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Clinical Trial
. 2015 Sep 14;10(9):e0138245.
doi: 10.1371/journal.pone.0138245. eCollection 2015.

Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers

Nicky D'Haene  1 , Marie Le Mercier  1 , Nancy De Nève  1 , Oriane Blanchard  1 , Mélanie Delaunoy  2 , Hakim El Housni  2 , Barbara Dessars  2 , Pierre Heimann  2 , Myriam Remmelink  1 , Pieter Demetter  1 , Sabine Tejpar  3 , Isabelle Salmon  1
Affiliations
Clinical Trial

Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers

Nicky D'Haene et al. PLoS One. .

Abstract

Objective: Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation.

Methods: We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed.

Results: Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%.

Conclusions: Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Mutational profiles of NSCLC.
Mutations in different genes (rows) are indicated for each NSCLC sample (columns). A grey square indicates that a mutation (reported in the COSMIC database (http://www.sanger.ac.uk/cosmic), excluding polymorphism) was found with the Ampliseq Colon and Lung panel in the gene, whereas an empty square indicates that no relevant mutation was found for the gene.
Fig 2
Fig 2. Mutational profiles of CRC.
Mutations in different genes (rows) are indicated for each CRC sample (columns). A grey square indicates that a mutation (reported in the COSMIC database (http://www.sanger.ac.uk/cosmic), excluding polymorphism) was found with the Ampliseq Colon and Lung panel in the gene, whereas an empty square indicates that no relevant mutation was found for the gene.
See this image and copyright information in PMC

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