Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: A multi-institutional research study

Cecily P. Vaughn; José Luis Costa; Harriet E. Feilotter; Rosella Petraroli; Varun Bagai; Anna Maria Rachiglio; Federica Zito Marino; Bastiaan Tops; Henriette M. Kurth; Kazuko Sakai; Andrea Mafficini; Roy R.L. Bastien; Anne Reiman; Delphine Le Corre; Alexander Boag; Susan Crocker; Michel Bihl; Astrid Hirschmann; Aldo Scarpa; José Carlos Machado; Hélène Blons; Orla Sheils; Kelli Bramlett; Marjolijn J.L. Ligtenberg; Ian A. Cree; Nicola Normanno; Kazuto Nishio; Pierre Laurent-Puig

doi:10.1186/s12885-018-4736-4

Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: A multi-institutional research study

Cecily P. Vaughn, José Luis Costa, Harriet E. Feilotter, Rosella Petraroli, Varun Bagai, Anna Maria Rachiglio, Federica Zito Marino, Bastiaan Tops, Henriette M. Kurth, Kazuko Sakai, Andrea Mafficini, Roy R.L. Bastien, Anne Reiman, Delphine Le Corre, Alexander Boag, Susan Crocker, Michel Bihl, Astrid Hirschmann, Aldo Scarpa, José Carlos MachadoHélène Blons, Orla Sheils, Kelli Bramlett, Marjolijn J.L. Ligtenberg, Ian A. Cree, Nicola Normanno, Kazuto Nishio, Pierre Laurent-Puig

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Abstract

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 (10ng) 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.

Original language	English
Article number	828
Number of pages	8
Journal	BMC Cancer
Volume	18
Issue number	1
DOIs	https://doi.org/10.1186/s12885-018-4736-4
Publication status	Published - 16 Aug 2018

Bibliographical note

Open Access This 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.

Keywords

Biomarker
Detection
FFPE
Gene fusions
Lung cancer
Next-generation sequencing

ASJC Scopus subject areas

Oncology
Genetics
Cancer Research

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1186/s12885-018-4736-4Licence: CC BY

PublishedFinal published version, 906 KBLicence: CC BY

Cite this

Vaughn, C. P., Costa, J. L., Feilotter, H. E., Petraroli, R., Bagai, V., Rachiglio, A. M., Marino, F. Z., Tops, B., Kurth, H. M., Sakai, K., Mafficini, A., Bastien, R. R. L., Reiman, A., Le Corre, D., Boag, A., Crocker, S., Bihl, M., Hirschmann, A., Scarpa, A., ... Laurent-Puig, P. (2018). Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: A multi-institutional research study. BMC Cancer, 18(1), Article 828. https://doi.org/10.1186/s12885-018-4736-4

Vaughn, CP, Costa, JL, Feilotter, HE, Petraroli, R, Bagai, V, Rachiglio, AM, Marino, FZ, Tops, B, Kurth, HM, Sakai, K, Mafficini, A, Bastien, RRL, Reiman, A, Le Corre, D, Boag, A, Crocker, S, Bihl, M, Hirschmann, A, Scarpa, A, Machado, JC, Blons, H, Sheils, O, Bramlett, K, Ligtenberg, MJL, Cree, IA, Normanno, N, Nishio, K & Laurent-Puig, P 2018, 'Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: A multi-institutional research study', BMC Cancer, vol. 18, no. 1, 828. https://doi.org/10.1186/s12885-018-4736-4

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title = "Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: A multi-institutional research study",

abstract = "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{\texttrademark} 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 (10ng) 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.",

keywords = "Biomarker, Detection, FFPE, Gene fusions, Lung cancer, Next-generation sequencing",

author = "Vaughn, {Cecily P.} and Costa, {Jos{\'e} Luis} and Feilotter, {Harriet E.} and Rosella Petraroli and Varun Bagai and Rachiglio, {Anna Maria} and Marino, {Federica Zito} and Bastiaan Tops and Kurth, {Henriette M.} and Kazuko Sakai and Andrea Mafficini and Bastien, {Roy R.L.} and Anne Reiman and {Le Corre}, Delphine and Alexander Boag and Susan Crocker and Michel Bihl and Astrid Hirschmann and Aldo Scarpa and Machado, {Jos{\'e} Carlos} and H{\'e}l{\`e}ne Blons and Orla Sheils and Kelli Bramlett and Ligtenberg, {Marjolijn J.L.} and Cree, {Ian A.} and Nicola Normanno and Kazuto Nishio and Pierre Laurent-Puig",

note = "Open Access This 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.",

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doi = "10.1186/s12885-018-4736-4",

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T2 - A multi-institutional research study

AU - Vaughn, Cecily P.

AU - Costa, José Luis

AU - Feilotter, Harriet E.

AU - Petraroli, Rosella

AU - Bagai, Varun

AU - Rachiglio, Anna Maria

AU - Marino, Federica Zito

AU - Tops, Bastiaan

AU - Kurth, Henriette M.

AU - Sakai, Kazuko

AU - Mafficini, Andrea

AU - Bastien, Roy R.L.

AU - Reiman, Anne

AU - Le Corre, Delphine

AU - Boag, Alexander

AU - Crocker, Susan

AU - Bihl, Michel

AU - Hirschmann, Astrid

AU - Scarpa, Aldo

AU - Machado, José Carlos

AU - Blons, Hélène

AU - Sheils, Orla

AU - Bramlett, Kelli

AU - Ligtenberg, Marjolijn J.L.

AU - Cree, Ian A.

AU - Normanno, Nicola

AU - Nishio, Kazuto

AU - Laurent-Puig, Pierre

N1 - Open Access This 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.

PY - 2018/8/16

Y1 - 2018/8/16

N2 - 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 (10ng) 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.

AB - 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 (10ng) 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.

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KW - Lung cancer

KW - Next-generation sequencing

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Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: A multi-institutional research study

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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Anne Reiman

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Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: A multi-institutional research study

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Profiles

Anne Reiman

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