Development of a method to implement whole-genome bisulfite sequencing of cfDNA from cancer patients and a mouse tumor model

Elaine C. Maggi, Silvia Gravina, Haiying Cheng, Bilal Piperdi, Ziqiang Yuan, Xiao Dong, Steven K. Libutti, Jan Vijg, Cristina Montagna

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


The goal of this study was to develop a method for whole genome cell-free DNA (cfDNA) methylation analysis in humans and mice with the ultimate goal to facilitate the identification of tumor derived DNA methylation changes in the blood. Plasma or serum from patients with pancreatic neuroendocrine tumors or lung cancer, and plasma from a murine model of pancreatic adenocarcinoma was used to develop a protocol for cfDNA isolation, library preparation and whole-genome bisulfite sequencing of ultra low quantities of cfDNA, including tumor-specific DNA. The protocol developed produced high quality libraries consistently generating a conversion rate > 98% that will be applicable for the analysis of human and mouse plasma or serum to detect tumor-derived changes in DNA methylation.

Original languageEnglish (US)
Article number6
JournalFrontiers in Genetics
Issue numberJAN
StatePublished - Jan 23 2018

Bibliographical note

Funding Information:
We would like to thank the Molecular Cytogenetic Core at Albert Einstein College of Medicine and in particular Dr. Jidong Shan. Research reported in this publication was supported by the Albert Einstein Cancer Center support grant of the National Institutes of Health under award number P30CA013330. Part of this work was also supported by a grant from the National Institutes of Health [CA180126-05 to JV]

Publisher Copyright:
© 2018 Maggi, Gravina, Cheng, Piperdi, Yuan, Dong, Libutti, Vijg and Montagna.


  • Biomarker
  • Cell-free DNA
  • CfDNA
  • Circulating DNA, mouse cfDNA
  • DNA methylation
  • Non-invasive blood based screening
  • Pancreatic cancer


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