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Open Access 01-12-2018 | Technical advance

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

Authors: 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

Published in: BMC Cancer | Issue 1/2018

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 (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.

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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
Authors: 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
Publication date: 01-12-2018
Publisher: BioMed Central
Published in: BMC Cancer / Issue 1/2018
Electronic ISSN: 1471-2407
DOI: https://doi.org/10.1186/s12885-018-4736-4

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