Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis-Reference-Cited by-同舟云学术

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

Published:2016-08 Issue:8 Volume:8 Page:1061-1077
ISSN:1750-1911
Container-title:Epigenomics
language:en
Short-container-title:Epigenomics

Author:

Jeong Hae Min¹,Lee Sangseon²,Chae Heejoon³,Kim RyongNam¹⁴,Kwon Mi Jeong⁵⁶,Oh Ensel⁷⁸,Choi Yoon-La⁷⁸⁹,Kim Sun¹⁰¹¹¹²,Shin Young Kee¹⁴¹²¹³¹⁴

Affiliation:

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.

Publisher

Future Medicine Ltd

Subject

Cancer Research,Genetics

Link

https://www.futuremedicine.com/doi/pdf/10.2217/epi-2016-0038

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