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527 A Personalized Whole Genome-Informed Assay Targeting Single Mutant in Circulating Tumor DNA Can Identify MRD and Predict Relapse in DLBCL

Program: Oral and Poster Abstracts
Type: Oral
Session: 621. Lymphomas: Translational – Molecular and Genetic: Signaling Pathways and MRD in Lymphoma
Hematology Disease Topics & Pathways:
Research, adult, non-Hodgkin lymphoma, Translational Research, Lymphomas, assays, B Cell lymphoma, Diseases, aggressive lymphoma, Lymphoid Malignancies, emerging technologies, Technology and Procedures, Human, Study Population, Minimal Residual Disease , molecular testing, omics technologies
Sunday, December 10, 2023: 1:00 PM

Reid W. Merryman, MD1, Justin Rhoades2*, Kan Xiong2*, Katherine Antel, MD, PhD3,4, Hyun Hwan An5*, Robert A. Redd, MS6*, Mikaela M. McDonough, BS5*, Lillian Guerrero3*, Andela Crnjac2*, Sainetra Sridhar2*, Timothy Blewett2*, Ju Chen2*, Parastoo B. Dahi, MD7*, Yago Nieto, MD, PhD8, Yi-Bin Chen, MD, MS9, Alex F. Herrera, MD9, Robin M. Joyce, MD10*, Philippe Armand, MD, PhD11, Mark Alan Murakami, MD, MA, MMSc5 and Viktor Adalsteinsson2*

1Brigham and Women's Hospital, Boston, MA
2Broad Institute, Boston, MA
3Dana-Farber Cancer Institute, BOSTON, MA
4Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
5Dana-Farber Cancer Institute, Boston, MA
6Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
7Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
8Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
9City of Hope, Duarte, CA
10Massachusetts General Hospital, Boston, MA
11Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA

Introduction: Minimal residual disease (MRD) detected by circulating tumor DNA (ctDNA) has emerged as a promising biomarker in diffuse large B-cell lymphoma (DLBCL). MAESTRO (minor-allele-enriched sequencing through recognition oligonucleotides) was recently developed to aid the detection of low-frequency mutations by enriching for mutant alleles using probes preferentially capturing single-nucleotide variants. We have extended this application – termed MAESTRO-Pool – to analyze personalized MRD variant detection within a cohort-level single assay. We demonstrate high sensitivity to detect MRD using MAESTRO-Pool and the detection of emergent mutations using targeted sequencing of the same samples.

Methods: Fifty-nine plasma specimens from 9 patients with relapsed/refractory (R/R) DLBCL treated on a phase II trial (NCT02362997) of post-autologous stem cell transplant (ASCT) pembrolizumab maintenance were tested. Cases were selected based on the availability of genomic DNA from tumor tissue, patient-matched germline DNA, and serial post-ASCT plasma samples (≥ 3 time points). MAESTRO probes were designed to target patient tumor-specific somatic variants using results of baseline tumor-normal whole genome sequencing. Probes were then pooled into an integrated, cohort-level assay (MAESTRO-Pool). Serial samples were compared with an orthogonal, whole-genome, tumor-informed MRD test which does not use mutation enrichment (MRD Tracker; Parsons, HA et al. Clin Cancer Res 26, 2556-2564 (2020)) for sensitivity and specificity of variant detection. In addition, sensitivity to detect MRD and predict relapse was compared to that observed with immunoglobulin locus high-throughput sequencing (IgHTS). Additional baits were designed to capture single nucleotide variants (SNVs) previously reported in R/R DLBCL (63 loci in 12 genes), enabling detection of treatment-emergent mutations not identified in baseline tumor specimens.

Results: Tumor-normal WGS revealed a median of 433 somatic SNVs per tumor (range 81-1653). The pooled assay comprised 6044 SNV-specific probes. MRD identification was similar for MAESTRO-Pool and MRD Tracker. Among 59 samples, a discrepant MRD call was observed for a single sample where ctDNA was detected at 4 ppm using MRD Tracker, but not detected using MAESTRO-Pool (limit of detection [LoD] 16 ppm). Estimated tumor fractions using MRD Tracker and MAESTRO-Pool were concordant. Even with reduced sequencing requirements of MAESTRO-Pool, we observed a similar median limit of detection (LoD) for MAESTRO-Pool (median 30 ppm, range 1-18,243) and MRD Tracker (median 40 ppm, range 1-4,727 ppm).

MAESTRO-Pool identified ctDNA prior to recurrence for all 5 patients who relapsed, including at the earliest available post-ASCT timepoint for 4 of 5 relapsing patients. The time from ctDNA detection to clinical relapse (lead time) was the same or longer for each patient using MAESTRO-Pool (median 178 days, range 69-518) compared to IgHTS (median 44 days, range not detected to 518 days) (p=0.37) (Fig.1a). MAESTRO-POOL was associated with improved sensitivity compared to IgHTS (MAESTRO-Pool sensitivity of 90.5% for samples with matched IgHTS results versus IgHTS sensitivity of 61.9%, p=0.006). Superior sensitivity was primarily driven by MAESTRO-Pool’s improved detection of low-frequency (<1000 ppm) mutant alleles. In addition to tracking molecular tumor burden, we identified several de novo mutations in relapsing patients using targeted sequencing of the same samples. Notably, plasma from a patient who progressed at 18.5 months post-ASCT (DL-015) manifested an emergent CREBBP R1446H mutation not detected in the baseline tumor whose allele frequency steadily increased from 0.048% one week after ASCT to 30.533% at relapse (Fig 1b).

Conclusion: In this pilot study, MAESTRO-Pool enabled ultrasensitive detection and quantification of MRD with superior sensitivity compared to IgHTS. Complementary targeted sequencing also characterized genetic evolution, including detection of treatment-emergent mutations. Our results support the incorporation of ctDNA testing using MAESTRO-Pool in future prospective trials in DLBCL.

Disclosures: Merryman: Genentech/Roche: Research Funding; BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding; Alphasights: Membership on an entity's Board of Directors or advisory committees; Epizyme: Membership on an entity's Board of Directors or advisory committees; Genmab: Membership on an entity's Board of Directors or advisory committees, Research Funding; Intellia: Membership on an entity's Board of Directors or advisory committees; Seattle Genetics: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Merck: Research Funding; Adaptive Biotechnology: Membership on an entity's Board of Directors or advisory committees. Nieto: Affimed: Research Funding; Secura Bio: Research Funding; Astra Zeneca: Research Funding. Herrera: Adicet Bio: Consultancy; Caribou Biosciences: Consultancy; Takeda: Consultancy; Tubulis GmbH: Consultancy; Pfizer: Consultancy; Merck: Consultancy, Research Funding; Genmab: Consultancy; Allogene Therapeutics: Consultancy; Seattle Genetics: Consultancy, Research Funding; ADC Therapeutics: Consultancy, Research Funding; AbbVie: Consultancy; BMS: Consultancy, Other: Travel/Accommodations/Expenses, Research Funding; Regeneron: Consultancy; Karyopharm Therapeutics: Consultancy; AstraZeneca/MedImmune: Consultancy; Kite, a Gilead Company: Research Funding; Genentech/Roche: Consultancy, Research Funding; Gilead Sciences: Research Funding; AstraZeneca: Research Funding. Armand: MSD: Consultancy, Research Funding; Affimed Therapeutics: Research Funding; Enterome: Consultancy; Xencor: Consultancy; Regeneron: Consultancy; Tessa Therapeutics: Consultancy; Kite - a Gilead company: Research Funding; ATB Therapeutics: Consultancy; Genentech/Roche: Consultancy, Research Funding; Foresight Diagnostics: Consultancy; ADC Therapeutics: Consultancy; GenMab: Consultancy; AstraZeneca: Consultancy, Research Funding; IGM: Research Funding; Adaptive Biotechnologies: Research Funding; Bristol Myers Squibb: Consultancy, Research Funding; Merck: Consultancy, Honoraria, Research Funding. Murakami: Novartis AG: Membership on an entity's Board of Directors or advisory committees; imCORE (Genentech/Roche): Research Funding. Adalsteinsson: Exact Sciences: Current equity holder in private company.

*signifies non-member of ASH