Comprehensive Genomic Profiling (CGP) of Acute Myeloid Leukemias with Foundation One Heme Identifies Actionable Genomic Alterations and Biomarkers

Introduction: Targeted therapies have become increasingly important in acute myeloid leukemia (AML), with FDA-approved drugs including IDH1/IDH2, BCL-2, and FLT3 inhibitors. Notable investigational drugs include menin inhibitors for AML with NPM1 mutations, NUP98 or KMT2A rearrangement. The 5th edition of WHO classification of myeloid neoplasms has outlined recurrent genomic alterations that allow the diagnosis of AML regardless of blast count, as well as somatic mutations that can render a diagnosis of myelodysplasia-related AML. Furthermore, the NCCN guidelines recommend risk stratification of AML patients incorporating mutational status of NPM1, CEBPA, FLT3, and TP53, for guiding treatment decisions. This highlights the clinical relevance of diagnostic and prognostic AML biomarkers without existing or emerging associated targeted therapies. With the plethora of actionable genomic alterations and biomarkers, CGP using next-generation sequencing (NGS) can facilitate the simultaneous interrogation of these important alterations in a single assay. We describe the molecular landscape of a large AML cohort tested on the FoundationOne Heme (F1H) platform, a CGP assay, demonstrating the advantages of CGP in clinical decision making and management.

Methods: F1H is a hybrid-capture NGS assay that analyzes all classes of genomic alterations in DNA (exons from 406 genes, select introns from 31 genes) and rearrangements in RNA (265 genes) from fresh blood, bone marrow, or formalin-fixed paraffin-embedded (FFPE) tumor samples. All patient samples with confirmed diagnoses of AML, undergoing F1H testing between December 2013 and September 2023 at Foundation Medicine (Cambridge, MA) were included in the study. Diagnoses were assigned by board-certified hematopathologists with molecular expertise who reviewed submitted test requisition forms, hematopathology reports, and accompanying H&E or Wright Giemsa-stained slides.

Results: A total of 3,793 unique AML patient samples were included, including 36% of peripheral blood, 47% of bone marrow aspirate, and 18% of FFPE. The cohort comprised 56% males and 44% females, with a median age of 61 (range <1 to >89). Many samples harbored pathogenic genomic alterations with diagnostic, classification, or therapeutic importance. Mutations were detected in FLT3 (20% of cases), TP53 (17%), ASXL1 (15%), NPM1 (15%), SRSF2 (12%), IDH2 (11%), IDH1 (7%), CEBPA (7%), BCOR (6%), STAG2 (6%), U2AF1 (6%), SF3B1 (4%), and EZH2 (3%). Of note, 55% of pathogenic FLT3 variants were internal tandem duplications, and 28% were tyrosine kinase domain mutations. 96% of pathogenic NPM1 variants involved the W288 codon, a mutational hotspot. Overall, 19% of cases harbored recurrent AML gene rearrangements defined by the WHO classification. Commonly detected rearrangements included KMT2A (7%), RUNX1::RUNX1T1 (4%), CBFB::MYH11 (3%), KMT2A::MLLT3 (3%), BCR::ABL1 (2%), NUP98 (2%), PML::RARA (1%), DEK::NUP214 (<1%), and RBM15::MRTFA (<1%), with 68% of rearrangements detectable by RNA sequencing only. KMT2A and NUP98 exhibited various rearrangement partners, which would not be easily characterized by fluorescence in situ hybridization (FISH) studies with break-apart probes.

Conclusions: The analysis of 3,793 AML patient samples comprising a variety of molecular subtypes demonstrated that the F1H assay platform detects important pathogenic genomic alterations with diagnostic, prognostic, and therapeutic significance. Current best practices for the diagnosis, classification, prognostication, and treatment of AML call for the assessment of the presence and absence of numerous genomic alterations. Therefore, in contrast to single-gene or small-panel molecular testing, the F1H platform can simplify such assessment via a CGP approach.

Ho:Loxo Oncology at Lilly: Ended employment in the past 24 months; Foundation Medicine: Current Employment, Current equity holder in publicly-traded company. Danziger:Foundation Medicine: Current Employment. Lee:Foundation Medicine: Current Employment. Lin:Foundation Medicine: Current Employment. Huang:Foundation Medicine: Current Employment. Marcus:Foundation Medicine: Current Employment. Mata:Foundation Medicine: Current Employment.