Evaluating the Clinical Utility of Real-Time Comprehensive Whole Exome Sequencing and RNA-Seq for Patients with Diffuse Large B-Cell Lymphoma
Authors: Chihara Dai , Balakrishnan Kumudha , Masand Gita , Harkins Robert Andrew , Akkad Neha , 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 , Samokhina Anna , Yong Sheila T , Nomie Krystle , Fowler Nathan H. , Flowers Christopher R. , Westin Jason R. 
Published: December 2024

Introduction: Due to the rapidly evolving landscape of targeted therapies, there is an unmet need for comprehensive molecular profiling to guide treatment decisions for patients with lymphoma. The POLARIX trial showed significant impact of cell-of-origin (COO) in response to polatuzumab-vedotin, demonstrating the unmet need for a reliable real-time assay for molecular profiling to better assign novel treatment to patients with diffuse large B-cell lymphoma (DLBCL) who require treatments within a few weeks from the diagnosis or recurrence. To address this need, we designed a pilot study to assess the feasibility and turnaround time (TAT) of a comprehensive whole exome sequencing (WES) and transcriptome sequencing (RNA-seq) assay in patients with DLBCL for clinical decision-making (NCT05464823).
Methods: Patients aged ≥18 years with DLBCL were eligible. Formalin-fixed paraffin-embedded tissues at diagnosis or recurrent disease 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;150x for tumor and/or &lt;100x for normal samples were labeled as quantity not sufficient (QNS). Genomic and transcriptomic data were profiled to define DLBCL COO (Alizadeh et al. Nature 2000), dark zone signature (Dzsig; Ennishi et al. J Clin Oncol. 2019), LymphGen (Wright et al. Cancer Cell 2020), and lymphoma microenvironment (LME; Kotlov et al. Cancer Discov. 2021) classification to uncover clinically relevant biomarkers and match patients with clinical trials on ClinicalTrials.gov.
Results: Among 92 patients analyzed to date, 77 patients (40 with newly diagnosed disease and 37 with relapsed/refractory disease) received WES and RNA-seq, yielding 73 reports with clinical information (treatment options and clinical trial matching) and 4 QNS reports without actionable findings. The remaining 15 samples were rejected as they failed pathology quality control for next-generation sequencing. COO, Dzsig, LymphGen, and LME were classifiable in approximately 90% of patients. The median TAT was 8 days for the result reports (range: 5-22 days), and 73% of custom reports had at TAT ≤10 days.
WES identified frequent TP53 (n=23, 30%) and MYD88 (n=13, 17%) alterations. COOs were designated as activated B-cell type (ABC) in 31 patients (46%) or germinal center B-cell type in 37 patients (54%). The LymphGen classifier showed subtypes MCD (n=8, 12%), EZB MYC- (n=8, 12%), and other (n=18, 26%) as the most common. LME classification revealed most LMEs as mesenchymal (n=49, 70%) and immune-depleted (n=14, 20%), immune-inflamed (n=5, 7%), and germinal center-like (n=2, 3%) were less frequent. Clinically actionable and relevant findings, such as ABC subtype (n=31), TP53 loss (n=23), Dzsig+ (n=10), and CARD11 mutations which are associated with ibrutinib resistance (n=3), were identified in 58 samples. Molecular profiling supported screening for clinical trials, and on average, 8 potential clinical trials were identified from ClinicalTrials.gov per the full report although majority of trials were not lymphoma focused trials.
Conclusion: We demonstrated clinical utility and acceptable TAT using a comprehensive WES and RNA-seq assay in a cohort of patients with DLBCL. The full test reports included findings on significant alterations, COO, Dzsig, LymphGen, and LME subtypes, treatment options, and clinical trial matches. These robust findings, coupled with rapid TAT, demonstrate the real-world feasibility of using integrated WES and RNA-seq to design biology-driven trials and guide clinical decision-making for patients with lymphoma initiating a new line of therapy.