Abstract
Background: Next generation sequencing (NGS)-based multi-gene panel tests have been performed to predict the treatment response and prognosis in patients with colorectal cancer (CRC). Whether the multi-gene mutation results of formalin-fixed paraffin-embedded (FFPE) tissues are identical to those of fresh frozen tissues remains unknown.Methods: A 22-gene panel with 103 hotspots was used to detect mutations in paired fresh frozen tissue and FFPE tissue from 118 patients with CRC.Results: In our study, 117 patients (99.2%) had one or more variants, with 226 variants in FFPE tissue and 221 in fresh frozen tissue. Of the 129 variants identified in this study, 96 variants were present in both FFPE and fresh frozen tissues; 27 variants were found in FFPE tissues only; 6 variants were found only in fresh frozen tissues. The mutation results demonstrated >94.0% concordance in all variants, with Kappa coefficient >0.500 in 64.3% (83/129) of variants. At the gene level, concordance ranged from 73.8 to 100.0%, with Kappa coefficient >0.500 in 81.3% (13/16) of genes.Conclusions: The results of mutation analysis performed with a multi-gene panel and FFPE and fresh frozen tissue were highly concordant in patients with CRC, at both the variant and gene levels. There were, however, some important differences in mutation results between the two tissue types. Therefore, fresh frozen tissue should not routinely be replaced with FFPE tissue for mutation analysis with a multi-gene panel. Rather, FFPE tissue is a reasonable alternative for fresh frozen tissue when the latter is unavailable.
Highlights
The survival of patients with colorectal cancer (CRC) has improved greatly in recent decades, because of advancements in surgical technique, chemoradiotherapy, and targeted therapy [1, 2]
We showed the utility of this 22-gene panel when used with Next generation sequencing (NGS) to detect gene mutations in formalin-fixed paraffin-embedded (FFPE) tissue from 207 patients with CRC [15]
We found that 117 patients (99.2%) had one or more variants, with 226 variants in FFPE tissues and 221 in fresh frozen tissues
Summary
The survival of patients with colorectal cancer (CRC) has improved greatly in recent decades, because of advancements in surgical technique, chemoradiotherapy, and targeted therapy [1, 2]. Somatic gene mutations of KRAS (KRAS proto-oncogene, GTPase), NRAS (NRAS proto-oncogene, GTPase), and BRAF (B-Raf protooncogene, serine/threonine kinase) have been used to predict the outcomes of EGFR (epidermal growth factor receptor)—targeted therapy for metastatic CRC [4]. Research studies of targeted therapy and individualized medicine have identified additional genes associated with the development and treatment of CRC [6]. The classification of CRC based on multiple gene detection may help to explain inter-individual differences in treatment response and long-term outcomes. The detection of multiple gene mutations could offer more options for new targeted treatment efforts in drug-resistant patients [11]. Generation sequencing (NGS)-based multi-gene panel tests have been performed to predict the treatment response and prognosis in patients with colorectal cancer (CRC). Whether the multi-gene mutation results of formalin-fixed paraffin-embedded (FFPE) tissues are identical to those of fresh frozen tissues remains unknown
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