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Epigenomics. 2016 Aug;8(8):1061-77. doi: 10.2217/epi-2016-0038. Epub 2016 Jun 8.

Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis.

Jeong HM1, Lee S2, Chae H3, Kim R1,4, Kwon MJ5,6, Oh E7,8, Choi YL7,8,9, Kim S10,11,12, Shin YK1,4,12,13,14.

Author information

1
Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
2
School of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea.
3
Computer Science Department, School of Informatics & Computing, Indiana University, Bloomington, IN, USA.
4
Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Republic of Korea.
5
College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.
6
Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.
7
Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
8
Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.
9
Laboratory of Cancer Genomics & Molecular Pathology, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea.
10
Department of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea.
11
Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.
12
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
13
The Center for Anti-Cancer Companion Diagnostics, School of Biological Science, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Republic of Korea.
14
Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.

Abstract

AIMS:

We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage.

MATERIALS & METHODS:

The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results.

RESULTS:

MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods.

CONCLUSION:

MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.

KEYWORDS:

DNA methylation analysis; methylated DNA immunoprecipitation-bisulphite sequencing; next-generation sequencing

PMID:
27266718
DOI:
10.2217/epi-2016-0038
[Indexed for MEDLINE]
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