title: Comparison of next-generation sequencing and mutation-specific platforms in clinical practice.
abstract: OBJECTIVE
  To compare next-generation sequencing (NGS) platforms with mutation-specific analysis platforms in a clinical setting, in terms of sensitivity, mutation specificity, costs, capacity, and ease of use.
  
  
  METHODS
  We analyzed 25 formalin-fixed, paraffin-embedded lung cancer samples of different size and tumor percentage for known KRAS and EGFR hotspot mutations with two dedicated genotyping platforms (cobas [Roche Diagnostics, Almere, The Netherlands] and Rotor-Gene [QIAGEN, Venlo, The Netherlands]) and two NGS platforms (454 Genome Sequencer [GS] junior [Roche Diagnostics] and Ion Torrent Personal Genome Machine [Life Technologies, Bleiswijk, The Netherlands]).
  
  
  RESULTS
  All platforms, except the 454 GS junior, detected the mutations originally detected by Sanger sequencing and high-resolution melting prescreening and detected an additional KRAS mutation. The dedicated genotyping platforms outperformed the NGS platforms in speed and ease of use. The large sequencing capacity of the NGS platforms enabled them to deliver all mutation information for all samples at once.
  
  
  CONCLUSIONS
  Sensitivity for detecting mutations was highly comparable among all platforms. The choice for either a dedicated genotyping platform or an NGS platform is basically a trade-off between speed and genetic information.
authors.affiliation: From the Departments of Pathology and j.w.j.hinrichs@umcutrecht.nl.
authors.forename: John W J
authors.initials: JW
authors.lastname: Hinrichs
authors.affiliation: From the Departments of Pathology and.
authors.forename: W T Marja
authors.initials: WT
authors.lastname: van Blokland
authors.affiliation: From the Departments of Pathology and.
authors.forename: Michiel J
authors.initials: MJ
authors.lastname: Moons
authors.affiliation: From the Departments of Pathology and.
authors.forename: Remco D
authors.initials: RD
authors.lastname: Radersma
authors.affiliation: From the Departments of Pathology and.
authors.forename: Joyce H
authors.initials: JH
authors.lastname: Radersma-van Loon
authors.affiliation: From the Departments of Pathology and.
authors.forename: Carmen M A
authors.initials: CM
authors.lastname: de Voijs
authors.affiliation: From the Departments of Pathology and.
authors.forename: Sophie B
authors.initials: SB
authors.lastname: Rappel
authors.affiliation: Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Marco J
authors.initials: MJ
authors.lastname: Koudijs
authors.affiliation: Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Nicolle J M
authors.initials: NJ
authors.lastname: Besselink
authors.affiliation: From the Departments of Pathology and.
authors.forename: Stefan M
authors.initials: SM
authors.lastname: Willems
authors.affiliation: From the Departments of Pathology and.
authors.forename: Roel A
authors.initials: RA
authors.lastname: de Weger
mesh_terms: D001483:Base Sequence; D002289:Carcinoma, Non-Small-Cell Lung / Q000175:diagnosis / Q000235:genetics*; D003365:Costs and Cost Analysis; D004252:DNA Mutational Analysis / Q000191:economics / Q000379:methods*; D004273:DNA, Neoplasm / Q000737:chemistry / Q000302:isolation & purification; D004502:Education, Medical, Continuing; D066246:ErbB Receptors / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000175:diagnosis / Q000235:genetics*; D009154:Mutation; D016612:Paraffin Embedding; D011518:Proto-Oncogene Proteins / Q000235:genetics*; D016283:Proto-Oncogene Proteins p21(ras); D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D013997:Time Factors; D018631:ras Proteins / Q000235:genetics*
chemical_list: D004273:DNA, Neoplasm; C117307:KRAS protein, human; D011518:Proto-Oncogene Proteins; C512478:EGFR protein, human; D066246:ErbB Receptors; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins
keywords: EGFR; KRAS; Lung adenocarcinoma; Mutation analysis platform; Next-generation sequencing