Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods.

ABSTRACT: Illumina Infinium DNA Methylation (5mC) arrays are a popular technology for low-cost, high-throughput, genome-scale measurement of 5mC distribution, especially in cancer and other complex diseases. After the success of its HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers. Despite the widespread use of 850k, analysis of the corresponding data remains suboptimal: it still relies mostly on Illumina's default annotation, which underestimates enhancerss and long noncoding RNAs. Results: We have thus developed an approach, based on the ENCODE and LNCipedia databases, which greatly improves upon Illumina's default annotation of enhancers and long noncoding transcripts. We compared the re-annotated 850k with both 450k an

SUBMITTER: Bizet M 

PROVIDER: S-EPMC9665128 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature