Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model
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 tu...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fgene.2018.00006/full |
| _version_ | 1828811420385411072 |
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| author | Elaine C. Maggi Silvia Gravina Haiying Cheng Bilal Piperdi Ziqiang Yuan Xiao Dong Steven K. Libutti Jan Vijg Jan Vijg Jan Vijg Cristina Montagna Cristina Montagna |
| author_facet | Elaine C. Maggi Silvia Gravina Haiying Cheng Bilal Piperdi Ziqiang Yuan Xiao Dong Steven K. Libutti Jan Vijg Jan Vijg Jan Vijg Cristina Montagna Cristina Montagna |
| author_sort | Elaine C. Maggi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T09:27:32Z |
| format | Article |
| id | doaj.art-9d957a29de5c4a079f02b0ce9d94941b |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T09:27:32Z |
| publishDate | 2018-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-9d957a29de5c4a079f02b0ce9d94941b2022-12-22T00:28:59ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-01-01910.3389/fgene.2018.00006300628Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor ModelElaine C. Maggi0Silvia Gravina1Haiying Cheng2Bilal Piperdi3Ziqiang Yuan4Xiao Dong5Steven K. Libutti6Jan Vijg7Jan Vijg8Jan Vijg9Cristina Montagna10Cristina Montagna11Department of Genetics, Albert Einstein College of Medicine, New York, NY, United StatesDepartment of Genetics, Albert Einstein College of Medicine, New York, NY, United StatesDepartment of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, United StatesDepartment of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, United StatesDepartment of Surgery, Albert Einstein College of Medicine, New York, NY, United StatesDepartment of Genetics, Albert Einstein College of Medicine, New York, NY, United StatesDepartment of Surgery, Albert Einstein College of Medicine, New York, NY, United StatesDepartment of Genetics, Albert Einstein College of Medicine, New York, NY, United StatesDepartment of Ophthalmology and Visual Science, Albert Einstein College of Medicine, New York, NY, United StatesObstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, New York, NY, United StatesDepartment of Genetics, Albert Einstein College of Medicine, New York, NY, United StatesDepartment of Pathology, Albert Einstein College of Medicine, New York, NY, United StatesThe 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.http://journal.frontiersin.org/article/10.3389/fgene.2018.00006/fullcell-free DNAcfDNADNA methylationnon-invasive blood based screeningbiomarkerpancreatic cancer |
| spellingShingle | Elaine C. Maggi Silvia Gravina Haiying Cheng Bilal Piperdi Ziqiang Yuan Xiao Dong Steven K. Libutti Jan Vijg Jan Vijg Jan Vijg Cristina Montagna Cristina Montagna Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model Frontiers in Genetics cell-free DNA cfDNA DNA methylation non-invasive blood based screening biomarker pancreatic cancer |
| title | Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model |
| title_full | Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model |
| title_fullStr | Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model |
| title_full_unstemmed | Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model |
| title_short | Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model |
| title_sort | development of a method to implement whole genome bisulfite sequencing of cfdna from cancer patients and a mouse tumor model |
| topic | cell-free DNA cfDNA DNA methylation non-invasive blood based screening biomarker pancreatic cancer |
| url | http://journal.frontiersin.org/article/10.3389/fgene.2018.00006/full |
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