Whole Genome Sequencing Informed Patient Personalized Measurable Residual Disease Assays for Acute Myeloid Leukemia

ABSTRACT

Post-treatment measurable residual disease (MRD) in acute myeloid leukemia (AML) patients is associated with adverse clinical outcomes. Validated molecular methods for AML MRD are preferable to flow cytometry assays but are not available for all patients. The limit of detection (LOD) of next-generation sequencing (NGS) assays for single nucleotide variants is restricted by technical error rates. Structural alterations are common genetic features of AML, but MRD approaches for detecting this class of variants have primarily relied on RNA. However, RNA has suboptimal stability, not all structural alterations are expressed as transcripts, and the impact of anti-leukemic therapy on transcription may make leukemic disease burden quantification inaccurate. In this study, we demonstrate a whole genome sequencing (WGS)-based approach to identify genomic DNA breakpoints of chromosomal rearrangements that allowed design of highly sensitive patient-personalized digital droplet PCR (ddPCR) MRD assays. Acute myeloid leukemia (AML) is an aggressive malignancy of the hematopoietic precursor cells that predominantly affects older individuals. Oncogenic transformation occurring through the acquisition of structural chromosomal aberrations is noted in 35% of AML cases, and can result in the formation of fusion proteins that confer proliferation and survival advantages (1). When compared to classical cytogenetics for the identification of structural variants at diagnosis, newer techniques such as optical genome mapping can identify clinically pertinent aberrations that may be cryptic or smaller than the resolution of conventional karyotyping and FISH (2). Similarly, short-read whole genome sequencing (WGS) has been shown to increase diagnostic yield and better refine risk stratification when compared to traditional cytogenetic testing in myeloid malignancies (3). Additionally, WGS can be utilized to identify genomic breakpoints of chromosomal rearrangements at a basepair (bp) resolution.