ALLCatchR, a machine-learning classifier identifies now 20 T-ALL subtypes across cohorts and age groups

T cell acute lymphoblastic leukemia (T-ALL) comprises molecular diverse subtypes, currently lacking robust cross-cohort validations and operational gene expression definitions. To establish a gene expression anchored framework for T-ALL subtyping, we aggregated 2,314 transcriptomes (15 cohorts, age: 0.8 to 90.8 years). An extended unsupervised approach defined 17 main clusters and 3 sub-clusters in high blast fraction samples. Supervised analysis added an overarching immature ETP-like definition and resolved the LMO2{gamma}{delta} -like subtype. All clusters were populated by samples from at least two cohorts. Characteristic genomic driver enrichment agreed across cohorts, while gene expression clusters did not correspond exclusively to single driver events but also reflected developmental origins. A machine learning classifier based on ALLCatchR - our B-ALL classifier - identified these 21 transcriptomic definitions with 0.995-1.0 accuracy in a validation set (n=203). Testing the classifier on a hold-out data set (n=265 samples) showed that 92.7% of predictions matched with corresponding driver alterations. Across all samples, 88.5% of cases were high-confidence, 6.5% candidate predictions and 5.0% remained unclassified, largely due to low blast fractions. We identified a novel gene expression cluster markedly enriched (P<0.001) for clonal hematopoiesis mutations (IDH2 R140Q, DNMT3A) and a stem-/progenitor cell-like gene expression. This novel clonal hematopoiesis-related T-ALL subtype was observed in six cohorts representing 8.9% of adults and 39.5% of patients aged >50 years. We advanced ALLCatchR, a free R package which now enables B- /T- lineage separation, gene-expression subtyping, blast estimation, and developmental annotation to harmonize T-ALL classification across studies and clinical contexts. Visual Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/697268v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@19f60a5org.highwire.dtl.DTLVardef@821873org.highwire.dtl.DTLVardef@113339dorg.highwire.dtl.DTLVardef@1a1b307_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIEstablished on 2,314 T-ALL transcriptomes, ALLCatchR now assigns 20 RNA-Seq subtypes and their developmental underpinnings across ages. C_LIO_LIClonal hematopoiesis related T-ALL (DNMT3A, IDH2 R140Q) defines an immature gene expression cluster in [~]40% of patients >50 years. C_LI