jarvis

AU - Davey Smith, George

AU - De Vivo, Immaculata

AU - Simpkin, Andrew J

AU - Tilling, Kate M

AU - Waterman, Pamela

AU - Krieger, Nancy

AU - Suderman, Matthew J

AU - Relton, Caroline L

N1 - Funding Information: This work was funded by the National Institutes of Health (NIH)/National Institute on Minority Health and Health Disparities (NIMHD) (5R01MD014304). The prior MBMS study was funded by the National Institutes of Health/National Institute on Aging (1 R01 AG027122). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. GDS, CR, KT, MS and SHW work within the MRC Integrative Epidemiology Unit at the University of Bristol, which is supported by the Medical Research Council (MC_UU_00011/1, 3 & 5). We are extremely grateful to all the MBMS participants who took part in this study, the staff at the four participating community health centers, and the researchers who conducted participant recruitment and interviews. We thank Elmer Freeman, Director of the Center for Community Health Education Research and Services, Inc (Northeastern University, Boston) and Brent Coull, Professor of Biostatistics and Environmental Health (Harvard TH Chan School of Public Health) for their involvement with the original MBMS study and continued engagement with this project. Funding Information: The MBMS study protocol, implemented in accordance with the Helsinki Declaration of 1975, as revised in 2000, was approved by the Harvard School of Public Health Office of Human Research Administration (protocol #11950–127, which covered 3 of the 4 health centers through reciprocal IRB agreements), and was also separately approved by the fourth community health center’s Institutional Review Board. All participants provided written informed consent. Additionally, the protocol for the current study, funded by the National Institutes of Health/National Institute of Minority Health and Health Disparities (R01MD014304), was approved by the Harvard T.H. Chan School of Public Health Office of Human Research Administration (Protocol # IRB19-0524). Publisher Copyright: © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

PY - 2022/10/14

Y1 - 2022/10/14

N2 - DNA methylation (DNAm) is commonly assayed using the Illumina Infinium MethylationEPIC BeadChip, but there is currently little published evidence to define the lower limits of the amount of DNA that can be used whilst preserving data quality. Such evidence is valuable for analyses utilising precious or limited DNA sources. We used a single pooled sample of DNA in quadruplicate at three dilutions to define replicability and noise, and an independent population dataset of 328 individuals (from a community-based study including US-born non-Hispanic Black and white persons) to assess the impact of total DNA input on the quality of data generated using the Illumina Infinium MethylationEPIC BeadChip. We found that data are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; and that low DNA input is associated with a reduction in power to detect EWAS associations, requiring larger sample sizes. We conclude that DNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.

AB - DNA methylation (DNAm) is commonly assayed using the Illumina Infinium MethylationEPIC BeadChip, but there is currently little published evidence to define the lower limits of the amount of DNA that can be used whilst preserving data quality. Such evidence is valuable for analyses utilising precious or limited DNA sources. We used a single pooled sample of DNA in quadruplicate at three dilutions to define replicability and noise, and an independent population dataset of 328 individuals (from a community-based study including US-born non-Hispanic Black and white persons) to assess the impact of total DNA input on the quality of data generated using the Illumina Infinium MethylationEPIC BeadChip. We found that data are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; and that low DNA input is associated with a reduction in power to detect EWAS associations, requiring larger sample sizes. We conclude that DNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.

U2 - 10.1080/15592294.2022.2123898

DO - 10.1080/15592294.2022.2123898

M3 - Article (Academic Journal)

C2 - 36239035

SN - 1559-2294

VL - 17

SP - 2366

EP - 2376

JO - Epigenetics

JF - Epigenetics

IS - 13

ER -

The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip

Abstract

Bibliographical note

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Projects

IEU: MRC Integrative Epidemiology Unit Quinquennial renewal

Datasets

The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip

Equipment

Research Data Storage Facility (RDSF)

Cite this