Evidence map›Paper›PMID 34710202›Full record

ArticleFrontiers in cell and developmental biology2021

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

Amira Bouzidi, Karim Labreche, Marine Baron, Marianne Veyri, Jérôme Alexandre Denis, Mehdi Touat, Marc Sanson, Frédéric Davi, Erell Guillerm, Stéphanie Jouannet and 11 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in cell and developmental biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.5field-weighted citation impact, top 43% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 9 citations in OpenAlex.

  1. Review
  2. Review
  3. Review
  4. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors at 5 institutions in 1 country.

Amira BouzidiSorbonne University, INSERM, Research Unit on Cardiovascular and Metabolic Disease UMR ICAN, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Karim LabrecheSorbonne University, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
Marine BaronSorbonne University, Center for Immunology and Infectious Diseases (CIMI-Paris), Department of Hematology, APHP, Hôpital Pitié Salpêtrière, Paris, France.
Marianne VeyriSorbonne University, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Theravir Team, Medical Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Jérôme Alexandre DenisSorbonne University, INSERM, Saint-Antoine Research Center, Cancer Biology and Therapeutics, CRSA, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Mehdi TouatSorbonne University, INSERM, CNRS, Brain and Spine Institute, ICM, Department of Neurology 2-Mazarin, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Marc SansonSorbonne University, INSERM, CNRS, Brain and Spine Institute, ICM, Department of Neurology 2-Mazarin, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Frédéric DaviSorbonne University, INSERM, Centre de Recherche des Cordeliers, Department of Biological Hematology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Erell GuillermSorbonne University, INSERM, Saint-Antoine Research Center, Microsatellites Instability and Cancer, CRSA, Genetics Department, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Stéphanie JouannetSorbonne University, Neurosurgery Department, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Frédéric CharlotteSorbonne University, Anatomy and Pathologic Cytology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Franck BielleSorbonne University, Neuropathology Department, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Sylvain ChoquetSorbonne University, Center for Immunology and Infectious Diseases (CIMI-Paris), Department of Hematology, APHP, Hôpital Pitié Salpêtrière, Paris, France.
Pierre-Yves BoëlleSorbonne University, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
Jacques CadranelSorbonne University, Chest Department and Thoracic Oncology, GRC 04, Theranoscan, AP-HP, Hôpital Tenon, Paris, France.
Véronique LeblondSorbonne University, Center for Immunology and Infectious Diseases (CIMI-Paris), Department of Hematology, APHP, Hôpital Pitié Salpêtrière, Paris, France.
Brigitte AutranSorbonne University, INSERM, CNRS, Center for Immunology and Infectious Diseases (CIMI-Paris), AP-HP, Pitié-Salpêtrière Hospital, Paris, France.
Jean-Marc LacorteSorbonne University, INSERM, Research Unit on Cardiovascular and Metabolic Disease UMR ICAN, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Jean-Philippe SpanoSorbonne University, INSERM, Research Unit on Cardiovascular and Metabolic Disease UMR ICAN, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
Florence CouletSorbonne University, INSERM, Research Unit on Cardiovascular and Metabolic Disease UMR ICAN, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.
IDEATION study group
Sorbonne Université · FRAssistance Publique – Hôpitaux de Paris · FRInserm · FRPitié-Salpêtrière Hospital · FRInstitut Pierre Louis d‘Épidémiologie et de Santé Publique · FR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

cancercfDNACNA profileimmunodeficiencyliquid biopsy

Identifiers

PMID34710202
PMCPMC8369887
OpenAlexW3190555587

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.