Evaluating the clinical utility of comprehensive whole exome sequencing (WES) and RNA-seq for patients with lymphoma
Authors
Dai Chihara¹, Kumudha Balakrishnan¹, Gita Masand¹, Anna Novokreshchenova², Alexander Bagaev², Nikita Kotlov², Ekaterina Postovalova², Eduardo Shugaev-Mendosa², Yuliya Gracheva², Kelley Lauziere², Leznath Kaneunyenye², Brianna McKenna², Amber Berlinski², McKenna Walsh², Linnea Larson², Mariam Kotsinyan², Anna Samokhina², Sheila T. Yong², Krystle Nomie², Nathan Fowler², Andrew Harkins¹, Neha Akkad¹, Christopher R. Flowers¹, Jason Westin¹
- 1 The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- 2 BostonGene Corp., Waltham, MA, USA
Abstract
Introduction:
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. 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 clinical whole exome sequencing (WES) and transcriptome sequencing (RNA-seq) assay in patients with LBCL for clinical decision-making (NCT05464823).
Methods:
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 <20% tumor purity and median coverage of <150x for tumor and/or <100x for normal samples were labeled as quantity not sufficient (QNS). Genomic and transcriptomic data were profiled to define LBCL COO (Alizadeh et al. Nature 2000), double hit signature(DHITSig; 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 (n=68), DHITSig(n=10), LymphGen (n=69), and LME (n=68) classifications were generated.The median TAT was 8 days for the result reports (range: 5–22 days), and 73.3% of custom reports had a TAT ≤10 days.
WES identified frequent TP53 (n=23, 29.9%) and MYD88 (n=13, 16.9%) alterations. COOs were designated as activated (n=31, 45.6%) or germinal center (n=37, 54.4%). The LymphGen classifier showed subtypes MCD (n=8, 11.6%), EZB MYC- (n=8, 11.6%), and other (n=18, 26.1%) as the most prevalent. LME classification revealed most LMEs as mesenchymal (n=49, 70%). Immune-depleted (n=14, 20%), immune-inflamed (n=5, 7.1%), and germinal center-like (n=2, 2.9%) LMEs were less prevalent. Clinically actionable and relevant findings, such as ABC subtype (n=31), TP53 loss (n=23), DHITSig+(n=10), and CARD11 mutations 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, DHITSig, 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.
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. 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 clinical whole exome sequencing (WES) and transcriptome sequencing (RNA-seq) assay in patients with LBCL for clinical decision-making (NCT05464823).
Methods:
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 <20% tumor purity and median coverage of <150x for tumor and/or <100x for normal samples were labeled as quantity not sufficient (QNS). Genomic and transcriptomic data were profiled to define LBCL COO (Alizadeh et al. Nature 2000), double hit signature(DHITSig; 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 (n=68), DHITSig(n=10), LymphGen (n=69), and LME (n=68) classifications were generated.The median TAT was 8 days for the result reports (range: 5–22 days), and 73.3% of custom reports had a TAT ≤10 days.
WES identified frequent TP53 (n=23, 29.9%) and MYD88 (n=13, 16.9%) alterations. COOs were designated as activated (n=31, 45.6%) or germinal center (n=37, 54.4%). The LymphGen classifier showed subtypes MCD (n=8, 11.6%), EZB MYC- (n=8, 11.6%), and other (n=18, 26.1%) as the most prevalent. LME classification revealed most LMEs as mesenchymal (n=49, 70%). Immune-depleted (n=14, 20%), immune-inflamed (n=5, 7.1%), and germinal center-like (n=2, 2.9%) LMEs were less prevalent. Clinically actionable and relevant findings, such as ABC subtype (n=31), TP53 loss (n=23), DHITSig+(n=10), and CARD11 mutations 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, DHITSig, 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.
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