Murugesan, Alli

7546 Background: MRD assessment informs relapse risk in MM but is typically bone marrow-based and invasive. We therefore compared two minimally invasive MRD assays: BM-informed cfDNA whole-genome sequencing (cfWGS) and plasma proteomic MRD (EasyM). Methods: 71 longitudinal plasma samples (22 diagnosis, 49 follow-up) from 22 newly diagnosed MM patients across 8 Canadian sites (TFRIM4) had paired cfWGS and EasyM (Rapid Novor Inc). cfWGS MRD used patient-specific mutation lists from diagnostic BM WGS (Abelman et al., medRxiv 2025). EasyM used mass spectrometry to quantify residual M-protein from baseline. The primary endpoint was progression-free survival (PFS). Results: Among 22 MM patients (8 male, 14 female; median age at diagnosis 62 years), 8 progressed at a median follow-up of 52.6 months (range: 10-79 months). At 1-year maintenance (n = 18 available), cfWGS MRD+ (6/18) predicted inferior PFS (HR 20.12, 95% CI 2.23-181.60, p = 0.007). EasyM any-detect positivity was frequent (16/18, reflecting delayed clearance) and not prognostic (p = 0.99), with poor agreement vs cfWGS (44.4%, κ = 0.118). An exploratory EasyM clearance threshold of 0.93% (hypothesis-generating) classified 5/18 patients as MRD+ and stratified PFS (HR 8.78, 95% CI 1.55-49.82, p = 0.004), improving agreement with cfWGS (17/18, 94.4%, κ = 0.870). Progression clustered in cfWGS+/EasyM-high patients (EasyM >0.93%; 4/5; median 11.9 months post-collection [1.9–22.8]) and occurred once in cfWGS−/EasyM-low patients (1/12, 27.6 months). The only discordant case (cfWGS+/EasyM−) progressed 8.7 months after collection. Higher quantitative MRD burden was associated with inferior PFS (cfWGS: HR 2.92 per 1 SD, 95% CI 1.29-6.59, p = 0.01; EasyM: HR 5.48 per 1 SD, 95% CI 0.79-37.90, p = 0.085). At ~100 days post-autologous stem cell transplantation (ASCT; n = 16 available), EasyM was uniformly MRD+ (16/16) while cfWGS was MRD+ in 7/16 patients. Applying an EasyM clearance threshold (2.13%; 9 cleared vs 7 residual) improved agreement with cfWGS (14/16; 87.5%; κ = 0.746). Of two discordant cases, one cfWGS+/EasyM-cleared patient relapsed 38.6 months post-collection and one cfWGS−/EasyM-residual patient remained progression-free at last follow-up. At post-ASCT, both assays showed consistent but underpowered associations with PFS (cfWGS HR 6.32, 95% CI 0.70–56.76, p = 0.100; EasyM-clearance HR 2.36, 95% CI 0.39–14.18, p = 0.335). Across all post-treatment samples (n = 49), continuous cfWGS burden correlated with EasyM residual M-protein (rho = 0.535, p < 0.001). Conclusions: BM-informed cfWGS MRD strongly stratified PFS, whereas EasyM required a clearance definition due to near-universal early positivity. Concordant plasma burdens support complementary MRD information. Future work will validate these findings in larger cohorts and quantify the incremental value of combined cfWGS and proteomic MRD for early relapse prediction.

Abstract Introduction: Early relapse limits durable remissions in multiple myeloma (MM). Cell-free DNA (cfDNA) fragment patterns capture tumor burden and nucleosome positioning. We tested whether a fragmentomics signature trained at MRD time points stratifies progression-free survival (PFS) when applied to pretreatment plasma. Methods: We performed 30-40× whole-genome sequencing of plasma cfDNA from 43 newly diagnosed MM patients, with 65 additional MRD timepoint samples from 41 of those patients (post-ASCT n=30; 1-year maintenance n=30; other maintenance n=5) across eight Canadian sites (TFRIM4 and IMMAGINE studies) and one U.S. site (Mayo SPORE). MRD testing used multiparameter flow cytometry for all follow-up samples (n=65) and clonoSEQ in a subset (n=31). Logistic and elastic-net models were trained at MRD timepoints on fragmentomics features (short-fragment burden; a combined model integrating fragment-length distributions with inferred nucleosome positioning at MM-specific chromatin accessibility regions [Ordoñez et al., Genome Res. 2020]). A decision threshold was fixed by the Youden index during training and applied unchanged to diagnosis samples. PFS was analyzed by Kaplan-Meier, log-rank, and Cox models. Results: After a median follow-up of 49.1 months, 16 of 43 patients (37%) progressed. Using the prespecified locked threshold, patients classified as MRD+ by the proportion-of-short-fragments model had significantly shorter PFS than MRD- patients (HR = 5.12; 95% CI 1.16-22.57; log-rank p = 0.016), with median PFS of 49.2 months for MRD+ cases versus not reached for the MRD- group. Fixed-horizon PFS favored MRD- samples at 24/36/48 months (100/94/87% vs 85/81/53% for MRD+). A combined model integrating weighted fragment lengths with inferred nucleosome positioning also separated outcomes (log-rank p=0.054); the Cox HR was not estimable because no MRD- patients relapsed. At 24, 36, and 48 months, baseline MRD positivity by the short-fragment model identified 100%, 83%, and 86% of patients who relapsed within those intervals (specificity 44%, 43%, and 52%), while the combined model detected all early relapses across the same horizons (specificity 15-21%), indicating consistently high sensitivity but modest specificity for predicting early progression. Conclusions: A cfDNA fragmentomics signature trained at MRD time points stratified PFS when applied to diagnostic plasma, identifying patients at risk of early relapse. Short-fragment burden was most discriminative, and a combined model with nucleosome positioning recapitulated it with higher sensitivity, albeit lower specificity. These data support cfDNA fragmentomics as a practical liquid-biopsy risk biomarker in MM and suggest higher signals may proxy aggressive disease with greater tumor shedding and chromatin disorganization. Future work will validate findings in larger cohorts and integrate cytogenetic and immune features. Citation Format: Dor David Abelman, Jenna Eagles, Aimee Wong, Saumil Shah, Jeffrey Bruce, Stephanie Pedersen, David S. Scott, Cecilia Bonolo de Campos, Signy Chow, Darrell White, Irwindeed Sandhu, Kevin Song, Esteban Braggio, Shaji Kunnathu Kumar, Alli Murugesan, Tony Reiman, A. Keith Stewart, Suzanne Trudel, Trevor J. Pugh. Baseline cfDNA fragmentomics identifies multiple myeloma patients at risk of early progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2597.

Abstract Introduction: Monitoring minimal residual disease (MRD) is critical in multiple myeloma (MM) to predict outcomes and guide therapy. Traditional bone marrow (BM) aspirates for MRD detection are invasive and limited by sample quality. We therefore explored cell-free DNA (cfDNA) fragmentation as a less invasive alternative for MRD detection. Methods: We performed 30-40X whole-genome sequencing (WGS) on peripheral blood cfDNA from 45 MM patients, collecting baseline (n = 45) and follow-up samples (n = 98) from eight Canadian sites (M4 and IMMAGINE studies) and one U.S. site (SPORE study), plus 25 healthy controls. Samples were collected post-induction therapy (n = 13), 100 days post-autologous stem cell transplantation (ACST, n = 36), and during maintenance therapy (n = 49). Multiparameter flow cytometry (MFC) MRD testing was conducted on 77 samples. We evaluated insert size metrics and MM-specific chromatin accessibility (from Ordoñez et al., 2020) using Griffin (described in Doebley et al., 2022). Results: Baseline samples had a higher proportion of short fragments (20-150 bp) than follow-up samples (p = 0.0037) and healthy controls (p = 0.019). A fragment score (FS) based on weighted fragment distribution (per Vessies et al., 2022) was highest at baseline (mean = -0.384), followed by MRD-positive (mean = -0.495) and MRD-negative (mean = -0.550) samples. MRD-negative FS was lower than baseline samples (p &lt; 0.001) but higher than healthy controls (mean = -0.639; p = 0.016). Baseline samples had lower coverage at MM-specific chromatin regions than MRD timepoints (p &lt; 0.05; baseline mean = 0.982; MRD-positive = 0.989; MRD-negative = 0.994; healthy = 0.993), suggesting higher transcriptional activity pre-treatment. MRD-negative samples had higher coverage than MRD-positive cases (p &lt; 0.01). Using logistic regression, we assessed the predictive performance of FS and coverage at MM-specific sites. FS alone achieved an AUC of 0.632 (sensitivity [SN] 39.4%, specificity [SP] 92.1%, accuracy [AC] 67.6%). Coverage yielded an AUC of 0.681 (SN 75.8%, SP 60.5%, AC 67.6%). Combining FS and coverage at MM sites improved performance (AUC = 0.734; SN 48.5%, SP 92.1%, AC 71.8%). We next evaluated whether adjusting the BM tumor cell percentage cutoff by MFC could improve performance. At 0.017% (1 in 5, 789 cells) for MRD positivity, the combined model’s accuracy reached 83% with an AUC of 0.757 (SN 17%, SP 97%). Conclusions: cfDNA fragmentomic analysis achieved high specificity (92-97%) in detecting MRD, providing a less invasive alternative to facilitate serial monitoring. While sensitivity remains an area for improvement, the high specificity of cfDNA makes it valuable for confirming MRD negativity and reducing invasive procedures. Future efforts aim to enhance sensitivity by integrating additional fragmentomic features. Citation Format: Dor D. Abelman, Jenna Eagles, Aimee Wong, Saumil Shah, Stephanie Pedersen, Stephenie Prokopec, David S. Scott, Sarah Bridges, Darrell White, Irwindeep Sandhu, Kevin Song, Esteban Braggio, Alli Murugesan, Anthony Reiman, Suzanne Trudel, Trevor J. Pugh. Tumor-independent monitoring of minimal residual disease in multiple myeloma using cfDNA fragmentomics [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 3250.

Abstract Introduction: In multiple myeloma, randomized trials of maintenance therapy using thalidomide or lenalidomide following autologous transplant (ASCT) demonstrated prolonged progression-free survival (PFS), but overall survival benefit was inconsistent. The MY.10 trial (n=332) demonstrated improved PFS with thalidomide-prednisone maintenance therapy, but quality of life was inferior and overall survival was not improved. As a randomized trial with a no-treatment control arm and biospecimen collection, MY.10 provides a unique opportunity to identify predictors of benefit from therapy that could be used to personalize treatment. Immunomodulatory drug action is mediated in part through binding to cereblon (CRBN) and downregulation of IRF4. Candidate single nucleotide polymorphisms (SNPs) were selected from the CRBN/IRF4 pathway and other genes previously associated with myeloma prognosis, drug response and toxicity from literature review. The aim of this study was to investigate associations between candidate SNPs and benefit from immunomodulatory compound-based maintenance therapy, as well as prognostic impact. Methods: Genomic DNA was extracted from samples preserved in Trizol¨. SNPs were genotyped using TaqMan¨ genotyping assays on the ViiA7 qPCR platform. Analysis was performed on 187 patients with available samples and clinical data (86 in treatment arm; 101 in observation arm). Cox regression models were performed using SAS clinical 2.0 for prognostic impact of a single SNP on PFS, assessed with and without adjusted covariates (age, stage, performance status and response to ASCT). In treatment benefit analysis, PFS was modeled with genotype, treatment assignment and their interaction term. Results: SNPs with significant prognostic impact for PFS in all 187 patients were found in CRBN (rs1672753) (HR 0.59, 95%CI 0.4-0.86; p=0.006) and the following SNPs which had been found to be prognostic in prior studies were validated: CYP1A1 (rs1048943) (HR 1.98, 95%CI 1.19-3.27; p=0.008), CYP1B1 (rs1056836) (HR 0.72, 95%CI 0.52-0.99; p=0.043), and trend toward significance for SNP in CYP1A2 (rs2069514) (HR 2.02, 95%CI 0.98-4.15; p=0.057). Of these, only the CYP1A1 SNP was found to be possibly predictive of greater benefit from maintenance therapy. A SNP in ABCA1 (rs363717), previously associated with thalidomide-induced neuropathy,‎ was prognostic in this study (HR 1.44, 95%CI 1.03-2.02; p=0.033) but not predictive of treatment benefit. Table 1 lists SNPs associated with a differential level of benefit from maintenance therapy, including SNPs in FAM179a and ICAM1 that were possibly associated with harm from maintenance therapy. Table 1. SNPs and treatment interaction with significant impact on PFS. HR represent hazard ratio of treatment versus observation for a given genotype group. Asterisk Indicates trend toward significance. Wildtype Heterozygote & mutant p-value interaction Gene dbSNP ID SNP HR 95% CI HR 95% CI FAM179A rs1053667 T>C 0.46 0.33, 0.66 2.28 0.78, 6.65 0.003 ICAM1 rs1799969 G>A 0.51 0.36, 0.73 1.75 0.83, 3.70 0.007 CASP3 rs1049216 A>G 0.82 0.54, 1.25 0.41 0.25, 0.69 0.029 IRF4 rs12203592 C>T 0.69 0.47, 1.02 0.38 0.21, 0.69 0.062* CYP1A1 rs1048943 A>G 0.62 0.44, 0.87 0.11 0.02, 0.52 0.079* Conclusion: Previously identified SNPs in drug metabolism and drug efflux genes were validated to be prognostic in this cohort. The prognostic but not predictive significance of a SNP in CRBN suggests a possible role for CRBN in multiple myeloma disease biology independent of immunomodulatory therapy. SNPs predictive of differing degrees of benefit from immunomodulatory maintenance were found in genes involved in immunomodulatory activation, drug action and cell adhesion mediated drug resistance; SNPs in FAM179A and ICAM1 were possibly associated with harm from thalidomide maintenance and could potentially be used to identify patients unsuitable for immunomodulatory maintenance therapy. These results may be applicable to lenalidomide and pomalidomide, since immunomodulatory compounds exhibit similar chemical structures and mechanisms of action. Validation of these SNPs in prospective clinical trials involving other immunomodulatory can test this hypothesis. Further studies are needed to confirm our findings. Disclosures Off Label Use: thalidomide and prednisone maintenance for multiple myeloma. Bahlis:Celgene: Consultancy, Honoraria, Research Funding, Speakers Bureau; Amgen: Consultancy; Johnson & Johnson: Speakers Bureau; Johnson & Johnson: Consultancy; Johnson & Johnson: Research Funding. Song:Celgene Canada: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. White:Celgene Canada: Honoraria, Research Funding. Chen:Celgene: Consultancy, Honoraria, Research Funding. Seftel:Celgene: Honoraria, Research Funding. Howsen-Jan:Celgene: Honoraria, Research Funding. Reece:Amgen: Honoraria; Bristol-Myers Squibb: Research Funding; Merck: Research Funding; Novartis: Honoraria, Research Funding; Onyx: Consultancy; Millennium Takeda: Research Funding; Lundbeck: Honoraria; Otsuka: Research Funding; Janssen-Cilag: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding. Shepherd:Celgene: Honoraria, Research Funding. Chen:Celgene: Honoraria, Research Funding. Djurfeldt:Celgene: Research Funding. Reiman:Soricimed Biopharma Inc: Consultancy, Other: Scientific Advisory Board for Soricimed.