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

Keita Hasegawa1,2, Kazuhiko Nakabayashi3, Keisuke Ishiwata1

  • 1Department of Maternal-Fetal Biology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.

BMC Research Notes
|July 6, 2023
PubMed
Summary

A new capture methyl-seq protocol (EMCap) reduces costs and DNA input for clinical methylome sequencing. This method offers comparable data quality to standard protocols, making it ideal for large-scale studies.

Keywords:
APOBECCapture methyl-seqDNA methylationEnzymatic conversionTET2

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Area of Science:

  • Genomics
  • Epigenetics

Background:

  • Sequencing-based methylome analysis is crucial for clinical research.
  • Current methods can be costly and require substantial genomic DNA input.

Purpose of the Study:

  • To develop a cost-effective capture methyl-seq protocol for clinical samples.
  • To reduce the amount of genomic DNA needed for library preparation.

Main Methods:

  • Established a capture methyl-seq protocol (EMCap) involving pre-pooling of libraries.
  • Utilized TET2/APOBEC-mediated conversion of unmethylated cytosine to thymine.
  • Compared EMCap with the standard SureSelect XT Human Methyl-Seq Kit.

Main Results:

  • EMCap demonstrated comparable DNA methylation data quality to the standard protocol.
  • The EMCap protocol is more cost-effective.
  • EMCap significantly reduces the required input genomic DNA.

Conclusions:

  • EMCap is a suitable alternative for clinical methylome sequencing.
  • The protocol's efficiency makes it advantageous for large-scale clinical applications.