Methyl-binding DNA capture sequencing for patient tissues

Rohit R. Jadhav, Yao V. Wang, Ya Ting Hsu, Joseph Liu, Dawn Garcia, Zhao Lai, Hui-ming Huang, Victor X Jin

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Methylation is one of the essential epigenetic modifications to the DNA, which is responsible for the precise regulation of genes required for stable development and differentiation of different tissue types. Dysregulation of this process is often the hallmark of various diseases like cancer. Here, we outline one of the recent sequencing techniques, Methyl-Binding DNA Capture sequencing (MBDCap-seq), used to quantify methylation in various normal and disease tissues for large patient cohorts. We describe a detailed protocol of this affinity enrichment approach along with a bioinformatics pipeline to achieve optimal quantification. This technique has been used to sequence hundreds of patients across various cancer types as a part of the 1,000 methylome project (Cancer Methylome System).

Original languageEnglish (US)
Article numbere54131
JournalJournal of Visualized Experiments
Volume2016
Issue number116
DOIs
StatePublished - Oct 31 2016

Fingerprint

Methylation
DNA Sequence Analysis
DNA
Tissue
Bioinformatics
Neoplasms
Pipelines
Genes
Computational Biology
Epigenomics

Keywords

  • Bioinformatics
  • Differential methylation
  • DNA methylation
  • Epigenetics
  • Genetics
  • Issue 116
  • MBD-seq
  • Sequencing

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Jadhav, R. R., Wang, Y. V., Hsu, Y. T., Liu, J., Garcia, D., Lai, Z., ... Jin, V. X. (2016). Methyl-binding DNA capture sequencing for patient tissues. Journal of Visualized Experiments, 2016(116), [e54131]. https://doi.org/10.3791/54131

Methyl-binding DNA capture sequencing for patient tissues. / Jadhav, Rohit R.; Wang, Yao V.; Hsu, Ya Ting; Liu, Joseph; Garcia, Dawn; Lai, Zhao; Huang, Hui-ming; Jin, Victor X.

In: Journal of Visualized Experiments, Vol. 2016, No. 116, e54131, 31.10.2016.

Research output: Contribution to journalArticle

Jadhav, RR, Wang, YV, Hsu, YT, Liu, J, Garcia, D, Lai, Z, Huang, H & Jin, VX 2016, 'Methyl-binding DNA capture sequencing for patient tissues', Journal of Visualized Experiments, vol. 2016, no. 116, e54131. https://doi.org/10.3791/54131
Jadhav RR, Wang YV, Hsu YT, Liu J, Garcia D, Lai Z et al. Methyl-binding DNA capture sequencing for patient tissues. Journal of Visualized Experiments. 2016 Oct 31;2016(116). e54131. https://doi.org/10.3791/54131
Jadhav, Rohit R. ; Wang, Yao V. ; Hsu, Ya Ting ; Liu, Joseph ; Garcia, Dawn ; Lai, Zhao ; Huang, Hui-ming ; Jin, Victor X. / Methyl-binding DNA capture sequencing for patient tissues. In: Journal of Visualized Experiments. 2016 ; Vol. 2016, No. 116.
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