Abstract 1035: Identification of fibroblast growth factor receptors (FGFRs) alterations (alts) at DNA and RNA-level by one-step next-generation sequencing (NGS) panel
Authors: Min Qing, Xuejun Chen, Wenqing Su, Xiaofang Zhuo, Ting Shen, Chengjuan Xiong, Xuesong Lyu, Renee Tate, Qibiao Wu, Longen Zhou, Shibu Thomas, Wangwang Ning, Jianqing Wang, Huihui Yan, Zhiqiang Yin, Zhan Huang, Yaxin Xue, Changbin Zhu
Journal: Cancer Research (2024)

Abstract Background: FGFR inhibitors are currently in clinical development or approved for urothelial cancer and cholangiocarcinoma with FGFR fusion (FUS) or/and mutation (MUT). AmoyDx FGFR 1-4 NGS Panel (FGFR-P) was developed for FGFR alts detection based on both DNA and RNA. The goal of this study is to validate and assess the performance of FGFR-P in pan-cancer FGFR alts detection by comparing with an AmoyDx comprehensive genomic profiling test (CGP) and a health authority approved DNA-based NGS panel (DNA-P). Methods: Both FGFR-P and CGP are DNA (MUT) and RNA (FUS) based for detecting FGFR alts with optimized bioinformatics pipeline to eliminate baseline noise caused by deamination events, which is commonly found in aged FFPE samples. Cell lines, cell line/patient derived xenografts (CDXs/PDXs) and 397 samples of 26 cancer types (90 samples &amp;gt;10 years) were used for validation of FGFR-P. Total 382 and 50 pan-cancer samples were respectively tested to compare FGFR-P with CGP and DNA-P. Results: To validate accuracy, 36 FFPE samples from cell lines and CDXs/PDXs with known FGFR status (25 FUSs, 5 MUTs, 6 wild-types) were tested by FGFR-P with concordance rate 100%. In clinical sample testing, FGFR-P also showed high agreement with CGP (99.5%) and DNA-P (98.0%). Conflicting result confirmed by FISH revealed 1 FUS missed by DNA-P but detected by FGFR-P, which demonstrated advantage of FGFR alts detection by DNA+RNA. In addition, an optimized bioinformatics pipeline by mimic samples with deamination events effectively filtered out C:G&amp;gt;T:A false positive signals. FGFR-P achieved high success rate in testing pan-tumor samples (89.9%) including samples &amp;gt;10 years (75.6%). Conclusions: FGFR-P provides a novel opportunity to identify FGFR alt pan-cancer patients using a robust DNA+RNA NGS platform, which shows high success rate even in aged samples and will be a potent tool for sensitive and reliable detection of FGFR alts for clinical diagnostics. CGP FGFR-P MUT Positive Negative Total Positive 29 0 29 Negative 1 194 195 Total 30 194 224 FUS Positive Negative Total Positive 20 1 21 Negative 0 137 137 Total 20 138 158 The overall percent agreement 99.5% Citation Format: Min Qing, Xuejun Chen, Wenqing Su, Xiaofang Zhuo, Ting Shen, Chengjuan Xiong, Xuesong Lyu, Renee Tate, Qibiao Wu, Longen Zhou, Shibu Thomas, Wangwang Ning, Jianqing Wang, Huihui Yan, Zhiqiang Yin, Zhan Huang, Yaxin Xue, Changbin Zhu. Identification of fibroblast growth factor receptors (FGFRs) alterations (alts) at DNA and RNA-level by one-step next-generation sequencing (NGS) panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1035.