Highly sensitive liquid biopsy Duplex sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants.

Autor:	Hallermayr A; MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.; Pettenkofer School of Public Health, Munich, Germany.; Institute for Medical Information Processing, Biometry, and Epidemiology -IBE, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany., Neuhann TM; MGZ - Medizinisch Genetisches Zentrum, Munich, Germany., Steinke-Lange V; MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.; Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany., Scharf F; MGZ - Medizinisch Genetisches Zentrum, Munich, Germany., Laner A; MGZ - Medizinisch Genetisches Zentrum, Munich, Germany., Ewald R; Limbus Medical Technologies GmbH, Rostock, Germany., Liesfeld B; Limbus Medical Technologies GmbH, Rostock, Germany., Holinski-Feder E; MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.; Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany., Pickl JMA; MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.; Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany.
Jazyk:	angličtina
Zdroj:	Frontiers in oncology [Front Oncol] 2022 Dec 27; Vol. 12, pp. 1014592. Date of Electronic Publication: 2022 Dec 27 (Print Publication: 2022).
DOI:	10.3389/fonc.2022.1014592
Abstrakt:	Background: Liquid biopsy (LB) is a promising complement to tissue biopsy for detection of clinically relevant genetic variants in cancer and mosaic diseases. A combined workflow to enable parallel tissue and LB analysis is required to maximize diagnostic yield for patients. Methods: We developed and validated a cost-efficient combined next-generation sequencing (NGS) workflow for both tissue and LB samples, and applied Duplex sequencing technology for highly accurate detection of low frequency variants in plasma. Clinically relevant cutoffs for variant reporting and quantification were established. Results: We investigated assay performance characteristics for very low amounts of clinically relevant variants. In plasma, the assay achieved 100% sensitivity and 92.3% positive predictive value (PPV) for single nucleotide variants (SNVs) and 91.7% sensitivity and 100% PPV for insertions and deletions (InDel) in clinically relevant hotspots with 0.5-5% variant allele frequencies (VAFs). We further established a cutoff for reporting variants (i.e. Limit of Blank, LOB) at 0.25% VAF and a cutoff for quantification (i.e. Limit of Quantification, LOQ) at 5% VAF in plasma for accurate clinical interpretation of analysis results. With our LB approach, we were able to identify the molecular cause of a clinically confirmed asymmetric overgrowth syndrome in a 10-year old child that would have remained undetected with tissue analysis as well as other molecular diagnostic approaches. Conclusion: Our flexible and cost-efficient workflow allows analysis of both tissue and LB samples and provides clinically relevant cutoffs for variant reporting and precise quantification. Complementing tissue analysis by LB is likely to increase diagnostic yield for patients with molecular diseases. Competing Interests: Authors RE and BL were employed by Limbus Medical Technologies GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Hallermayr, Neuhann, Steinke-Lange, Scharf, Laner, Ewald, Liesfeld, Holinski-Feder and Pickl.)
Databáze:	MEDLINE
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