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

• Published in: PloS one Vol. 10; no. 9; p. e0138245
• Main Authors: D'Haene, Nicky, Le Mercier, Marie, De Nève, Nancy, Blanchard, Oriane, Delaunoy, Mélanie, El Housni, Hakim, Dessars, Barbara, Heimann, Pierre, Remmelink, Myriam, Demetter, Pieter, Tejpar, Sabine, Salmon, Isabelle
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 14-09-2015; Public Library of Science (PLoS)
• Subjects: Aerospace technology transfer; Audio frequencies; Cancer; Carcinoma, Non-Small-Cell Lung - genetics; Colon; Colon cancer; Colonic Neoplasms - genetics; Colorectal cancer; Deoxyribonucleic acid; DNA; DNA Mutational Analysis - methods; DNA, Neoplasm - genetics; Epidermal growth factor receptors; Female; Gene Frequency; Gene mutation; Gene sequencing; Genes; Genetics; Genomes; Genomics; High-Throughput Nucleotide Sequencing - methods; Humans; Lung cancer; Lung carcinoma; Lung diseases; Lung Neoplasms - genetics; Male; Mutation; Neoplasm Proteins - genetics; Non-small cell lung cancer; Non-small cell lung carcinoma; Pathology; Point mutation; Sensitivity analysis; Sensitivity and Specificity; Small cell lung carcinoma; Technology application; Technology transfer; United Kingdom > UK; Belgium
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0138245

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.
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.
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%.
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.