Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study

Autor: Sutton, Lesley-Ann, Ljungström, Viktor, Enjuanes, Anna, Cortese, Diego, Skaftason, Aron, Tausch, Eugen, Kozubik, Katerina Stano, Nadeu, Ferran, Armand, Marine, Malcikova, Jikta, Djureinovic, Tatjana, Forster, Jade, Davis, Zadie, Oscier, David, Rossi, Davide, Ghia, Paolo, Strefford, Jonathan C., Pospisilova, Sarka, Stilgenbauer, Stephan, Davi, Frederic, Campo, Elias, Stamatopoulos, Kostas, Rosenquist, Richard
Přispěvatelé: Karolinska Institutet [Stockholm], Uppsala University, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), University of Ulm (UUlm), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Service d'Hématologie clinique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Sorbonne Université - Faculté de Médecine (SU FM), Sorbonne Université (SU), University of Southampton, Oncology Institute of Southern Switzerland (IOSI), Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), IRCCS Ospedale San Raffaele [Milan, Italy], Karolinska University Hospital [Stockholm], Sutton, Lesley-Ann, Ljungström, Viktor, Enjuanes, Anna, Cortese, Diego, Skaftason, Aron, Tausch, Eugen, Stano Kozubik, Katerina, Nadeu, Ferran, Armand, Marine, Malcikova, Jikta, Pandzic, Tatjana, Forster, Jade, Davis, Zadie, Oscier, David, Rossi, Davide, Ghia, Paolo, Strefford, Jonathan C, Pospisilova, Sarka, Stilgenbauer, Stephan, Davi, Frederic, Campo, Elia, Stamatopoulos, Kosta, Rosenquist, Richard
Jazyk: angličtina
Rok vydání: 2020
Předmět:
Zdroj: Haematologica
Haematologica, Ferrata Storti Foundation, 2020, 106 (3), pp.682-691. ⟨10.3324/haematol.2019.234716⟩
ISSN: 1592-8721
0390-6078
DOI: 10.3324/haematol.2019.234716⟩
Popis: International audience; Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads ≥100x ranged from 94.2- 99.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) >0.5%. Reproducibility was assessed by looking at the inter-laboratory variation in detecting mutations and 107 of 115 (93% concordance) mutations were detected by all six centers, while the remaining eight variants (7%) were undetected by a single center. Notably, 6 of 8 of these variants concerned minor subclonal mutations (VAF 5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.
Databáze: OpenAIRE
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