Next-Generation Sequencing on Circulating Tumor DNA in Advanced Solid Cancer: Swiss Army Knife for the Molecular Tumor Board? A Review of the Literature Focused on FDA Approved Test

Vasseur, Damien; Sahli, H.; Bayle, Arnaud; Tagliamento, Marco; Besse, Benjamin; Marzac, Christophe; Arbab, Ahmadreza; Auger, Nathalie; Cotteret, Sophie; Aldea, Mihaela; Blanc‐Durand, Félix; Géraud, Arthur; Gazzah, Anas; Loriot, Yohann; Hollebecque, Antoine; Martín-Romano, Patricia; Ngo-Camus, Maud; Nicotra, Claudio; Ponce, Santiago; Sakkal, Madona; Caron, Olivier; Smolenschi, Cristina; Micol, Jean-Baptiste; Italiano, Antoîne; Rouleau, Etienne; Lacroix, Ludovic

doi:10.3390/cells11121901

Cited by 15 publications

(10 citation statements)

References 72 publications

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“…Furthermore, it has been suggested that both the specific sequences, mutations and methylation profiles observed in cfDNA can serve as indicative biomarkers of cancer (8,9). In line with this, there are already FDA-approved linear cfDNA testing methods for specific alleles (reviewed in (10)), indicating the potential of cfDNA as a tool in disease diagnostics and monitoring.…”

Section: Introductionmentioning

confidence: 91%

Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors

Zole,

Hansen,

Haskó

et al. 2024

Preprint

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Human plasma DNA originates from all tissues and organs, holding the potential as a versatile marker for diseases such as cancer, as fragments of cancer-specific alleles can be found circulating in the blood. While linear DNA has been studied intensely as a liquid biomarker, the role of circular circulating DNA in cancer is more unknown due, in part, to a lack of comprehensive testing methods. Our developed method profiles extrachromosomal circular DNA (eccDNA) in plasma, integrating Solid-Phase Reversible Immobilization (SPRI) bead purification, the removal of linear DNA and mitochondrial DNA, and DNA sequencing. As an initial assessment, we examined the method, biological variations, and technical variations using plasma samples from four patients with lung adenocarcinoma and four healthy and physically fit individuals. Despite the small sample group, we observed a significant eccDNA increase in cancer patients in two independent laboratories and that eccDNA covered up to 0.4 % of the genome/mL plasma. We found a subset of eccDNA from recurrent genes present in cancer samples but not in every control. In conclusion, our data reflect the large variation found in eccDNA sequence content and show that the variability observed among replicates in eccDNA stems from a biological source and can cause inconclusive findings for biomarkers. This suggests the need to explore other biological markers, such as epigenetic features on eccDNA.

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Section: Introductionmentioning

confidence: 91%

Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors

Zole,

Hansen,

Haskó

et al. 2024

Preprint

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“…The panels designed for ctDNA detection use barcode enrichment to identify rare DNA sequence alterations. Both panels can detect a rare pathogenic variant with the variant allele frequency (VAF) ranging from 0.40% to 0.82% and a probability of 95% ( Vasseur et al, 2022 ). The panels have additional benefits by detecting CNVs important for the diagnosis of glioma ( Jonsson et al, 2019 ; Sharaf et al, 2021 ) except for Guradant360 CDx.…”

Section: The Market For Glioma Molecular Profilementioning

confidence: 99%

Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects

Penkova,

Kuziakova,

Gulaia

et al. 2023

Front. Mol. Biosci.

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Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.

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“…The variety of the parameters tested with sensitivity and specificity (single nucleotide variations (SNV), fusion genes, copy number alterations, tumor mutational burden, microsatellite status, tumor fraction (TF)) 9 vouches for the clinical applicability of cfDNA technology in the field of precision oncology and immunotherapy. FDA recently approved two next-generation sequencing (NGS) large cancer-related genes panel (large CGP) on circulating cell free DNA (cfDNA): FoundationOne® Liquid CDx (Foundation Medicine, Inc; Cambridge, MA) and Guardant360® CDx (Guardant Health, Inc.; Redwood, CA, USA).…”

Section: Introductionmentioning

confidence: 99%

“…Besides it’s utilization in the clinical setting, these characteristics make liquid biopsy a useful tool for molecular tumor boards and clinical trials inclusion 9 – 11 as an excellent complement to tissue biopsy 12 , still considered the gold standard. Clinical trials increasingly allow the use of liquid biopsy only as a screening tool for trial eligibility.…”

Section: Introductionmentioning

confidence: 99%

Genomic landscape of liquid biopsy mutations in TP53 and DNA damage genes in cancer patients

Vasseur,

Arbab,

Giudici

et al. 2024

npj Precis. Onc.

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Next-generation sequencing (NGS) assays based on plasma cell-free DNA (cfDNA) are increasingly used for clinical trials inclusion. Their optimized limit of detection applied to a large number of genes leads to the identification of mutations not confirmed in tissue. It becomes essential to describe the characteristics and consequences of these liquid biopsy-only mutations. In the STING protocol (Gustave Roussy, NCT04932525), 542 patients with advanced solid cancer had cfDNA-based and tissue-based NGS analysis (performed by FoundationOne® Liquid CDx and FoundationOne CDx™, respectively). Mutations identified in the liquid biopsy but not in the paired tissue were considered as liquid biopsy-only mutations irrespective of their variant allelic frequency (VAF). Out of 542 patients, 281 (51.8%) harbored at least one liquid biopsy-only mutation. These patients were significantly older, and more heavily pretreated. Liquid biopsy-only mutations occurring in TP53, and in DDR genes (ATM, CHEK2, ATR, BRCA2, and BRCA1) accounted for 90.8% of all the mutations. The median VAF of these mutations was generally low (0.37% and 0.40% for TP53 and DDR genes respectively). The variant type repartition depended on the gene. Liquid biopsy-only mutations affected hotspot in TP53 codon 273, 125, 195, 176, 237 or 280 and ATM codon 2891 and 3008. In a subset of 37 patients, 75.0%, 53.5% and 83.3% of the liquid biopsy-only mutations occurring respectively in ATM, TP53, and CHEK2 were confirmed in the matching whole blood sample. Although liquid biopsy-only mutations makes the interpretation of liquid biopsy results more complex, they have distinct characteristics making them more easily identifiable.

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Next-Generation Sequencing on Circulating Tumor DNA in Advanced Solid Cancer: Swiss Army Knife for the Molecular Tumor Board? A Review of the Literature Focused on FDA Approved Test

Cited by 15 publications

References 72 publications

Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors

Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors

Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects

Genomic landscape of liquid biopsy mutations in TP53 and DNA damage genes in cancer patients

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