A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

Keita Hasegawa, Kazuhiko Nakabayashi, Keisuke Ishiwata, Yoshifumi Kasuga, Kenichiro Hata, Mamoru Tanaka

Research output: Contribution to journalArticlepeer-review

Abstract

Objective: The opportunities for sequencing-based methylome analysis of clinical samples are increasing. To reduce its cost and the amount of genomic DNA required for library preparation, we aimed to establish a capture methyl-seq protocol, which adopts pre-pooling of multiple libraries before hybridization capture and TET2/APOBEC-mediated conversion of unmethylated cytosine to thymine. Results: We compared a publicly available dataset generated by the standard Agilent protocol of SureSelect XT Human Methyl-Seq Kit and our dataset obtained by our modified protocol, EMCap, that adopted sample pre-pooling and enzymatic conversion. We confirmed that the quality of DNA methylation data was comparable between the two datasets. As our protocol, EMCap, is more cost-effective and reduces the amount of input genomic DNA, it would serve as a better choice for clinical methylome sequencing.

Original languageEnglish
Article number141
JournalBMC Research Notes
Volume16
Issue number1
DOIs
Publication statusPublished - 2023 Dec

Keywords

  • APOBEC
  • Capture methyl-seq
  • DNA methylation
  • Enzymatic conversion
  • TET2

ASJC Scopus subject areas

  • General Biochemistry,Genetics and Molecular Biology

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