Rapid diagnosis of acute leukemia with integrated epigenomic and genomic profiling | LC26

Abstract
Acute leukemia (AL) diagnosis is a time-consuming process that requires integration of multiple different diagnostic modalities, including morphology, immunophenotyping, and molecular genetics. Given this complexity, new approaches are needed to provide rapid diagnosis with molecular precision. In prior work, we developed a DNA methylation-based classifier (MARLIN) that can generate accurate AL classifications in ‘real-time’ after just a few minutes of nanopore sequencing. Here, we adapt this approach to achieve methylation-based classification in tandem with Adaptive Sampling-based enrichment on a PromethION sequencer for a comprehensive panel of 264 genomic regions of interest (ROI) relevant to leukemia classification. We assembled a patient cohort of 20 retrospective cases encompassing the spectrum of AL (2 T-ALL, 6 B-ALL, and 12 AML). For each sample, we devoted 90% of the flow cell pores to Adaptive Sampling and 10% to genome-wide methylation and copy number profiles. We achieved a median coverage of 103.1x (range: 64.9x–175.6x) over the 264 ROIs included in our Adaptive Sampling panel. Using established variant callers (Clair3, Sniffles) and manual review in Integrative Genomics Viewer (IGV), we identified all mutations (54/54, 100%) and AL-defining fusions (10/10, 100%) reported by conventional assessments, as well as the majority of copy-number/cytogenetic changes (21/24, 87.5%). Methylation-based MARLIN predictions were concordant with standard-of-care diagnoses in all cases (20/20, 100%). Prospective application of our approach in ‘real-time’ also generated accurate methylation- (<4 hr) and genetics- (~24 hr) based classifications for 5/5 patients, demonstrating proof-of-concept for our integrated epigenomic-genomic approach for rapid AL diagnosis.

Biography
Maria Reyes Capilla-Guerra is an early-career biomedical sciences graduate with dual Master’s degrees in Molecular Genetics and Bioinformatics. Currently she works at Dana-Farber Cancer Institute, where her work focuses on cancer genomics and epigenomics, particularly in hematological malignancies.