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

Introduction: Targeted therapies are important in the treatment of B- and T-cell acute lymphoblastic leukemia (ALL), particularly for BCR::ABL1 or BCR::ABL1-like B-ALL, which can be treated with tyrosine kinase inhibitors. B-ALL and T-ALL are both characterized by recurrent gene rearrangements, including subtype-defining rearrangements for B-ALL defined by the 5th edition of WHO classification. BCR::ABL1-like B-ALL is characterized by more than dozens of different gene translocations, some of which are cryptic when visualized by karyotyping, posing challenges for their detection by conventional cytogenetics studies. Furthermore, NCCN guidelines recommend that the risk stratification of B-ALL incorporates specific gene rearrangements, as well as TP53, IKZF1, and PAX5 alteration status. For T-ALL, NCCN recommends determination of mutations in NRAS, KRAS, PTEN, NOTCH1, and FBXW7. CGP using next-generation sequencing (NGS) facilitates the simultaneous interrogation of many genes and a variety of alteration types in a single assay. We describe the molecular landscape of a large ALL cohort tested on the FoundationOne Heme (F1H) assay, highlighting the clinical utility of CGP with F1H in patient 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 diagnoses of ALL 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 the submitted test requisition forms, hematopathology reports, and accompanying H&E or Wright Giemsa-stained slides.

Results: A total of 2,637 unique ALL patient samples were included, comprising 75% B-ALL and 25% T-ALL cases, including 24% peripheral blood, 53% bone marrow aspirate, and 23% formalin-fixed, paraffin-embedded (FFPE) samples. The median age was 23 years (range <1 to >89) and 59% of the patients were male, 41% were female. A majority of samples harbored pathogenic genomic alterations with diagnostic, prognostic, or therapeutic significance. Mutations were detected in NRAS (14% of cases), TP53 (13%), KRAS (15%), NOTCH1 (10%), FBXW7 (4%), and PTEN (2%). PAX5 alterations were detected in 8% of cases. Homozygous gene deletions were detected in CDKN2A (30%), CDKN2B (24%), and IKZF1 (6%). Commonly detected rearrangements included BCR::ABL1 (12%), ETV6::RUNX1 (5%), KMT2A (5%), CRLF2 (4%, mostly P2RY8::CRLF2), TCF3::PBX1 (2%), other ABL1/ABL2 (1.5%), JAK2 (1.5%), IGH::EPOR (<1%), TCF3::HLF (<1%), and MYC (<1%), some of which facilitated the diagnosis of BCR::ABL1-like B-ALL. A diversity of rearrangement partners was detected, many of which would be challenging and time consuming to characterize using conventional fluorescence in situ hybridization (FISH) studies with break-apart probes.

Conclusions: This analysis of 2,637 samples comprising a variety of molecular subtypes of ALL demonstrated that the F1H assay detects pathogenic genomic alterations with diagnostic, prognostic, and therapeutic significance. As both the treatment landscape and disease classification system in ALL have continued to evolve over time, CGP assays such as F1H can play a critical role in clinical decision making by simultaneously assessing the presence and absence of numerous actionable genomic alterations and biomarkers with a single assay.