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

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posted on 2022-10-14, 07:40 authored by Sarah Holmes Watkins, Karen Ho, Christian Testa, Louise Falk, Patrice Soule, Linda V. Nguyen, Sophie FitzGibbon, Catherine Slack, Jarvis T. Chen, George Davey Smith, Immaculata De Vivo, Andrew J. Simpkin, Kate Tilling, Pamela D. Waterman, Nancy Krieger, Matthew Suderman, Caroline Relton

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.


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).