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

• Published in: Epigenetics Vol. 11; no. 1; pp. 36 - 48
• Main Authors: Teh, Ai Ling, Pan, Hong, Lin, Xinyi, Lim, Yubin Ives, Patro, Chinari Pawan Kumar, Cheong, Clara Yujing, Gong, Min, MacIsaac, Julia L., Kwoh, Chee-Keong, Meaney, Michael J., Kobor, Michael S., Chong, Yap-Seng, Gluckman, Peter D., Holbrook, Joanna D., Karnani, Neerja
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 02.01.2016
• Subjects: DNA Methylation; Epigenesis, Genetic; Epigenome-wide association study; Ethnic Groups - genetics; Female; Genome, Human; Humans; Infinium HumanMethylation450 array; Male; Methyl-Capture Sequencing; next generation sequencing; Oligonucleotide Array Sequence Analysis - methods; Research Paper; Sequence Alignment; Sequence Analysis, DNA - methods; Methyl-Capture Sequencing; DNA methylation; Epigenome-wide association study; Infinium HumanMethylation450 array; next generation sequencing
• ISSN: 1559-2294; 1559-2308; 1559-2308
• DOI: 10.1080/15592294.2015.1132136

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 to study interindividual variation, we demonstrate the utility of MC Seq in studying interindividual variation in subjects from different ethnicities.