Abstract 6304: RUO LymphoTrack Enterprise Software v3.0.1 - A comprehensive suite to standardize analyses of IG and TCR sequencing data

This study introduces the LymphoTrack Enterprise Software v3.0.1 (LTE), a high-throughput Research Use Only (RUO) software suite for analyzing all RUO LymphoTrack Assays offered by Invivoscribe on a single platform. LTE provides a comprehensive solution for the analysis of immunoglobulin and T-cell receptor nucleotide sequences. LTE is specifically designed to meet the needs of higher volume laboratories seeking compatibility with a broader range of sequencers and increased automation flexibility. Unlike the desktop RUO LymphoTrack Software - MiSeq for clonality and MRD analyses, which caters to smaller-scale users, LTE offers an advanced enterprise architecture featuring containerization, a REST API for seamless integration, and scalable infrastructure to handle large datasets efficiently. These enhancements make LTE an ideal choice for labs focused on high-throughput analysis and integration into automated workflows. Notably, LTE significantly reduced MiSeq processing time to 2.2 ± 0.34 minutes (n=3 runs, 24 samples each) vs. 30.3 ± 1.50 minutes in RUO LymphoTrack v2.4.6—an ∼92.8% reduction. LTE also includes compatibility with more assay and sequencing platforms, supporting Illumina NextSeq1000 and Complete Genomics DNBSEQ-G99, with planned support for NovaSeq6000 in future releases to further increase compatibility. For example, it recognizes DNBSEQ-G99 FASTQ files, performs adapter trimming, and proceeds to clonality analysis, with total analysis times of 20.1 ± 0.56 minutes for a NextSeq550 run (n = 3 runs, 12-25 samples each run), 8.98 ± 2.23 minutes for a NextSeq1000 run (n = 4 runs, 96 samples), and 70.3 ± 6.35 minutes (n = 3 runs, 24 samples each run) for a DNBSEQ-G99 run (including 65.7 ± 7.06 minutes for adapter trimming step). Key advancements in this release include enhanced CDR3 region identification, a critical feature for immunogenomics, enabling rapid and precise immune repertoire and clonality analyses. Testing over 220,000 unique sequences, the RUO LymphoTrack Enterprise v3.0.1 algorithm achieved a CDR3 identification rate of 98.6%, a substantial improvement from the 58.4% rate observed with the previous version. The software also supports multiple immunogenetic databases, including IgBlast, IMGT/V-QUEST, and IMGT/GENE-DB, allowing for customized antibody and T-cell receptor profiling. By offering faster processing, broader platform compatibility, and enhanced analytical capabilities, RUO LymphoTrack Enterprise v3.0.1 provides a robust, all-in-one solution for researchers seeking to streamline immunogenomic workflows. This upgraded version establishes a new standard in cancer genomics, with potential to significantly advance biomarker discovery, immune response characterization, and cancer subtype differentiation. Citation Format: Tran Nguyen, Jacob Witsotsky, Julian D’Angelo, Javier Velazquez-Muriel, Angelo Arias, Jelena Jablanovic, Jeffrey Miller. RUO LymphoTrack Enterprise Software v3.0.1 - A comprehensive suite to standardize analyses of IG and TCR sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6304.