For patients enrolled from April 2014 to July 2017, sequencing was via amplicon-based Ion AmpliSeq Cancer Hotspot v2 (50 genes, Appendix A), performed in our institution on Ion Torrent/PGM System (Life Technologies, Camarillo, CA, USA) as previously described (22 (link)). Patients enrolled after August 2017 to January 31, 2022, underwent tumour sequencing via FoundationOne CDx (FM1) after an institutional change in panel use. Formalin-fixed, paraffin-embedded (FFPE) tissue was processed per institutional practice, and slides were submitted to Foundation Medicine (Cambridge, MA, USA) for testing. If adequate tissue was not available in patients with no plans for further biopsy, two tubes of whole blood were submitted to Foundation Medicine for analysis under the FoundationOne Liquid CDx platform. Variants identified by FoundationOne CDx are represented as pathogenic or likely pathogenic and variants of unknown significance. For the purposes of this analysis, the variants of uncertain significance were excluded. FoundationOne CDx specimens were also simultaneously profiled for TMB as well as MSI status (23 (link)).
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