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 utilizing 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.

KEYWORDS:

• DNA methylation
• Illumina Infinium MethylationEPIC BeadChip
• DNA input
• low DNA
• reliability

Acknowledgments

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.

Disclosure statement

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).

Data availability statement

Due to the nature of this research, participants of this study did not agree for their data to be shared publicly, so supporting data is not available. Supplementary table 3 can be found on zenodo.org, DOI = 10.5281/zenodo.7006990, URL = https://zenodo.org/record/7006990#.YySK9HbMKUk

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15592294.2022.2123898

Additional information

Funding

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).