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Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations

Cell-free DNA (cfDNA) analysis is a minimally invasive method that can be used to detect genomic abnormalities by directly testing a blood sample. This method is particularly useful for immunosuppressed patients, who are at high risk of complications from tissue biopsy. The cfDNA tumor fraction (TF)...

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Autores principales: Bouzidi, Amira, Labreche, Karim, Baron, Marine, Veyri, Marianne, Denis, Jérôme Alexandre, Touat, Mehdi, Sanson, Marc, Davi, Frédéric, Guillerm, Erell, Jouannet, Stéphanie, Charlotte, Frédéric, Bielle, Franck, Choquet, Sylvain, Boëlle, Pierre-Yves, Cadranel, Jacques, Leblond, Véronique, Autran, Brigitte, Lacorte, Jean-Marc, Spano, Jean-Philippe, Coulet, Florence
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369887/
https://www.ncbi.nlm.nih.gov/pubmed/34710202
http://dx.doi.org/10.3389/fcell.2021.661272
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author Bouzidi, Amira
Labreche, Karim
Baron, Marine
Veyri, Marianne
Denis, Jérôme Alexandre
Touat, Mehdi
Sanson, Marc
Davi, Frédéric
Guillerm, Erell
Jouannet, Stéphanie
Charlotte, Frédéric
Bielle, Franck
Choquet, Sylvain
Boëlle, Pierre-Yves
Cadranel, Jacques
Leblond, Véronique
Autran, Brigitte
Lacorte, Jean-Marc
Spano, Jean-Philippe
Coulet, Florence
author_facet Bouzidi, Amira
Labreche, Karim
Baron, Marine
Veyri, Marianne
Denis, Jérôme Alexandre
Touat, Mehdi
Sanson, Marc
Davi, Frédéric
Guillerm, Erell
Jouannet, Stéphanie
Charlotte, Frédéric
Bielle, Franck
Choquet, Sylvain
Boëlle, Pierre-Yves
Cadranel, Jacques
Leblond, Véronique
Autran, Brigitte
Lacorte, Jean-Marc
Spano, Jean-Philippe
Coulet, Florence
author_sort Bouzidi, Amira
collection PubMed
description Cell-free DNA (cfDNA) analysis is a minimally invasive method that can be used to detect genomic abnormalities by directly testing a blood sample. This method is particularly useful for immunosuppressed patients, who are at high risk of complications from tissue biopsy. The cfDNA tumor fraction (TF) varies greatly across cancer type and between patients. Thus, the detection of molecular alterations is highly dependent on the circulating TF. In our study, we aimed to calculate the TF and characterize the copy number aberration (CNA) profile of cfDNA from patients with rare malignancies occurring in immunosuppressed environments or immune-privileged sites. To accomplish this, we recruited 36 patients: 19 patients with non-Hodgkin lymphoma (NHL) who were either human immunodeficiency virus (HIV)-positive or organ transplant recipients, 5 HIV-positive lung cancer patients, and 12 patients with glioma. cfDNA was extracted from the patients’ plasma and sequenced using low-coverage whole genome sequencing (LC-WGS). The cfDNA TF was then calculated using the ichorCNA bioinformatic algorithm, based on the CNA profile. In parallel, we performed whole exome sequencing of patient tumor tissue and cfDNA samples with detectable TFs. We detected a cfDNA TF in 29% of immune-suppressed patients (one patient with lung cancer and six with systemic NHL), with a TF range from 8 to 70%. In these patients, the events detected in the CNA profile of cfDNA are well-known events associated with NHL and lung cancer. Moreover, cfDNA CNA profile correlated with the CNA profile of matched tumor tissue. No tumor-derived cfDNA was detected in the glioma patients. Our study shows that tumor genetic content is detectable in cfDNA from immunosuppressed patients with advanced NHL or lung cancer. LC-WGS is a time- and cost-effective method that can help select an appropriate strategy for performing extensive molecular analysis of cfDNA. This technique also enables characterization of CNAs in cfDNA when sufficient tumor content is available. Hence, this approach can be used to collect useful molecular information that is relevant to patient care.
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spelling pubmed-83698872021-08-18 Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations Bouzidi, Amira Labreche, Karim Baron, Marine Veyri, Marianne Denis, Jérôme Alexandre Touat, Mehdi Sanson, Marc Davi, Frédéric Guillerm, Erell Jouannet, Stéphanie Charlotte, Frédéric Bielle, Franck Choquet, Sylvain Boëlle, Pierre-Yves Cadranel, Jacques Leblond, Véronique Autran, Brigitte Lacorte, Jean-Marc Spano, Jean-Philippe Coulet, Florence Front Cell Dev Biol Cell and Developmental Biology Cell-free DNA (cfDNA) analysis is a minimally invasive method that can be used to detect genomic abnormalities by directly testing a blood sample. This method is particularly useful for immunosuppressed patients, who are at high risk of complications from tissue biopsy. The cfDNA tumor fraction (TF) varies greatly across cancer type and between patients. Thus, the detection of molecular alterations is highly dependent on the circulating TF. In our study, we aimed to calculate the TF and characterize the copy number aberration (CNA) profile of cfDNA from patients with rare malignancies occurring in immunosuppressed environments or immune-privileged sites. To accomplish this, we recruited 36 patients: 19 patients with non-Hodgkin lymphoma (NHL) who were either human immunodeficiency virus (HIV)-positive or organ transplant recipients, 5 HIV-positive lung cancer patients, and 12 patients with glioma. cfDNA was extracted from the patients’ plasma and sequenced using low-coverage whole genome sequencing (LC-WGS). The cfDNA TF was then calculated using the ichorCNA bioinformatic algorithm, based on the CNA profile. In parallel, we performed whole exome sequencing of patient tumor tissue and cfDNA samples with detectable TFs. We detected a cfDNA TF in 29% of immune-suppressed patients (one patient with lung cancer and six with systemic NHL), with a TF range from 8 to 70%. In these patients, the events detected in the CNA profile of cfDNA are well-known events associated with NHL and lung cancer. Moreover, cfDNA CNA profile correlated with the CNA profile of matched tumor tissue. No tumor-derived cfDNA was detected in the glioma patients. Our study shows that tumor genetic content is detectable in cfDNA from immunosuppressed patients with advanced NHL or lung cancer. LC-WGS is a time- and cost-effective method that can help select an appropriate strategy for performing extensive molecular analysis of cfDNA. This technique also enables characterization of CNAs in cfDNA when sufficient tumor content is available. Hence, this approach can be used to collect useful molecular information that is relevant to patient care. Frontiers Media S.A. 2021-08-03 /pmc/articles/PMC8369887/ /pubmed/34710202 http://dx.doi.org/10.3389/fcell.2021.661272 Text en Copyright © 2021 Bouzidi, Labreche, Baron, Veyri, Denis, Touat, Sanson, Davi, Guillerm, Jouannet, Charlotte, Bielle, Choquet, Boëlle, Cadranel, Leblond, Autran, Lacorte, Spano, Coulet and the IDEATION study group. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cell and Developmental Biology
Bouzidi, Amira
Labreche, Karim
Baron, Marine
Veyri, Marianne
Denis, Jérôme Alexandre
Touat, Mehdi
Sanson, Marc
Davi, Frédéric
Guillerm, Erell
Jouannet, Stéphanie
Charlotte, Frédéric
Bielle, Franck
Choquet, Sylvain
Boëlle, Pierre-Yves
Cadranel, Jacques
Leblond, Véronique
Autran, Brigitte
Lacorte, Jean-Marc
Spano, Jean-Philippe
Coulet, Florence
Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations
title Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations
title_full Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations
title_fullStr Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations
title_full_unstemmed Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations
title_short Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations
title_sort low-coverage whole genome sequencing of cell-free dna from immunosuppressed cancer patients enables tumor fraction determination and reveals relevant copy number alterations
topic Cell and Developmental Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369887/
https://www.ncbi.nlm.nih.gov/pubmed/34710202
http://dx.doi.org/10.3389/fcell.2021.661272
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