The SEQC2 epigenomics quality control (EpiQC) study [methylation array]

We present a multi-platform assessment and a global resource for epigenetics research from the FDA's Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus on 5-methylcytosine modifications. Microarray experiments were run at three different labs, denoted labs A, B, and C. The resulting dataset contains 30 samples, with each of the seven cell lines (HG001-HG007) having between three and six replicates (biological or technical). Two technical replicates were generated for each cell line at lab A, one replicate from each cell line was generated at lab B, and three technical replicates were generated for the Han Chinese family trio cell lines (HG005-HG007) at lab C.