Consistency and reproducibility of next‐generation sequencing in cytopathology: A second worldwide ring trial study on improved cytological molecular reference specimens Article Swipe
Pasquale Pisapia
,
Umberto Malapelle
,
Gianluca Roma
,
Sonika Saddar
,
Qi Zheng
,
Francesco Pepe
,
Dario Bruzzese
,
Elena Vigliar
,
Claudio Bellevicine
,
Rajyalakshmi Luthra
,
Yuri E. Nikiforov
,
Clara Mayo‐de‐las‐Casas
,
Miguel Ángel Molina‐Vila
,
Rafael Rosell
,
Michel Bihl
,
Spasenija Savic
,
Lukas Bubendorf
,
Dario de Biase
,
Giovanni Tallini
,
David H. Hwang
,
Lynette M. Sholl
,
Sara Vander Borght
,
Birgit Weynand
,
Daniel Stieber
,
Philippe Vielh
,
Alessandra Rappa
,
Massimo Barberis
,
Matteo Fassan
,
Massimo Rugge
,
Carlos E. de Andrea
,
María D. Lozano
,
Cristiana Lupi
,
Gabriella Fontanini
,
Fernando Schmitt
,
Catherine I. Dumur
,
Bettina Bisig
,
Massimo Bongiovanni
,
Sabine Merkelbach‐Bruse
,
Reinhard Büttner
,
Marina N. Nikiforova
,
Sinchita Roy‐Chowdhuri
,
Giancarlo Troncone
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1002/cncy.22134
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1002/cncy.22134
Background Artificial genomic reference standards in a cytocentrifuge/cytospin format with well‐annotated genomic data are useful for validating next‐generation sequencing (NGS) on routine cytopreparations. Here, reference standards were optimized to be stained by different laboratories before DNA extraction and to contain a lower number of cells (2 × 10 5 ). This was done to better reflect the clinical challenge of working with insufficient cytological material. Methods A total of 17 worldwide laboratories analyzed customized reference standard slides (slides A‐D). Each laboratory applied its standard workflow. The sample slides were engineered to harbor epidermal growth factor receptor ( EGFR ) c.2235_2249del15 p.E746_A750delELREA, EGFR c.2369C>T p.T790M, Kirsten rat sarcoma viral oncogene homolog ( KRAS ) c.38G>A p.G13D, and B‐Raf proto‐oncogene, serine/threonine kinase ( BRAF ) c.1798_1799GT>AA p.V600K mutations at various allele frequencies (AFs). Results EGFR and KRAS mutation detection showed excellent interlaboratory reproducibility, especially on slides A and B (10% and 5% AFs). On slide C (1% AF), either the EGFR mutation or the KRAS mutation was undetected by 10 of the 17 laboratories (58.82%). A reassessment of the raw data in a second‐look analysis highlighted the mutations (n = 10) that had been missed in the first‐look analysis. BRAF c.1798_1799GT>AA p.V600K showed a lower concordance rate for mutation detection and AF quantification. Conclusions The data show that the detection of low‐abundance mutations is still clinically challenging and may require a visual inspection of sequencing reads to detect. Genomic reference standards in a cytocentrifuge/cytospin format are a valid tool for regular quality assessment of laboratories performing molecular studies on cytology with low‐AF mutations.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/cncy.22134
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cncy.22134
- OA Status
- bronze
- Cited By
- 48
- References
- 37
- Related Works
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- OpenAlex ID
- https://openalex.org/W2940592398
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2940592398Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/cncy.22134Digital Object Identifier
- Title
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Consistency and reproducibility of next‐generation sequencing in cytopathology: A second worldwide ring trial study on improved cytological molecular reference specimensWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2019Year of publication
- Publication date
-
2019-04-25Full publication date if available
- Authors
-
Pasquale Pisapia, Umberto Malapelle, Gianluca Roma, Sonika Saddar, Qi Zheng, Francesco Pepe, Dario Bruzzese, Elena Vigliar, Claudio Bellevicine, Rajyalakshmi Luthra, Yuri E. Nikiforov, Clara Mayo‐de‐las‐Casas, Miguel Ángel Molina‐Vila, Rafael Rosell, Michel Bihl, Spasenija Savic, Lukas Bubendorf, Dario de Biase, Giovanni Tallini, David H. Hwang, Lynette M. Sholl, Sara Vander Borght, Birgit Weynand, Daniel Stieber, Philippe Vielh, Alessandra Rappa, Massimo Barberis, Matteo Fassan, Massimo Rugge, Carlos E. de Andrea, María D. Lozano, Cristiana Lupi, Gabriella Fontanini, Fernando Schmitt, Catherine I. Dumur, Bettina Bisig, Massimo Bongiovanni, Sabine Merkelbach‐Bruse, Reinhard Büttner, Marina N. Nikiforova, Sinchita Roy‐Chowdhuri, Giancarlo TronconeList of authors in order
- Landing page
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https://doi.org/10.1002/cncy.22134Publisher landing page
- PDF URL
-
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cncy.22134Direct link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
bronzeOpen access status per OpenAlex
- OA URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cncy.22134Direct OA link when available
- Concepts
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KRAS, Medicine, Mutation, Cytopathology, Molecular diagnostics, DNA sequencing, Concordance, Cancer, Pathology, Genetics, Biology, Internal medicine, Gene, Cytology, Colorectal cancerTop concepts (fields/topics) attached by OpenAlex
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48Total citation count in OpenAlex
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2025: 7, 2024: 6, 2023: 6, 2022: 7, 2021: 8Per-year citation counts (last 5 years)
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37Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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