Abstract 1326: A novel system that produces pre-qualified cancer NGS panels with customizable content
Authors: Steven Roman, Charles Scafe, Yun Zhu, Fernando Farfan, Brooke McKnight, Santoshi Bandla, Chenchen Yang, Yu-Ting Tseng, Xiaoping Duan, Jigar Patel, Natasha Arksey, Seth Sadis, Fiona Hyland
Journal: Cancer Research (2020)

Abstract Introduction Next-generation sequencing (NGS) is the preferred method to simultaneously characterize multiple relevant genetic variants in cancer samples. In addition to pan-cancer applications, researchers are increasingly interested in cancer type specific and custom solutions. We describe a flexible system for providing optimized, pre-tested primers for PCR-based NGS library preparation that generates cancer type specific panels with customizable content for use with FFPE tumor tissue samples. Methods A multifactorial scoring method was used to assign gene targets to 10 different cancer types for a total of approximately 300 genes. Fifteen to thirty genes most relevant to each particular cancer type were chosen for inclusion into core panels and an additional 15-50 genes were identified as supplemental content for each cancer type. The system is designed so that core panels can be modified by adding, dropping, or substituting any of the core genes with any of the other genes inventoried in the system. The assay system uses Ion AmpliSeq™ technology with manual or automated library preparation and sequencing on the Ion Torrent GeneStudio™ S5 sequencing platform. Ten ng of purified DNA per library pool (20 ng total) is used as input for library preparation. An automated tumor-only workflow for variant calling and sample quality reporting is provided within Ion Reporter. Streamlined access to reporting of variant relevance is enabled by Oncomine Reporter. Results Following primer design optimization and performance testing, core panels for Bladder, Colorectal &amp; Pancreatic, Kidney, Liver, Melanoma, Prostate, Lymphoma (B-cell types), and Gynecological cancers, as well as a panel for BRCA1/2 and homologous recombination repair, were characterized with cell lines, commercial reference controls, and FFPE samples. Panel base uniformity was &amp;gt; 90% across all panels. Sensitivity for hotspot variants (both SNVs and indels) was 95% down to Minor Allele Frequency (MAF) of 5%. Positive Predictive Value (PPV) for hotspots variants (both SNVs and indels) was 99%. The sensitivity of CNV gain was 90%. Conclusions A novel system to provide high-quality NGS library prep reagents for pre-defined or customized cancer panels and representative performance data are described in detail. For Research use only. Not for use in diagnostic procedures. Citation Format: Steven Roman, Charles Scafe, Yun Zhu, Fernando Farfan, Brooke McKnight, Santoshi Bandla, Chenchen Yang, Yu-Ting Tseng, Xiaoping Duan, Jigar Patel, Natasha Arksey, Seth Sadis, Fiona Hyland. A novel system that produces pre-qualified cancer NGS panels with customizable content [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1326.