Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts

Steffan Noe Christiansen*, Jeppe Dyrberg Andersen, Marie-Louise Kampmann, Jing Liu, Mikkel Meyer Andersen, Jacob Tfelt-Hansen, Niels Morling

*Corresponding author for this work
2 Citations (Scopus)

Abstract

The Infinium MethylationEPIC BeadChip (EPIC) is a reliable method for measuring the DNA methylation of more than 850,000 CpG positions. In clinical and forensic settings, it is critical to be able to work with low DNA amounts without risking reduced reproducibility. We evaluated the EPIC for a range of DNA amounts using two-fold serial dilutions investigated on two different days. While the β-value distributions were generally unaffected by decreasing DNA amounts, the median squared Pearson's correlation coefficient (R2) of between-days β-value comparisons decreased from 0.994 (500 ng DNA) to 0.957 (16 ng DNA). The median standard deviation of the β-values was 0.005 and up to 0.017 (median of medians: 0.014) for β-values around 0.6-0.7. With decreasing amounts of DNA from 500 ng to 16 ng, the percentage of probes with standard deviations ≤ 0.1 decreased from 99.9% to 99.4%. This study showed that high reproducibility results are obtained with DNA amounts in the range 125-500 ng DNA, while DNA amounts equal to 63 ng or below gave less reproducible results.

Original languageEnglish
JournalEpigenetics
Volume17
Issue number12
Pages (from-to)1636-1645
Number of pages10
ISSN1559-2294
DOIs
Publication statusPublished - Dec 2022

Keywords

  • CpG Islands
  • DNA
  • DNA Methylation
  • Oligonucleotide Array Sequence Analysis/methods
  • Reproducibility of Results
  • correlation
  • reproducibility
  • illumina MethylationEPIC array
  • DNA methylation
  • low DNA amounts
  • variability

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