Reliability of liquid biopsy analysis: an inter-laboratory comparison of circulating tumor DNA extraction and sequencing with different platforms

Koessler, Thibaud; Paradiso, Viola; Piscuoglio, Salvatore; Nienhold, Ronny; Ho, Liza; Christinat, Yann; Terracciano, Luigi; Cathomas, Gieri; Wicki, Andreas; Mckee, Thomas Alexander; Nouspikel, Thierry

doi:10.1038/s41374-020-0459-7

Cited by 17 publications

(23 citation statements)

References 28 publications

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“…DNA was quantified with the Qubit dsDNA High Sensitivity Kit (ThermoFisher). Enrichment of the characteristic mononucleosomal fragment peak (160–200 bp) and absence of contaminating high molecular weight genomic DNA [ 28 , 29 ] were verified using the Bioanalyzer 2100 High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

Longitudinal therapy monitoring of ALK-positive lung cancer by combined copy number and targeted mutation profiling of cell-free DNA

et al. 2020

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Section: Methodsmentioning

confidence: 99%

Longitudinal therapy monitoring of ALK-positive lung cancer by combined copy number and targeted mutation profiling of cell-free DNA

et al. 2020

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“…The current study focusses on how the potential clinical utility of liquid rebiopsies in ALK + NSCLC depends on the anatomical pattern of treatment failure, and on the prognostic information that their results additionally provide about the subsequent disease course and patient survival. We present this article in accordance with the STROBE reporting checklist (available at http:// dx.doi.org/10.21037/tlcr- [21][22][23][24][25][26][27][28][29][30][31][32].…”

Section: Introductionmentioning

confidence: 99%

“…Conversely, most oligoprogressive ALK + NSCLC patients with negative liquid biopsies appear to have a more indolent course without need for immediate change of systemic treatment.Conflicts of Interest:All authors have completed the ICMJE uniform disclosure form (available at http://dx.doi. org/10.21037/tlcr-[21][22][23][24][25][26][27][28][29][30][31][32]. PC reports grants and personal fees from Novartis, grants and personal fees from Roche, grants and personal fees from AstraZeneca, personal fees from Pfizer, grants and personal fees from Takeda, personal fees from Chugai, personal fees from Boehringer, outside the submitted work; SD reports personal fees from Roche, outside the submitted work; DK reports personal fees from Pfizer, personal fees from BMS, personal fees from AstraZeneca, outside the submitted work; AV reports personal fees from AstraZeneca, outside the submitted work; MR reports personal fees from Amgen, personal fees from AstraZeneca, personal fees from BMS, personal fees from Boehringer, personal fees from Lilly, personal fees from Merck, personal fees from MSD, personal fees from Novartis, personal fees from Pfizer, personal fees from Roche, personal fees from Samsung, outside the submitted work; AS reports personal fees from AstraZeneca, personal fees from Lilly, personal fees from Bayer, personal fees from BMS, personal fees from Illumina, personal fees from Janssen, personal fees from MSD, personal fees from Novartis, personal fees from Pfizer, personal fees from Roche, personal fees from Seattle Genomics, outside the submitted work; MT reports grants from AstraZeneca, personal fees from Lilly, personal fees from BMS, personal fees from MSD, personal fees from Novartis, personal fees from Roche, personal fees from Boehringer, personal fees from Celgene, personal fees from Takeda, personal fees from AbbVie, outside the submitted work; HS reports grants and personal fees from Roche, outside the submitted work.…”

mentioning

confidence: 99%

Earlier extracranial progression and shorter survival in ALK- rearranged lung cancer with positive liquid rebiopsies

Christopoulos¹,

Dietz²,

Angeles³

et al. 2021

Transl Lung Cancer Res

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Background: Liquid rebiopsies can detect resistance mutations to guide therapy of anaplastic lymphoma kinase-rearranged (ALK + ) non-small-cell lung cancer (NSCLC) failing tyrosine kinase inhibitors (TKI).Here, we analyze how their results relate to the anatomical pattern of disease progression and patient outcome.Methods: Clinical, molecular, and radiologic characteristics of consecutive TKI-treated ALK + NSCLC patients were analyzed using prospectively collected plasma samples and the 17-gene targeted AVENIO kit, which covers oncogenic drivers and all TP53 exons.Results: In 56 patients, 139 instances of radiologic changes were analyzed, of which 133 corresponded to disease progression. Circulating tumor DNA (ctDNA) alterations were identified in most instances of extracranial progression (58/94 or 62%), especially if concomitant intracranial progression was also present (89%, P<0.001), but rarely in case of isolated central nervous system (CNS) progression (8/39 or 21%, P<0.001). ctDNA detectability correlated with presence of "short" echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion variants (mainly V3, E6:A20) and/or TP53 mutations (P<0.05), and presented therapeutic opportunities in <50% of cases. Patients with extracranial progression and positive liquid biopsies had shorter survival from the start of palliative treatment (mean 52 vs. 69 months, P=0.002), regardless of previous and subsequent therapy and initial ECOG performance status. Furthermore, for patients with extracranial progression, ctDNA detectability was associated with shorter next-line progressionfree survival (PFS) (3 vs. 13 months, P=0.003) if they were switched to another systemic therapy (49/86 samples), and with shorter time-to-next-treatment (TNT) (3 vs. 8 months, P=0.004) if they were continued ^ ORCID: 0000-0002-7966-8980.

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“…The methodologies depend on the purpose of ctDNA [44][45][46][47][48] : (1) Quantitative PCR (qPCR): This procedure is used for the evaluation of total cfDNA amount and/or cfDNA integrity. To be sure to identify properly ctDNA coming from EC (and not from others tumors or pathologies), it is necessary to refer to specific mutations present in the tumor.…”

Section: Methodologies For Detection Of Ctdnamentioning

confidence: 99%

Liquid biopsy in endometrial cancer

Malentacchi¹,

Sgromo²,

Antonuzzo³

et al. 2020

JCMT

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Liquid biopsy (LB) is an emerging tool for the evaluation of relapse in several cancers and nowadays is used in lung cancer for primary detection and molecular characterization when tumoral tissue is not available. It can represent an innovative biospecimen for the screening, diagnosis, and monitoring of all types of cancer and for monitoring of therapeutic efficacy. LB includes several biofluids such as blood, urine, peritoneal fluid/lavage, and analytes (circulating tumor cells, circulating tumor DNA, long noncoding RNA, microRNA, vesicles, mRNA, and protein) that can play different roles in diagnosis, prognosis, and patient management as well as in the improvement of the knowledge of cancer evolution. Endometrial cancer (EC) is a tumor usually detected at low stage with a good prognosis, but few low risk cases, unexpectedly, can evolve to bad prognosis. Up to now, no molecular target exists to treat advanced stage or to define the evolution of low stage EC. This review focuses on how the LB may help in the management and characterization of patients affected by EC.

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Reliability of liquid biopsy analysis: an inter-laboratory comparison of circulating tumor DNA extraction and sequencing with different platforms

Cited by 17 publications

References 28 publications

Longitudinal therapy monitoring of ALK-positive lung cancer by combined copy number and targeted mutation profiling of cell-free DNA

Longitudinal therapy monitoring of ALK-positive lung cancer by combined copy number and targeted mutation profiling of cell-free DNA

Earlier extracranial progression and shorter survival in ALK- rearranged lung cancer with positive liquid rebiopsies

Liquid biopsy in endometrial cancer

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