Abstract
Introduction: Genetic profiling is essential for optimal management of patients with acute myeloid leukemia (AML). Whole genome sequencing (WGS) has been proposed as a replacement for the multiple testing modalities currently in use but has not yet been widely adopted. WGS may also reveal new or underappreciated biology with potential utility in diagnostics and drug discovery. We report here, from 18 major cancer centers in the USA, the largest cohort of WGS from AML diagnosis (Dx) and complete remission (CR) described to date.
Methods: Adults with AML in CR screened for the prospective multicenter national protocol MEASURE (NCT05224661) were selected based on availability of stored Dx material. WGS data was generated (Illumina NovaSeq) centrally and interpreted independently to clinical molecular and cytogenetics reports. Dx-only and CR-only analysis used the DRAGEN 4.4 Heme WGS pipeline on Illumina Connected Analytics and was interpreted using Illumina Connected Insights 5.1. Paired Dx-CR analysis used DRAGEN MRD-Fingerprint and Somatic pipelines. Filters were established to identify variants in AML-related genes and cancer hotspots.
Results: Of 255 patients (pts) included, 53% were male, median age was 59 years (range: 19-79y) and 70% were non-Hispanic White. Most (89.4%) were in first CR, and 26.7% had received induction less intensive than traditional cytotoxic chemotherapy. Considerable heterogeneity in clinical genetic profiling approaches between centers was observed.
Median WGS depth was 117X (range: 59–300X) at Dx and 37X (range: 24–89X) at CR. Dx-only WGS was able to detect the prognostic and predictive genomic features reported by clinical testing (488/527, 93%) and resulted in identical ELN 2022 prognostic risk classifications in most pts (237/255, 93%). In 11 pts (4.3%) however classification would be refined due to additional information from WGS, including 3 pts downstaged to favorable risk.
WGS frequently identified alterations commonly missed by standard clinical testing. KMT2A partial tandem duplication (KMT2A-PTD), reported as associated with adverse outcomes, was observed in 34 pts (13%). Tandem duplications were also identified in additional genes related to AML, including UBTF, RUNX1, EZH2, and CCDC26. Cytogenetically cryptic gene fusions were observed in 8 pts, involving NUP98 (5 pts), KMT2A (2 pts), and MECOM (1 pt). Copy-neutral loss of heterozygosity (CN-LOH) was observed in chromosome hotspots (eg: 2p, 11, 13q, 21q) in 43 pts (16.9%), overlapping with oncogenic variants in 30 of 43 pts (69.8%) including FLT3, RUNX1, DNMT3A, KMT2A, and WT1. Additional features were found, including microdeletions overlapping with AML driver genes, MYC amplification, deep intronic cryptic splice variants, and signatures of chromothripsis.
In the subset of 109 pts with cytogenetically normal AML, defined by a successful clinical metaphase cytogenetics test yielding a normal result, WGS identified structural abnormalities in 51 pts (47%) including KMT2A-PTD (22 pts), CN-LOH (20 pts), microdeletions (7 pts), cryptic fusion genes (5 pts), chromosomal gains or losses (2 pts), and a translocation (1 pt).
At CR, WGS profiling identified both persistent and emerging variants. A higher proportion of the less-intensively treated pts had at least one persistent mutation at CR (57.6% vs 33.3%; p<0.001) in genes recommended by ELN for testing at Dx. Oncogenic variants detected only in CR were seen in 30 pts, including PPM1D (7 pts), MPL (3 pts), U2AF1 (3 pts) and IDH1 and BRAF (1pt each). Finally, Dx-CR matched calling enabled the discovery of novel diagnostic features directly correlated with leukemic portion, including segregated variations from pre-leukemia clonal hematopoiesis and variations in regulatory regions not captured by standard clinical testing.
Conclusions: WGS is a single assay for the comprehensive AML genomic profiling required for diagnostic, prognostic, and predictive purposes. In this multicenter study, WGS revealed many structural and copy number abnormalities missed by current standard of care clinical testing, including potential therapeutic targets. The rate of tandem duplications identified by deep WGS was higher than has been reported previously by other methodologies. WGS can provide novel insights into AML disease biology, prognostication, treatment effects, MRD targets, and potential therapeutic susceptibilities. The MEASURE Genome Atlas is a unique new resource for the AML community.
