Abstract PO-016: Test-the-test: Clinical utility of comprehensive whole exome sequencing (WES) and RNA-seq for lymphoma patients
Authors: Chihara Dai , Balakrishnan Kumudha , Masand Gita , Novokreshchenova Anna , Bagaev Alexander , Kotlov Nikita , Postovalova Ekaterina , Shugaev-Mendosa Eduardo , Gracheva Yuliya , Lauziere Kelley , Kaneunyenye Leznath , McKenna Brianna , Berlinski Amber , Walsh McKenna , Larson Linnea , Kotsinyan Mariam , Yong Sheila T , Nomie Krystle , Fowler Nathan , Flowers Christopher R. , Westin Jason 
Published: June 2024

Abstract
Due to the rapidly evolving landscape of targeted therapies, there is an unmet need for comprehensive molecular profiling to guide treatment decisions for lymphoma patients. Here, we designed a pilot study to assess the feasibility and turnaround time (TAT) of a comprehensive clinical whole exome sequencing (WES) and transcriptome sequencing (RNA-seq) assay in large B-cell lymphoma (LBCL) patients for clinical decision-making (NCT05464823). Patients aged ≥18 years with histologically documented LBCL requiring therapy were eligible. Formalin-fixed paraffin-embedded tissues underwent WES, RNA-seq, and copy number analysis with concomitant peripheral blood or saliva for germline DNA sequencing. Samples with &lt;20% tumor purity and median coverage of &lt;142x for tumor and/or &lt;95x for normal samples were labeled as quantity not sufficient (QNS). Genomic and transcriptomic data were profiled to uncover clinically relevant biomarkers and match patients with clinical trials on ClinicalTrials.gov. Among 84 patients analyzed to date, 71 received WES and RNA-seq, yielding 67 reports with clinical information (treatment options and clinical trial matching) and 4 QNS reports without actionable findings. The remaining 13 samples were rejected as they failed pathology quality control for next-generation sequencing. Cell of origin (COO, n=62), LymphGen (n=62), and lymphoma microenvironment (LME, n=64) classifications were applied. The median TAT was 8 days for custom reports, and 70.4% of custom reports had a TAT ≤10 days. WES identified frequent TP53 (n=22) and MYD88 (n=11) alterations. COOs were designated as activated (n=26, 41.94%) or germinal center (n=36, 58.06%) LBCL. The LymphGen classifier (Wright et al. Cancer Cell. 2020) showed subtypes EZB MYC- (n=10, 16.13%), MCD (n=8, 12.9%), and A53 (n=6, 11.5%) as the most prevalent. LME classification revealed most LMEs as mesenchymal (n=46, 71.88%). Immune-depleted (n=12, 18.75%), immune-inflamed (n=4, 6.25%), and germinal center-like (n=2, 3.13%) LMEs were less prevalent, but the immune-depleted LME was more common in patients with relapse. Clinically significant findings, such as activated COO subtype (n=27), TP53 loss (n=21), DHITsig+ (n=9), and CARD11 mutations associated with ibrutinib resistance (n=3), were identified in 52 samples. On average, 8 clinical trials were identified per full report. Our results show the clinical utility and acceptable TAT of using a comprehensive WES and RNA-seq assay on a cohort of lymphoma patients. The full test reports included findings on significant alterations, LymphGen and LME subtypes, COOs, treatment options, and clinical trial matches. These robust findings, coupled with rapid TAT, demonstrate the feasibility of using integrated WES and RNA-seq to guide clinical decision-making for lymphoma patients.
Citation Format: Dai Chihara, Kumudha Balakrishnan, Gita Masand, Anna Novokreshchenova, Alexander Bagaev, Nikita Kotlov, Ekaterina Postovalova, Eduardo Shugaev-Mendosa, Yuliya Gracheva, Kelley Lauziere, Leznath Kaneunyenye, Brianna McKenna, Amber Berlinski, McKenna Walsh, Linnea Larson, Mariam Kotsinyan, Sheila T Yong, Krystle Nomie, Nathan Fowler, Christopher R. Flowers, Jason Westin. Test-the-test: Clinical utility of comprehensive whole exome sequencing (WES) and RNA-seq for lymphoma patients [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-016.