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Reference standards for gene fusion molecular assays on cytological samples : an international validation study

Malapelle, Umberto ; Pepe, Francesco ; Pisapia, Pasquale ; Altimari, Annalisa ; Bellevicine, Claudio ; Brunnström, Hans LU orcid ; Bruno, Rossella ; Büttner, Reinhard ; Cirnes, Luis and De Andrea, Carlos E. , et al. (2023) In Journal of Clinical Pathology 76(1). p.47-52
Abstract

Aims Gene fusions assays are key for personalised treatments of advanced human cancers. Their implementation on cytological material requires a preliminary validation that may make use of cell line slides mimicking cytological samples. In this international multi-institutional study, gene fusion reference standards were developed and validated. Methods Cell lines harbouring EML4(13)–ALK(20) and SLC34A2(4)–ROS1(32) gene fusions were adopted to prepare reference standards. Eight laboratories (five adopting amplicon-based and three hybridisation-based platforms) received, at different dilution points two sets of slides (slide A 50.0%, slide B 25.0%, slide C 12.5% and slide D wild type) stained by Papanicolaou (Pap) and May Grunwald Giemsa... (More)

Aims Gene fusions assays are key for personalised treatments of advanced human cancers. Their implementation on cytological material requires a preliminary validation that may make use of cell line slides mimicking cytological samples. In this international multi-institutional study, gene fusion reference standards were developed and validated. Methods Cell lines harbouring EML4(13)–ALK(20) and SLC34A2(4)–ROS1(32) gene fusions were adopted to prepare reference standards. Eight laboratories (five adopting amplicon-based and three hybridisation-based platforms) received, at different dilution points two sets of slides (slide A 50.0%, slide B 25.0%, slide C 12.5% and slide D wild type) stained by Papanicolaou (Pap) and May Grunwald Giemsa (MGG). Analysis was carried out on a total of 64 slides. Results Four (50.0%) out of eight laboratories reported results on all slides and dilution points. While 12 (37.5%) out of 32 MGG slides were inadequate, 27 (84.4%) out of 32 Pap slides produced libraries adequate for variant calling. The laboratories using hybridisation-based platforms showed the highest rate of inadequate results (13/24 slides, 54.2%). Conversely, only 10.0% (4/40 slides) of inadequate results were reported by laboratories adopting amplicon-based platforms. Conclusions Reference standards in cytological format yield better results when Pap staining and processed by amplicon-based assays. Further investigation is required to optimise these standards for MGG stained cells and for hybridisation-based approaches.

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Contribution to journal
publication status
published
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Journal of Clinical Pathology
volume
76
issue
1
pages
6 pages
publisher
BMJ Publishing Group
external identifiers
  • pmid:34429353
  • scopus:85126172352
ISSN
0021-9746
DOI
10.1136/jclinpath-2021-207825
language
English
LU publication?
yes
additional info
Funding Information: Monitoraggio ambientale, studio ed approfondimento della salute della popolazione residente inaree a rischio—In attuazione della D.G.R. Campanian. 180/2019. POR Campania FESR 2014–2020 Progetto “Sviluppo di Approcci Terapeutici Innovativi per patologie Neoplastiche resistenti ai trattamenti—SATIN”. Publisher Copyright: © Author(s) (or their employer(s)) 2023.
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ee5f0b95-b933-4553-bc6e-0b8dbff1644c
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2024-01-11 13:43:15
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2024-04-12 07:33:31
@article{ee5f0b95-b933-4553-bc6e-0b8dbff1644c,
  abstract     = {{<p>Aims Gene fusions assays are key for personalised treatments of advanced human cancers. Their implementation on cytological material requires a preliminary validation that may make use of cell line slides mimicking cytological samples. In this international multi-institutional study, gene fusion reference standards were developed and validated. Methods Cell lines harbouring EML4(13)–ALK(20) and SLC34A2(4)–ROS1(32) gene fusions were adopted to prepare reference standards. Eight laboratories (five adopting amplicon-based and three hybridisation-based platforms) received, at different dilution points two sets of slides (slide A 50.0%, slide B 25.0%, slide C 12.5% and slide D wild type) stained by Papanicolaou (Pap) and May Grunwald Giemsa (MGG). Analysis was carried out on a total of 64 slides. Results Four (50.0%) out of eight laboratories reported results on all slides and dilution points. While 12 (37.5%) out of 32 MGG slides were inadequate, 27 (84.4%) out of 32 Pap slides produced libraries adequate for variant calling. The laboratories using hybridisation-based platforms showed the highest rate of inadequate results (13/24 slides, 54.2%). Conversely, only 10.0% (4/40 slides) of inadequate results were reported by laboratories adopting amplicon-based platforms. Conclusions Reference standards in cytological format yield better results when Pap staining and processed by amplicon-based assays. Further investigation is required to optimise these standards for MGG stained cells and for hybridisation-based approaches.</p>}},
  author       = {{Malapelle, Umberto and Pepe, Francesco and Pisapia, Pasquale and Altimari, Annalisa and Bellevicine, Claudio and Brunnström, Hans and Bruno, Rossella and Büttner, Reinhard and Cirnes, Luis and De Andrea, Carlos E. and de Biase, Dario and Dumur, Catherine I. and Lindquist, Kajsa Ericson and Fontanini, Gabriella and Gautiero, Eugenio and Gentien, David and Hofman, Paul and Hofman, Veronique and Iaccarino, Antonino and Lozano, Maria Dolores and Mayo-De-Las-Casas, Clara and Merkelbach-Bruse, Sabine and Pagni, Fabio and Roman, Ruth and Schmitt, Fernando C. and Siemanowski, Janna and Roy-Chowdhuri, Sinchita and Tallini, Giovanni and Tresserra, Francesc and Borght, Sara Vander and Vielh, Philippe and Vigliar, Elena and Vita, Giulia Anna Carmen and Weynand, Birgit and Rosell, Rafael and Vila, Miguel Angel Molina and Troncone, Giancarlo}},
  issn         = {{0021-9746}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{47--52}},
  publisher    = {{BMJ Publishing Group}},
  series       = {{Journal of Clinical Pathology}},
  title        = {{Reference standards for gene fusion molecular assays on cytological samples : an international validation study}},
  url          = {{http://dx.doi.org/10.1136/jclinpath-2021-207825}},
  doi          = {{10.1136/jclinpath-2021-207825}},
  volume       = {{76}},
  year         = {{2023}},
}