Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

By Andrew E. Jaffe, Peter N. Murakami, Hwajin Lee, Jeffrey T. Leek, M. Fallin, Andrew P. Feinberg, Rafael A. Irizarry. International Journal of Epidemiology, 2012

650 citations recorded by the source corpus.

Subfields: Genetics, Health, Toxicology and Mutagenesis, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/de97265c2425bf2e32c0e81c62fa6a25c711c423

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In Genetics

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Citations in the corpus

Developmental regulation of human cortex transcription and its clinical relevance at base resolution (2014, neutral): “…model: (2) by constructing an F-statistic F i which are then thresholded across the genome, and contiguous regions above the threshold form candidate differentially expressed regions (DERs), ranked by their area statistic (average F-statistic times region width), described in Jaffe, et al. 48 .”
De novo identification of differentially methylated regions in the human genome (2015, methodology): “The three other candidate DMR-finding methods we tested were: • Bumphunter [25]: A method that also uses smoothed methylation values to detect DMRs • comb-p [26]: Finds regions of enrichment from spatially assigned P values • Probe Lasso [27]: A method that offsets CpG density bias via moderating th”
Accounting for cellular heterogeneity is critical in epigenome-wide association studies (2014, background): “In these studies, DNAm levels are measured genome-wide at thousands to millions of sites in hundreds of individuals to identify loci where these levels are associated with quantitative traits or disease [1,2].”
Analysing and interpreting DNA methylation data (2012, methodology): “…models 90 , Shannon entropy 91 , logistic M values 49 , feature selec‑ tion 92 , stratification of t tests 93 , aggregation of genomic regions by type 94 , statistical correction for copy‑number aberrations 95 or linear regression in combination with batch effect removal and peak detection 96 .”
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data (2012, neutral): “Contact: a.teschendorff@ucl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online Received on June 27, 2012; revised on October 9, 2012; accepted on November 16, 2012”