Navigating Illumina DNA methylation data: biology versus technical artefacts.

ABSTRACT: Illumina-based BeadChip arrays have revolutionized genome-wide DNA methylation profiling, pushing it into diagnostics. However, comprehensive quality assessment remains challenging within a wide range of available tissue materials and sample preparation methods. This study tackles two critical issues: differentiating between biological effects and technical artefacts in suboptimal quality samples and the impact of the first sample on the Illumina-like normalization algorithm. We introduce three quality control scores based on global DNA methylation distribution (DB-Score), bin distance from copy number variation analysis (BIN-Score) and consistently methylated CpGs (CM-Score) that rely on biological features rather than internal array controls. These scores, designed to be adjustable for d

SUBMITTER: Glaser S 

PROVIDER: S-EPMC11655293 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature