BMC cancer · 2018
Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study.
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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
Аннотация
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.
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.
Предметные рубрики MeSH
Anaplastic Lymphoma KinaseBiomarkers, TumorBiopsyCell Line, TumorFemaleHigh-Throughput Nucleotide SequencingHumansLung NeoplasmsLymph NodesMaleMembrane GlycoproteinsMultiplex Polymerase Chain ReactionOncogene Proteins, FusionProtein-Tyrosine KinasesProto-Oncogene ProteinsProto-Oncogene Proteins c-retReceptor Protein-Tyrosine KinasesReceptor, trkBReverse Transcriptase Polymerase Chain Reaction