Analytical Validation of a Pan-Cancer Next-Generation Sequencing Assay for In-House Liquid Biopsy Testing
Year: 2025
Type: article
Abstract: Liquid biopsy assays are transforming precision oncology by providing a less invasive alternative to tissue biopsies. These assays screen for tumor genetic alterations in circulating free DNA, which typically requires detecting variants at low allele frequencies and, therefore, a high sensitivity and specificity. This international, multicenter analytical performance study evaluated the Hedera Profiling 2 circulating tumor DNA test panel (HP2), a hybrid capture-based next-generation sequencing assay for the detection of somatic alterations in circulating free DNA. Covering 32 genes, HP2 enables the detection of single-nucleotide variants (SNVs), insertions and deletions (Indels), fusions, copy number variations, and microsatellite instability status from a single DNA-only workflow. The analytical performance was assessed using reference standards and a diverse cohort of 137 clinical samples precharacterized by orthogonal methods. In reference standards with variants spiked in at 0.5% allele frequency, sensitivity and specificity were 96.92% and 99.67%, respectively, for SNVs/Indels and 100% for fusions. In clinical samples, SNV/Indel detection showed high concordance (94% for European Society for Medical Oncology Scale of Clinical Actionability for Molecular Targets level I variants) with orthogonal methods. Evidence for solid sensitivity was also found for copy number variation detection and microsatellite instability status determination. Overall, the HP2 assay showed significant potential as a sensitive and efficient pan-cancer test for liquid biopsy testing in a decentralized molecular pathology laboratory setting.
Source: Journal of Molecular Diagnostics
Authors: Gaëlle Lescuyer, Alexandre Harlé, Hari Shankar Kumar, Pantelis Constantoulakis, Nicole Pfarr, Ellen Heitzer, Clémence Michon, Gianluca Russo, Ernst-Jan M. Speel, Marie Piecyk, Marie Husson, Georgia Christopoulou, Eva-Maria Mayr, Mai-Lan Koppermann, Christophe Passot, Ricarda Graf, Anes Hadjadj Aoul, Violaine Bourdon, Hendrikus J. Dubbink, Ronald van Marion, Imke Demers, Anne-Marie C. Dingemans, Giancarlo Troncone, Francesco Pepe, Laura Muinelo-Romay, Ángel Díaz-Lagares, Aitor Rodriguez-Casanova, Ramón Manuel Lago Lestón, Deepak Pathak, Parth Shah, Romain V. Parillaud, Oskar Martínez de Ilarduya, Jonas Behr, Alexis Rapin, Thomas Vetterli, Sanga Mitra Boppudi, Umberto Malapelle, Léa Payen
Institutions: Lyon 1 Université, Hospices Civils de Lyon, Hôpital Lyon Sud, Centre pour l'innovation en cancérologie de Lyon, Centre National de la Recherche Scientifique, Institut de Cancérologie de Lorraine, CRAN, Université de Lorraine, Technical University of Munich, Medical University of Graz, Institut de Cancérologie de l'Ouest, Federico II University Hospital, University of Naples Federico II, Maastricht University Medical Centre, Erasmus MC, Maastricht University, Erasmus MC Cancer Institute, Aix-Marseille Université, Institut Paoli-Calmettes, Complejo Hospitalario Universitario de Santiago, Instituto de Investigación Sanitaria de Santiago, Servicio Gallego de Salud, Centro de Investigación Biomédica en Red de Cáncer, Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $3,000
Awards: G5693523469, G7509453484
OpenAlex ID: W4414591229