Comparison of Next-Generation Sequencing and Mutation-Specific Platforms in Clinical Practice

John W. J. Hinrichs*, W. T. Marja Van Blokland, Michiel J. Moons, Remco D. Radersma, Joyce H. Radersma-Van Loon, Carmen M. A. de Voijs, Sophie B. Rappel, Marco J. Koudijs, Nicolle J. M. Besselink, Stefan M. Willems, Roel A. de Weger

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Objectives: To compare next-generation sequencing (NGS) plafforms 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 plafforms 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 plafform is basically a trade-off between speed and genetic information.

Original languageEnglish
Pages (from-to)573-578
Number of pages6
JournalAmerican journal of clinical pathology
Volume143
Issue number4
DOIs
Publication statusPublished - Apr 2015

Keywords

  • Base Sequence
  • Carcinoma, Non-Small-Cell Lung
  • Costs and Cost Analysis
  • DNA Mutational Analysis
  • DNA, Neoplasm
  • Education, Medical, Continuing
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Lung Neoplasms
  • Mutation
  • Paraffin Embedding
  • Proto-Oncogene Proteins
  • Proto-Oncogene Proteins p21(ras)
  • Receptor, Epidermal Growth Factor
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Time Factors
  • ras Proteins
  • Comparative Study
  • Journal Article

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