title: Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers.
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.
authors.affiliation: Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Nicky
authors.initials: N
authors.lastname: D'Haene
authors.affiliation: Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Marie
authors.initials: M
authors.lastname: Le Mercier
authors.affiliation: Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Nancy
authors.initials: N
authors.lastname: De Nève
authors.affiliation: Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Oriane
authors.initials: O
authors.lastname: Blanchard
authors.affiliation: Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Delaunoy
authors.affiliation: Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Hakim
authors.initials: H
authors.lastname: El Housni
authors.affiliation: Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Barbara
authors.initials: B
authors.lastname: Dessars
authors.affiliation: Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Pierre
authors.initials: P
authors.lastname: Heimann
authors.affiliation: Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Myriam
authors.initials: M
authors.lastname: Remmelink
authors.affiliation: Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Demetter
authors.affiliation: Department of Oncology, University Hospital Leuven, Leuven, Belgium.
authors.forename: Sabine
authors.initials: S
authors.lastname: Tejpar
authors.affiliation: Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Salmon
mesh_terms: D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D003110:Colonic Neoplasms / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods; D004273:DNA, Neoplasm / Q000235:genetics; D005260:Female; D005787:Gene Frequency; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D009363:Neoplasm Proteins / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D004273:DNA, Neoplasm; D009363:Neoplasm Proteins