Principles and challenges of genome-wide DNA methylation analysis

By Peter W. Laird. Nature reviews genetics, 2010

1,574 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6fb2a3e7a025fa2288c7fdf970f5201b50ada31e

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Citations in the corpus

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics (2013, methodology): “There are several techniques to profile DNA methylation, the most comprehensive being whole-genome bisulfite sequencing (WGBS; [4]), which has been used to profile methylation levels across entire genomes in a variety of organisms and cell types [5–7].”
Analysing and interpreting DNA methylation data (2012, methodology): “Various methods have been developed and are extensively reviewed 14,19,20 and benchmarked 64–66 elsewhere.”
DNA methylome analysis using short bisulfite sequencing data (2012, methodology): “Measuring methylation Several methods exist for measuring DNA methylation at specific genomic loci, and these have been reviewed recentl”
SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips (2012, background): “Each of these approaches has inherent strengths and weaknesses, which have been compared and discussed in several recent reviews [15-18].”
Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential (2018, background): “The first steps in marine macrophyte epigenetics can be taken with existing high-throughput techniques (Laird, 2010; Zhang and Jeltsch, 2010; Richards et al., 2017).”
edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets (2024, neutral): “BS-seq has become the gold-standard technology for studying DNA methylation [ 66 ].”
Epigenome-Wide Association Studies for common human diseases (2011, background): “The most common platforms of these two technologies have been extensively reviewe”
Epigenetic modifications and human disease (2010, background): “, which have proven to be crucial for the progress of the fiel”
Cancer epigenetics: from mechanism to therapy. (2012, background): “These technologies have provided comprehensive maps of nucleosome positioning (Segal and Widom, 2009), chromatin conformation (de Wit and de Laat, 2012), transcription factor binding sites (Farnham, 2009), and the localization of histone (Rando and Chang, 2009) and DNA (Laird, 2010) modifications.”
The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge (2015, background): “Abnormal profile of DNA methylation of CpG sites is among the earliest and most frequent alterations in cancer [21, 22].”
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis (2010, background): “good accuracy, small sample requirement and relatively low cost [1].”