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

doi:10.3389/fgene.2018.00006

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 journal › Article › peer-review

20 Scopus citations

Abstract

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 language	English (US)
Article number	6
Journal	Frontiers in Genetics
Volume	9
Issue number	JAN
DOIs	https://doi.org/10.3389/fgene.2018.00006
State	Published - Jan 23 2018

Keywords

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

ASJC Scopus subject areas

Molecular Medicine
Genetics
Genetics(clinical)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.3389/fgene.2018.00006

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

abstract = "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.",

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

author = "Maggi, {Elaine C.} and Silvia Gravina and Haiying Cheng and Bilal Piperdi and Ziqiang Yuan and Xiao Dong and Libutti, {Steven K.} and Jan Vijg and Cristina Montagna",

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doi = "10.3389/fgene.2018.00006",

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AU - Maggi, Elaine C.

AU - Gravina, Silvia

AU - Cheng, Haiying

AU - Piperdi, Bilal

AU - Yuan, Ziqiang

AU - Dong, Xiao

AU - Libutti, Steven K.

AU - Vijg, Jan

AU - Montagna, Cristina

PY - 2018/1/23

Y1 - 2018/1/23

N2 - 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.

AB - 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.

KW - Biomarker

KW - Cell-free DNA

KW - CfDNA

KW - Circulating DNA, mouse cfDNA

KW - DNA methylation

KW - Non-invasive blood based screening

KW - Pancreatic cancer

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JO - Frontiers in Genetics

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

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

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