Abstract
Background 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.
Materials and methods We use 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.
Results Data are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; however samples with a total input as low as 40ng pass standard quality control tests, and we observe little evidence that low input DNA obscures the associations between DNAm and two phenotypes, age and smoking status.
Conclusions DNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Funding, This work was funded by the National Institutes of Health/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.
Conflict of interest, The authors declare no conflicts of interest
