Technical and biological sources of unreliability of Infinium probes on Illumina methylation microarrays.

ABSTRACT: The Illumina Methylation array platform has facilitated countless epigenetic studies on DNA methylation (DNAme) in health and disease, yet relatively few studies have so studied its reliability, i.e., the consistency of repeated measures. Here we investigate the reliability of both type I and type II Infinium probes. We propose a method for excluding unreliable probes based on dynamic thresholds for mean intensity (MI) and 'unreliability', estimated by probe-level simulation of the influence of technical noise on methylation β values using the background intensities of negative control probes. We validate our method in several datasets, including newly generated Illumina MethylationEPIC BeadChip v1.0 data from paired whole blood samples taken six weeks apart and technical replicates spanni

SUBMITTER: Nazarenko T 

PROVIDER: S-EPMC11409515 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature