bims-tumhet Biomed News
on Tumor Heterogeneity
Issue of 2022‒05‒08
two papers selected by
Sergio Marchini
Humanitas Research

  1. Methods Mol Biol. 2022 ;2432 1-14
      The genome-wide patterns of methylation levels and identifications of differentially methylated genetic loci or regions of CpG sites are being important, because the methylome has the potential for large effects in disease etiology. There are several quantification methods of methylation level at each CpG site for a given sample, which include β-value, M-value, and N-value. The performance of three quantification methods of methylation levels has been examined with simulation study and 27K Illumina array data for obesity.
    Keywords:  Identification of differential methylation; Measure of methylation level; Normalization of signal intensity
  2. Methods Mol Biol. 2022 ;2432 15-24
      DNA methylation is a widely studied epigenetic phenomenon. Alterations in methylation patterns influence human phenotypes and risk of disease. The Illumina Infinium HumanMethylation450 (HM450) and MethylationEPIC (EPIC) BeadChip are widely used microarray-based platforms for epigenome-wide association studies (EWASs). In this chapter, we will discuss the use of intraclass correlation coefficient (ICC) for assessing technical variations induced by methylation arrays at single-CpG level. ICC compares variation of methylation levels within- and between-replicate measurements, ranging between 0 and 1. We further characterize the distribution of ICCs using a mixture of truncated normal and normal distributions, and cluster CpG sites on the arrays into low- and high-reliability groups. In practice, we recommend that extra caution needs to be taken for associations at the CpG sites with low ICC values.
    Keywords:  DNA methylation; Intraclass correlation; Normal mixture models; Technical error