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A Marchetti

A Uguen

A Vaishnavi

AK Virmani

Aldo Scarpa

Alexander Boag

Andrea Mafficini

Anna Maria Rachiglio

Anne Reiman

Astrid Hirschmann

Bastiaan Tops

Cancer Genome Atlas Research N

Cecily P. Vaughn

D Matsubara

Delphine Le Corre

E Ardini

F Li

Federica Zito Marino

Harriet E. Feilotter

Henriette M. Kurth

Hélène Blons

Ian A. Cree

JF Gainor

José Carlos Machado

José Luis Costa

JP Koivunen

K Rikova

K Takeuchi

Kazuko Sakai

Kazuto Nishio

KD Davies

Kelli Bramlett

KF To

L Ding

L Tembuyser

LM Sholl

M Soda

Marjolijn J. L. Ligtenberg

ME Lira

Michel Bihl

ML Wallander

N Pfarr

Nicola Normanno

Orla Sheils

Pierre Laurent-Puig

RM Phelps

Rosella Petraroli

Roy R. L. Bastien

S Scarpino

SM Ali

Susan Crocker

T Kohno

Varun Bagai

X Gao

Y Pan

Z Dai

BMC Cancer

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.</p

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

Coventry University Pure Portal

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

Crossref

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

Costa, J.L.

Rachiglio, A.M.

Tops, B.B.

Ligtenberg, M.J.L.

Laurent-Puig, P.

Radboud Repository

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

Directory of Open Access Journals

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.This work resulted from projects “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274), “GenomePT” (POCI-01-0145-FEDER-022184), “Advancing cancer research: from knowledge to application” (NORTE-01-0145-FEDER-000029) supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Norte Portugal Regional Programme (NORTE 2020), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by FCT - Fundação para a Ciência e a Tecnologia (PTDC/DTP-PIC/2500/2014). This work was supported by a grant from the Associazione Italiana per la Ricerca sul Cancro (AIRC) to N. Normanno (Grant number: IG17135)

Vaughn, C

Costa, JL

Feilotter, H

Petraroli, R

Bagai, V

Rachiglio, A

Marino, F

Tops, B

Kurth, H

Sakai, K

Mafficini, A

Bastien, R

Reiman, A

Le Corre, D

Boag, A

Crocker, S

Bihl, M

Hirschmann, A

Scarpa, A

Machado, JC

Blons, H

Sheils, O

Bramlett, K

Ligtenberg, M

Cree, I

Normanno, N

Nishio, K

Laurent-Puig, P

Repositório Aberto da Universidade do Porto

English

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

Vaughn C

Costa JL

Feilotter H

Petraroli R

Bagai V

Rachiglio A

Marino F

Tops B

Kurth H

Sakai K

Mafficini A

Bastien R

Reiman A

Le Corre D

Boag A

Crocker S

Bihl M

Hirschmann A

Scarpa A

Machado JC

Blons H

Sheils O

Bramlett K

Ligtenberg M

Cree I

Normanno N

Nishio K

Laurent-Puig P

Open Repository of the University of Porto

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

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

Abstract

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