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[Preprint]. 2023 Mar 27:2023.03.26.23287367.
doi: 10.1101/2023.03.26.23287367.

Quantification of measurable residual disease using duplex sequencing in adults with acute myeloid leukemia

Laura W Dillon  1 , Jake Higgins  2 , Hassan Nasif  3 , Megan Othus  3 , Lan Beppu  4 , Thomas H Smith  2 , Elizabeth Schmidt  2 , Charles C Valentine 3rd  2 , Jesse J Salk  2 , Brent L Wood  5 , Harry P Erba  6 , Jerald P Radich  4   7 , Christopher S Hourigan  1   8
Affiliations

Quantification of measurable residual disease using duplex sequencing in adults with acute myeloid leukemia

Laura W Dillon et al. medRxiv. .

Update in

Abstract

The presence of measurable residual disease (MRD) is strongly associated with treatment outcomes in acute myeloid leukemia (AML). Despite the correlation with clinical outcomes, MRD assessment has yet to be standardized or routinely incorporated into clinical trials. Discrepancies have been observed between different techniques for MRD assessment and there remains a need to compare centralized, high-quality multiparametric flow cytometry (MFC) and ultrasensitive next-generation sequencing (NGS) in AML patients with diverse mutational profiles. In 62 patients with AML, aged 18-60, in first complete remission after intensive induction therapy on the randomized phase 3 SWOG-S0106 clinical trial, MRD detection by MFC was compared with a 29 gene panel utilizing duplex sequencing (DS), an NGS method that generates double-stranded consensus sequences to reduce false positive errors. Using DS, detection of a persistent mutation utilizing defined criteria was seen in 22 (35%) patients and was strongly associated with higher rates of relapse (68% vs 13% at year 5; HR, 8.8; 95% CI, 3.2-24.5; P<0.001) and decreased survival (32% vs 82% at year 5; HR, 5.6; 95% CI, 2.3-13.8; P<0.001). MRD as defined by DS strongly outperformed MFC, which was observed in 10 (16%) patients and marginally associated with higher rates of relapse (50% vs 30% at year 5; HR, 2.4; 95% CI, 0.9-6.7; P=0.087) and decreased survival (40% vs 68% at year 5; HR, 2.5; 95% CI, 1.0-6.3; P=0.059). Furthermore, the prognostic significance of DS MRD status at the time of remission was similar on both randomized arms of the trial, predicting S0106 clinical trial outcomes. These findings suggest that DS is a powerful tool that could be used in patient management and for early treatment assessment in clinical trials.

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Conflict of interest statement

Conflict of Interest

The National Heart, Lung, and Blood Institute receives research funding for the laboratory of CSH from Sellas and the Foundation of the NIH AML MRD Biomarkers Consortium. MO consults for Merck and Biosight and serves on the data safety monitoring committee for Celgene, Glycomimetic, and Grifols. JH, THS, CCV, ES, and JJS are employees and stockholders of TwinStrand Biosciences. BLW consults for Amgen and Kite Pharma. HE: COI: AbbVie; Agios Pharmaceuticals; ALX Oncology; Amgen; Daiichi Sankyo; FORMA Therapeutics; Forty Seven; Gilead Sciences; GlycoMimetics; ImmunoGen; Jazz Pharmaceuticals; MacroGenics; Novartis; PTC Therapeutics; Research Funding: AbbVie; Agios Pharmaceuticals; Bristol Myers Squibb; Celgene; Incyte Corporation; Jazz Pharmaceuticals; Novartis; Speakers Bureau: AbbVie; Independent review committee: AbbVie; Agios Pharmaceuticals; Astellas; Bristol Myers Squibb; Celgene; Daiichi Sankyo; Genentech; GlycoMimetics; Incyte Corporation; Jazz Pharmaceuticals; Kura Oncology.

Figures

Figure 1.
Figure 1.. Clinical outcomes of S0106 AML patients analyzed for MRD.
Rates of (A) non-relapse related mortality (NRM), (B) relapse, (C) relapse-free survival (RFS), and (D) overall survival (OS) are shown for the 62-patient cohort from the S0106 clinical trial analyzed for measurable residual disease (MRD) by duplex sequencing and multiparametric flow cytometry.
Figure 2.
Figure 2.. Mutational spectrum, MRD status, and clinical outcomes of patients in complete remission.
The heatmap displays variants detected at diagnosis and the presence (divided into variant allele fraction (VAF) ≥ or < 5%) or absence at the time of complete remission by duplex sequencing (DS), DS measurable residual disease (MRD) status, multiparametric flow cytometry (MFC) MRD status, and clinical outcome at 5 years (relapse, no relapse, or non-relapse mortality (NRM). The presence of a mutation within a gene is denoted in the heatmap, with the color corresponding to the highest VAF within each gene per patient. Variants identified in remission that were not identified at diagnosis are also marked (*).
Figure 3.
Figure 3.. Impact of MRD status on clinical outcomes.
Rates of non-relapse mortality (NRM), relapse, relapse-free survival, and overall survival are shown based on measurable residual disease (MRD) status as determine by (A) multiparametric flow cytometry (MFC) and (B) duplex sequencing (DS). Positive, pos; Negative, neg.
Figure 4.
Figure 4.. Analysis of discordant MRD results by duplex sequencing and flow cytometry.
(A) Number and percentage of patients called MRD positive (pos) versus MRD negative (neg) by duplex sequencing (DS) versus multiparametric flow cytometry (MFC). (B) Clinical outcomes (non-relapse mortality (NRM), relapse, or no relapse) of MFC MRD versus DS MRD discordant cases. (C) Rates of relapse for patients grouped by MRD status as defined by MFC MRD and DS MRD. Complete remission, CR; Number, No.
Figure 5.
Figure 5.. Impact of treatment randomization and DS MRD status on relapse.
Rates of relapse for patients as defined by (A) treatment randomization to daunorubicin and cytarabine (DA) versus daunorubicin, cytarabine, and gemtuzumab ozogamicin (DA+GO) and (B) treatment randomization (DA or DA+GO) and duplex sequencing (DS) measurable residual disease (MRD) status. Positive, pos; Negative, neg.
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