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Identification and use of personalized genomic markers for monitoring circulating tumor DNA

Chen, Yilun LU ; George, Anthony M. LU ; Olsson, Eleonor LU and Saal, Lao H. LU (2018) In Methods in Molecular Biology 1768. p.303-322
Abstract

Digital PCR techniques are ideally suited for accurately quantifying trace amounts of target DNA sequences, such as tumor-derived mutant DNA that is present in the blood circulation of patients with cancer. Here, we describe an approach marrying low-coverage whole-genome sequencing of tumor tissues, to enumerate chromosomal rearrangement breakpoints, together with droplet digital PCR (ddPCR)-based personalized rearrangement assays to cost-effectively monitor circulating tumor DNA levels at multiple time-points during the clinical course. The method is generally applicable to essentially any cancer patient, as all cancers harbor unstable genomes, and may have uses for measuring minimal residual disease, response to therapy, and early... (More)

Digital PCR techniques are ideally suited for accurately quantifying trace amounts of target DNA sequences, such as tumor-derived mutant DNA that is present in the blood circulation of patients with cancer. Here, we describe an approach marrying low-coverage whole-genome sequencing of tumor tissues, to enumerate chromosomal rearrangement breakpoints, together with droplet digital PCR (ddPCR)-based personalized rearrangement assays to cost-effectively monitor circulating tumor DNA levels at multiple time-points during the clinical course. The method is generally applicable to essentially any cancer patient, as all cancers harbor unstable genomes, and may have uses for measuring minimal residual disease, response to therapy, and early detection of metastasis.

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Please use this url to cite or link to this publication:
author
organization
publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
subject
keywords
Cell-free circulating tumor DNA, Droplet digital PCR, Liquid biopsy, Noninvasive diagnosis, Personalized medicine, Whole-genome sequencing
in
Methods in Molecular Biology
volume
1768
pages
20 pages
publisher
Humana Press
external identifiers
  • scopus:85046362164
ISSN
1064-3745
DOI
10.1007/978-1-4939-7778-9_17
language
English
LU publication?
yes
id
292b7066-a4e0-4712-8a3e-8381c13467b0
date added to LUP
2018-05-17 14:34:24
date last changed
2018-05-29 09:43:40
@inbook{292b7066-a4e0-4712-8a3e-8381c13467b0,
  abstract     = {<p>Digital PCR techniques are ideally suited for accurately quantifying trace amounts of target DNA sequences, such as tumor-derived mutant DNA that is present in the blood circulation of patients with cancer. Here, we describe an approach marrying low-coverage whole-genome sequencing of tumor tissues, to enumerate chromosomal rearrangement breakpoints, together with droplet digital PCR (ddPCR)-based personalized rearrangement assays to cost-effectively monitor circulating tumor DNA levels at multiple time-points during the clinical course. The method is generally applicable to essentially any cancer patient, as all cancers harbor unstable genomes, and may have uses for measuring minimal residual disease, response to therapy, and early detection of metastasis.</p>},
  author       = {Chen, Yilun and George, Anthony M. and Olsson, Eleonor and Saal, Lao H.},
  issn         = {1064-3745},
  keyword      = {Cell-free circulating tumor DNA,Droplet digital PCR,Liquid biopsy,Noninvasive diagnosis,Personalized medicine,Whole-genome sequencing},
  language     = {eng},
  month        = {01},
  pages        = {303--322},
  publisher    = {Humana Press},
  series       = {Methods in Molecular Biology},
  title        = {Identification and use of personalized genomic markers for monitoring circulating tumor DNA},
  url          = {http://dx.doi.org/10.1007/978-1-4939-7778-9_17},
  volume       = {1768},
  year         = {2018},
}