Abstract
Background: Comprehensive genomic profiling (CGP) has transformed personalized medicine but is still not affordable to all patients, especially in developing countries. The price of CGP differs based on panel size. Aim: The aim of this study was to explore the benefits between a cancer hotspot panel and CGP in Asian lung cancer patients. Methods: One hundred sixty-two formalin-fixed, paraffin-embedded (FFPE) lung cancer clinical samples were subjected to next-generation sequencing using the Ion Torrent Proton System. Sixty-six cases were profiled using a 35-gene cancer hotspot panel and 96 with pathway-based CGP (400+ genes) for base substitutions (single nucleotide variants and small indels) and copy number variants (CNV). Results: In total, actionable variants were discovered in 86.4% (57/66) cases using the cancer hotspot panel, with 57.9% (33/57) derived from base substitutions, 10.5% (6/57) from CNVs and 31.6% (18/57) from both alterations. Contrarily, CGP identified actionability in 97.9% (94/96) patients, 17.0% (16/94) of which were from base substitutions, 22.3% (21/94) from CNVs and 60.6% (57/94) from both. EGFR mutations were identified in comparable frequency with both panels, with almost half (48.8%; 79/162) of all samples harboring activating mutations in the tyrosine kinase (TK) domain. Identification of EGFR TK inhibitor (TKI) resistance mechanisms, including EGFR mutations (T790M and C797S), EGFR amplification, abnormal downstream EGFR signaling ( KRAS, BRAF and PIK3CA mutations, PTEN loss) and activation of the bypass pathways ( MET amplification, HER2 mutation and amplification), was equivalent with both panels. Additional targetable genetic alterations were detected in 70.0% (21/30) and 83.3% (39/47) of EGFR-wild type patients using the cancer hotspot assay and CGP, respectively. Conclusion: In most Asian lung cancer patients, a cancer hotspot panel is sufficient to discover targetable genetic alterations and TKI resistance mechanisms.
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