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Pitfalls and Rewards of Setting Up a Liquid Biopsy Approach for the Detection of Driver Mutations in Circulating Tumor DNAs: Our Institutional Experience

We describe our institutional experience of developing a liquid biopsy approach using circulating tumor DNA (ctDNA) analysis for personalized medicine in cancer patients, focusing on the hurdles encountered during the multistep process in order to benefit other investigators wishing to set up this t...

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Autores principales: Chen, Michelle, Jian, Damon, Sidorov, Maxim, Woo, Rinette W. L., Kim, Angela, Stone, David E., Nazarian, Ari, Nosrati, Mehdi, Ice, Ryan J., de Semir, David, Dar, Altaf A., Luštrik, Roman, Kokošar, Janez, Ausec, Luka, Rowbotham, Michael C., Tranah, Gregory J., Kashani-Sabet, Mohammed, Soroceanu, Liliana, McAllister, Sean D., Desprez, Pierre-Yves
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9692455/
https://www.ncbi.nlm.nih.gov/pubmed/36579573
http://dx.doi.org/10.3390/jpm12111845
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author Chen, Michelle
Jian, Damon
Sidorov, Maxim
Woo, Rinette W. L.
Kim, Angela
Stone, David E.
Nazarian, Ari
Nosrati, Mehdi
Ice, Ryan J.
de Semir, David
Dar, Altaf A.
Luštrik, Roman
Kokošar, Janez
Ausec, Luka
Rowbotham, Michael C.
Tranah, Gregory J.
Kashani-Sabet, Mohammed
Soroceanu, Liliana
McAllister, Sean D.
Desprez, Pierre-Yves
author_facet Chen, Michelle
Jian, Damon
Sidorov, Maxim
Woo, Rinette W. L.
Kim, Angela
Stone, David E.
Nazarian, Ari
Nosrati, Mehdi
Ice, Ryan J.
de Semir, David
Dar, Altaf A.
Luštrik, Roman
Kokošar, Janez
Ausec, Luka
Rowbotham, Michael C.
Tranah, Gregory J.
Kashani-Sabet, Mohammed
Soroceanu, Liliana
McAllister, Sean D.
Desprez, Pierre-Yves
author_sort Chen, Michelle
collection PubMed
description We describe our institutional experience of developing a liquid biopsy approach using circulating tumor DNA (ctDNA) analysis for personalized medicine in cancer patients, focusing on the hurdles encountered during the multistep process in order to benefit other investigators wishing to set up this type of study in their institution. Blood samples were collected at the time of cancer surgery from 209 patients with one of nine different cancer types. Extracted tumor DNA and circulating cell-free DNA were sequenced using cancer-specific panels and the Illumina MiSeq machine. Almost half of the pairs investigated were uninformative, mostly because there was no trackable pathogenic mutation detected in the original tumor. The pairs with interpretable data corresponded to 107 patients. Analysis of 48 gene sequences common to both panels was performed and revealed that about 40% of these pairs contained at least one driver mutation detected in the DNA extracted from plasma. Here, we describe the choice of our overall approach, the selection of the cancer panels, and the difficulties encountered during the multistep process, including the use of several tumor types and in the data analysis. We also describe some case reports using longitudinal samples, illustrating the potential advantages and rewards in performing ctDNA sequencing to monitor tumor burden or guide treatment for cancer patients.
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spelling pubmed-96924552022-11-26 Pitfalls and Rewards of Setting Up a Liquid Biopsy Approach for the Detection of Driver Mutations in Circulating Tumor DNAs: Our Institutional Experience Chen, Michelle Jian, Damon Sidorov, Maxim Woo, Rinette W. L. Kim, Angela Stone, David E. Nazarian, Ari Nosrati, Mehdi Ice, Ryan J. de Semir, David Dar, Altaf A. Luštrik, Roman Kokošar, Janez Ausec, Luka Rowbotham, Michael C. Tranah, Gregory J. Kashani-Sabet, Mohammed Soroceanu, Liliana McAllister, Sean D. Desprez, Pierre-Yves J Pers Med Article We describe our institutional experience of developing a liquid biopsy approach using circulating tumor DNA (ctDNA) analysis for personalized medicine in cancer patients, focusing on the hurdles encountered during the multistep process in order to benefit other investigators wishing to set up this type of study in their institution. Blood samples were collected at the time of cancer surgery from 209 patients with one of nine different cancer types. Extracted tumor DNA and circulating cell-free DNA were sequenced using cancer-specific panels and the Illumina MiSeq machine. Almost half of the pairs investigated were uninformative, mostly because there was no trackable pathogenic mutation detected in the original tumor. The pairs with interpretable data corresponded to 107 patients. Analysis of 48 gene sequences common to both panels was performed and revealed that about 40% of these pairs contained at least one driver mutation detected in the DNA extracted from plasma. Here, we describe the choice of our overall approach, the selection of the cancer panels, and the difficulties encountered during the multistep process, including the use of several tumor types and in the data analysis. We also describe some case reports using longitudinal samples, illustrating the potential advantages and rewards in performing ctDNA sequencing to monitor tumor burden or guide treatment for cancer patients. MDPI 2022-11-04 /pmc/articles/PMC9692455/ /pubmed/36579573 http://dx.doi.org/10.3390/jpm12111845 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chen, Michelle
Jian, Damon
Sidorov, Maxim
Woo, Rinette W. L.
Kim, Angela
Stone, David E.
Nazarian, Ari
Nosrati, Mehdi
Ice, Ryan J.
de Semir, David
Dar, Altaf A.
Luštrik, Roman
Kokošar, Janez
Ausec, Luka
Rowbotham, Michael C.
Tranah, Gregory J.
Kashani-Sabet, Mohammed
Soroceanu, Liliana
McAllister, Sean D.
Desprez, Pierre-Yves
Pitfalls and Rewards of Setting Up a Liquid Biopsy Approach for the Detection of Driver Mutations in Circulating Tumor DNAs: Our Institutional Experience
title Pitfalls and Rewards of Setting Up a Liquid Biopsy Approach for the Detection of Driver Mutations in Circulating Tumor DNAs: Our Institutional Experience
title_full Pitfalls and Rewards of Setting Up a Liquid Biopsy Approach for the Detection of Driver Mutations in Circulating Tumor DNAs: Our Institutional Experience
title_fullStr Pitfalls and Rewards of Setting Up a Liquid Biopsy Approach for the Detection of Driver Mutations in Circulating Tumor DNAs: Our Institutional Experience
title_full_unstemmed Pitfalls and Rewards of Setting Up a Liquid Biopsy Approach for the Detection of Driver Mutations in Circulating Tumor DNAs: Our Institutional Experience
title_short Pitfalls and Rewards of Setting Up a Liquid Biopsy Approach for the Detection of Driver Mutations in Circulating Tumor DNAs: Our Institutional Experience
title_sort pitfalls and rewards of setting up a liquid biopsy approach for the detection of driver mutations in circulating tumor dnas: our institutional experience
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9692455/
https://www.ncbi.nlm.nih.gov/pubmed/36579573
http://dx.doi.org/10.3390/jpm12111845
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