Residual Allelic Burden Measured By Next-Generation Sequencing (NGS) at Remission Provides Limited Prognostic Value to Predict Relapse and Long-Term Outcome in Core Binding Factor Acute Myeloid Leukemia (CBF-AML)

Abstract

IntroductionNGS-based detection of minimal residual disease (MRD) has been successfully demonstrated for its correlation with relapse risk in AML. However, in a subtype of AML, CBF-AML, its clinical relevance of residual allelic burden at complete remission (CR) has not been fully explored. The standard MRD detection method in CBF-AML is quantitative PCR (qPCR). In this study, we aimed to explore applicability and feasibility of NGS-based MRD detection in CBF-AML taking various approaches, rather than simply using residual allele burden at CR.Patients and MethodsFifty-three patients (pts) diagnosed with CBF-AML were enrolled in this study (31 pts with RUNX1-RUNX1T1 and 22 pts with CBFB-MYH11). All 53 patients achieved complete remission (CR). We performed targeted deep sequencing on 84 genes in 106 samples collected at diagnosis and at CR as well as T-cell (n = 53, CD3+) fraction as a control using Illumina Hiseq 2500. Mean on-target coverage for 159 sequenced was 1,572x. The level of RUNX1-RUNX1T1 was measured at diagnosis and at CR for 29 patients using qPCR.ResultsAt diagnosis, 99 mutations from 49 pts (n = 49/53, 92%) were detected, where median number of mutations for 49 pts was 2 (range 1-6). Consistent with previous studies, KIT (36%), NRAS (32%), KRAS (17%), ASXL2 (15%) were commonly mutated. Among mutations detected at diagnosis, cKIT-D816 mutation and mutations in genes in DNA methylation pathway (DNMT3A and TET2) were associated with higher risk of relapse (5.29, [1.89 - 14.87], p = 0.002 and 3.15 [1.07 - 9.26], p= 0.037, respectively). In CR samples, 46 mutations from 32 pts were still detectable (46/99, 46%, mean VAF: 0.60%, range 0.04%-6.28%, Fig A). Only 4 mutations from 2 pts were over 2.5% (2 in TET2, 1 in ASXL1, and 1 in U2AF1). When tracing back at diagnosis, allelic burden of 46 mutations detected at remission were higher than 53 cleared mutations (p < 0.002), indicating clonal mutations are more likely to be detected at CR (Fig A). They were mostly in genes associated with activated signaling (32/46, 70%). When considering complete clearance rate, mutations in genes associated with activated signaling, DNA methylation, and spliceosome tended to be persistent at CR (32/64, 4/5, and 1/1), whereas mutations in cohesin complex and chromatin modifiers were mostly completely cleared (0/8 and 4/13).We then assessed clinical relevance of mutation clearance from various perspectives. We did not find association of mutation clearance at 0.3% (MC03) with OS (p = 0.43) or with relapse risk (p = 0.8, Fig B). Complete mutation clearance also did not show significant association with OS and relapse risk. Among 29 pts with RUNX1-RUNX1T1 with available qPCR data, 20 pts were MRD-positive by qPCR at CR. Nine pts who achieved MRD-negative also achieved MC03 as well. When considering only MRD-positive pts, achievement of MC03 did not affect OS (p = 0.69) and relapse incidence (p = 0.86, Fig C). Lastly, we assessed whether persistence of high risk mutations at CR (cKIT-D816, DNMT3A, and TET2) is associated with higher risk of relapse, but complete clearance of KIT-D816 mutation also did not affect OS and relapse incidence (p = 0.94 and p = 0.40, respectively, Fig D). We were not able to analyze DNMT3A and TET2 mutations as only 1/5 mutation was cleared.ConclusionCurrent study demonstrates that low residual allelic burden measured by NGS at CR does not provide additional clinically relevant information in addition to baseline mutation profile nor qPCR-based MRD in CBF-AML [Display omitted] DisclosuresNo relevant conflicts of interest to declare.