Abstract 173: Profiling T cell clonality in FFPE samples using a targeted sequencing approach: Critical parameters and limitations

With the rapid development of immuno-therapy approaches for cancer treatment, tools that characterize tumor-infiltrating immune cells fuel new opportunities to better understand the natural defense mechanisms against tumor cells. The AmpliSeqTM for Illumina Immune Repertoire Plus, TCR beta SR Panel is a targeted sequencing assay that assesses T cell clonal diversity by amplifying the CDR3 region of the TCRβ gene in both DNA or RNA. This study describes the performance of this assay on peripheral blood mononuclear cells (PBMC) as high-quality input as well as formalin-fixed paraffin embedded (FFPE) samples, using the MiXCR Immune Repertoire Analyzer app for clonotype analysis. Multiple replicate libraries prepared from RNA (n=6) and DNA (n=12) extracted from the same PBMC donor showed a minimum of 96.4% alignment, with high reproducibility between replicates for clonotypes ( Citation Format: Valerie N. Montel, Stephanie B. Greene, Jeff H. Tsai. Profiling T cell clonality in FFPE samples using a targeted sequencing approach: Critical parameters and limitations [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 173.