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Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study
BACKGROUND: Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097211/ https://www.ncbi.nlm.nih.gov/pubmed/30115026 http://dx.doi.org/10.1186/s12885-018-4736-4 |
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author | Vaughn, Cecily P. Costa, José Luis Feilotter, Harriet E. Petraroli, Rosella Bagai, Varun Rachiglio, Anna Maria Marino, Federica Zito Tops, Bastiaan Kurth, Henriette M. Sakai, Kazuko Mafficini, Andrea Bastien, Roy R. L. Reiman, Anne Le Corre, Delphine Boag, Alexander Crocker, Susan Bihl, Michel Hirschmann, Astrid Scarpa, Aldo Machado, José Carlos Blons, Hélène Sheils, Orla Bramlett, Kelli Ligtenberg, Marjolijn J. L. Cree, Ian A. Normanno, Nicola Nishio, Kazuto Laurent-Puig, Pierre |
author_facet | Vaughn, Cecily P. Costa, José Luis Feilotter, Harriet E. Petraroli, Rosella Bagai, Varun Rachiglio, Anna Maria Marino, Federica Zito Tops, Bastiaan Kurth, Henriette M. Sakai, Kazuko Mafficini, Andrea Bastien, Roy R. L. Reiman, Anne Le Corre, Delphine Boag, Alexander Crocker, Susan Bihl, Michel Hirschmann, Astrid Scarpa, Aldo Machado, José Carlos Blons, Hélène Sheils, Orla Bramlett, Kelli Ligtenberg, Marjolijn J. L. Cree, Ian A. Normanno, Nicola Nishio, Kazuto Laurent-Puig, Pierre |
author_sort | Vaughn, Cecily P. |
collection | PubMed |
description | BACKGROUND: Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. METHODS: We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples. RESULTS: Reproducibility between laboratories using diluted fusion-positive cell lines was 100%. A cohort of lung clinical research samples from different origins (tissue biopsies, tissue resections, lymph nodes and pleural fluid samples) were used to evaluate the panel. We observed 97% concordance for ALK (28/30 positive; 71/70 negative samples), 95% for ROS1 (3/4 positive; 19/18 negative samples), and 93% for RET (2/1 positive; 13/14 negative samples) between the AmpliSeq assay and other methodologies. CONCLUSION: This methodology enables simultaneous detection of multiple ALK, ROS1, RET, and NTRK1 gene fusion transcripts in a single panel, enhanced by an integrated analysis solution. The assay performs well on limited amounts of input RNA (10 ng) and offers an integrated single assay solution for detection of actionable fusions in lung adenocarcinoma, with potential savings in both cost and turn-around-time compared to the combination of all four assays by other methods. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12885-018-4736-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6097211 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60972112018-08-20 Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study Vaughn, Cecily P. Costa, José Luis Feilotter, Harriet E. Petraroli, Rosella Bagai, Varun Rachiglio, Anna Maria Marino, Federica Zito Tops, Bastiaan Kurth, Henriette M. Sakai, Kazuko Mafficini, Andrea Bastien, Roy R. L. Reiman, Anne Le Corre, Delphine Boag, Alexander Crocker, Susan Bihl, Michel Hirschmann, Astrid Scarpa, Aldo Machado, José Carlos Blons, Hélène Sheils, Orla Bramlett, Kelli Ligtenberg, Marjolijn J. L. Cree, Ian A. Normanno, Nicola Nishio, Kazuto Laurent-Puig, Pierre BMC Cancer Technical Advance BACKGROUND: Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. METHODS: We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples. RESULTS: Reproducibility between laboratories using diluted fusion-positive cell lines was 100%. A cohort of lung clinical research samples from different origins (tissue biopsies, tissue resections, lymph nodes and pleural fluid samples) were used to evaluate the panel. We observed 97% concordance for ALK (28/30 positive; 71/70 negative samples), 95% for ROS1 (3/4 positive; 19/18 negative samples), and 93% for RET (2/1 positive; 13/14 negative samples) between the AmpliSeq assay and other methodologies. CONCLUSION: This methodology enables simultaneous detection of multiple ALK, ROS1, RET, and NTRK1 gene fusion transcripts in a single panel, enhanced by an integrated analysis solution. The assay performs well on limited amounts of input RNA (10 ng) and offers an integrated single assay solution for detection of actionable fusions in lung adenocarcinoma, with potential savings in both cost and turn-around-time compared to the combination of all four assays by other methods. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12885-018-4736-4) contains supplementary material, which is available to authorized users. BioMed Central 2018-08-16 /pmc/articles/PMC6097211/ /pubmed/30115026 http://dx.doi.org/10.1186/s12885-018-4736-4 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Technical Advance Vaughn, Cecily P. Costa, José Luis Feilotter, Harriet E. Petraroli, Rosella Bagai, Varun Rachiglio, Anna Maria Marino, Federica Zito Tops, Bastiaan Kurth, Henriette M. Sakai, Kazuko Mafficini, Andrea Bastien, Roy R. L. Reiman, Anne Le Corre, Delphine Boag, Alexander Crocker, Susan Bihl, Michel Hirschmann, Astrid Scarpa, Aldo Machado, José Carlos Blons, Hélène Sheils, Orla Bramlett, Kelli Ligtenberg, Marjolijn J. L. Cree, Ian A. Normanno, Nicola Nishio, Kazuto Laurent-Puig, Pierre Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study |
title | Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study |
title_full | Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study |
title_fullStr | Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study |
title_full_unstemmed | Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study |
title_short | Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study |
title_sort | simultaneous detection of lung fusions using a multiplex rt-pcr next generation sequencing-based approach: a multi-institutional research study |
topic | Technical Advance |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097211/ https://www.ncbi.nlm.nih.gov/pubmed/30115026 http://dx.doi.org/10.1186/s12885-018-4736-4 |
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