Objectives: 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.

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