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

Research output: Contribution to journalArticle

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 languageEnglish
Article number828
JournalBMC Cancer
Volume18
Issue number1
DOIs
Publication statusPublished - Aug 16 2018

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Multiplex Polymerase Chain Reaction
Gene Fusion
Lung
Research
RNA
Tumor Biomarkers
Reproducibility of Results
Lung Neoplasms
Biomarkers
Lymph Nodes
Ions
Technology
Biopsy
Costs and Cost Analysis
Cell Line
Genes
Neoplasms
Adenocarcinoma of lung

Keywords

  • Biomarker
  • Detection
  • FFPE
  • Gene fusions
  • Lung cancer
  • Next-generation sequencing

ASJC Scopus subject areas

  • Oncology
  • Genetics
  • Cancer Research

Cite this

Vaughn, C. P., Costa, J. L., Feilotter, H. E., Petraroli, R., Bagai, V., Rachiglio, A. M., ... 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), [828]. https://doi.org/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. / 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.

In: BMC Cancer, Vol. 18, No. 1, 828, 16.08.2018.

Research output: Contribution to journalArticle

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
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. In: BMC Cancer. 2018 ; Vol. 18, No. 1.
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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.",
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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

PY - 2018/8/16

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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.

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