Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing

Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This approach generated up to 200 million reads for a single cfD...

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Autores principales: Lau, Billy T., Almeda, Alison, Schauer, Marie, McNamara, Madeline, Bai, Xiangqi, Meng, Qingxi, Partha, Mira, Grimes, Susan M., Lee, HoJoon, Heestand, Gregory M., Ji, Hanlee P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10155347/
https://www.ncbi.nlm.nih.gov/pubmed/37138315
http://dx.doi.org/10.1186/s13073-023-01178-3
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author Lau, Billy T.
Almeda, Alison
Schauer, Marie
McNamara, Madeline
Bai, Xiangqi
Meng, Qingxi
Partha, Mira
Grimes, Susan M.
Lee, HoJoon
Heestand, Gregory M.
Ji, Hanlee P.
author_facet Lau, Billy T.
Almeda, Alison
Schauer, Marie
McNamara, Madeline
Bai, Xiangqi
Meng, Qingxi
Partha, Mira
Grimes, Susan M.
Lee, HoJoon
Heestand, Gregory M.
Ji, Hanlee P.
author_sort Lau, Billy T.
collection PubMed
description Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This approach generated up to 200 million reads for a single cfDNA sample from cancer patients, an order of magnitude improvement over existing nanopore sequencing methods. We developed a single-molecule classifier to determine whether individual reads originated from a tumor or immune cells. Leveraging methylomes of matched tumors and immune cells, we characterized cfDNA methylomes of cancer patients for longitudinal monitoring during treatment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-023-01178-3.
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spelling pubmed-101553472023-05-04 Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing Lau, Billy T. Almeda, Alison Schauer, Marie McNamara, Madeline Bai, Xiangqi Meng, Qingxi Partha, Mira Grimes, Susan M. Lee, HoJoon Heestand, Gregory M. Ji, Hanlee P. Genome Med Method Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This approach generated up to 200 million reads for a single cfDNA sample from cancer patients, an order of magnitude improvement over existing nanopore sequencing methods. We developed a single-molecule classifier to determine whether individual reads originated from a tumor or immune cells. Leveraging methylomes of matched tumors and immune cells, we characterized cfDNA methylomes of cancer patients for longitudinal monitoring during treatment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-023-01178-3. BioMed Central 2023-05-03 /pmc/articles/PMC10155347/ /pubmed/37138315 http://dx.doi.org/10.1186/s13073-023-01178-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Lau, Billy T.
Almeda, Alison
Schauer, Marie
McNamara, Madeline
Bai, Xiangqi
Meng, Qingxi
Partha, Mira
Grimes, Susan M.
Lee, HoJoon
Heestand, Gregory M.
Ji, Hanlee P.
Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
title Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
title_full Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
title_fullStr Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
title_full_unstemmed Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
title_short Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing
title_sort single-molecule methylation profiles of cell-free dna in cancer with nanopore sequencing
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10155347/
https://www.ncbi.nlm.nih.gov/pubmed/37138315
http://dx.doi.org/10.1186/s13073-023-01178-3
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