Comparison of Methyl-capture Sequencing vs. Infinium 450K methylation array for methylome analysis in clinical samples

Epigenetics : Official Journal of the DNA Methylation Society
Ai Ling TehNeerja Karnani

Abstract

Interindividual variability in the epigenome has gained tremendous attention for its potential in pathophysiological investigation, disease diagnosis, and evaluation of clinical intervention. DNA methylation is the most studied epigenetic mark in epigenome-wide association studies (EWAS) as it can be detected from limited starting material. Infinium 450K methylation array is the most popular platform for high-throughput profiling of this mark in clinical samples, as it is cost-effective and requires small amounts of DNA. However, this method suffers from low genome coverage and errors introduced by probe cross-hybridization. Whole-genome bisulfite sequencing can overcome these limitations but elevates the costs tremendously. Methyl-Capture Sequencing (MC Seq) is an attractive intermediate solution to increase the methylome coverage in large sample sets. Here we first demonstrate that MC Seq can be employed using DNA amounts comparable to the amounts used for Infinium 450K. Second, to provide guidance when choosing between the 2 platforms for EWAS, we evaluate and compare MC Seq and Infinium 450K in terms of coverage, technical variation, and concordance of methylation calls in clinical samples. Last, since the focus in EWAS is ...Continue Reading

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Citations

Apr 8, 2016·Epigenomics·Xinyi LinJoanna D Holbrook
Apr 12, 2017·Clinical Epigenetics·Goran MicevicMarcus Bosenberg
Aug 24, 2018·Journal of Crohn's & Colitis·Hagar TamanRuth H Paulssen
Feb 13, 2019·Bioinformatics·Jordi Martorell-MarugánPedro Carmona-Sáez
Dec 14, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Kathleen CheungLouise N Reynard
Nov 4, 2017·Clinical Chemistry·Angela C Estampador, Paul W Franks
Sep 21, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Jonathan A HeissAllan C Just
Jul 8, 2020·International Journal of Molecular Sciences·Chia-Chun TsengShun-Jen Chang
Jul 13, 2021·Bio-protocol·Jordi Martorell-Marugán, Pedro Carmona-Sáez
Jun 23, 2021·Human Molecular Genetics·Suvo ChatterjeeFasil Tekola-Ayele
Sep 1, 2021·Epigenetics : Official Journal of the DNA Methylation Society·Philip TitcombeSheila J Barton

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Methods Mentioned

BETA
biopsies
WGBS
Immunoprecipitation
RRBS
MeDIP-Seq
Methyl-Capture Sequencing
Seq
Methyl-Seq
Assay
electrophoresis

Software Mentioned

bowtie2
Bismark
Homer annotatePeaks
bedtools
MeDIP
FastQC
Seq
R
MC Seq
UCSC genome browser

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