Genome-driven molecular stratification and clinical impact in pediatric solid tumors: Results from the STREAM program

The STREAM (Strategic TREatment And Magic for pediatric cancers) program, launched in March 2023, is a nation-wide precision-medicine platform for paediatric solid tumours and, unlike prior WGS studies centred on relapsed or high-risk disease, predominantly captures newly diagnosed patients. The programme integrates tumour-germline whole-genome sequencing, transcriptome and methylome profiling, in-vitro drug-response testing, centralised pathology review and multidisciplinary interpretation. Among 308 patients, somatic drivers were identified in 253 (82.1%), totalling 1,082 events across 404 genes. Pathogenic germline variants occurred in 32 of 303 evaluable patients (10.4%). Genomic profiling refined diagnosis in 85 cases, informed prognostic stratification in 20 and revealed 117 actionable targets across 99 patients. In-vitro drug screening from 58 patients yielded 496 sensitive and 1,376 resistant drug-tumour interactions. The genomic landscape showed lower mutational burden than adult cancers and was dominated by key pathways in cell-fate commitment, organ development and cell-cycle control. Using driver-gene alterations mapped to curated signalling programmes, we performed unsupervised clustering, identifying ten molecular sub-clusters. Several represented biologically coherent groups not captured by morphology: MAPK-driven pilocytic astrocytoma, Langerhans-cell histiocytosis and PLNTY formed one cluster; atypical teratoid/rhabdoid tumour and supratentorial ependymoma aligned through shared cell-cycle and epigenetic dysregulation; and medulloblastoma segregated into WNT, SHH and heterogeneous Group 3-4, the latter marked by SBS39 exposure linked to homologous-recombination deficiency. For prognostic evaluation, we analysed primary-diagnosis solid tumours (n=185), excluding relapse samples and haematologic malignancies. Survival differed significantly across clusters (OS p=0.0071). Cluster 6, composed mainly of Ewing sarcoma and rhabdomyosarcoma with growth-factor-receptor and secondary-signalling alterations, showed the highest mortality and relapse frequency and was the only group with a reached median OS. Clusters 2, 7 and 9 showed no deaths; Cluster 2 comprised Hedgehog-dominant medulloblastoma and related fibro-osseous tumours; Cluster 7 consisted of Group 3-leaning medulloblastoma and DNA-repair-altered tumours; and Cluster 9 included proliferative-signal-driven sarcomas and neuroblastoma, with no relapses observed. These molecular subgroups also showed strong concordance with in-vitro drug-response patterns. In this nation-wide cohort, molecular sub-clustering enhances diagnostic resolution, reveals pathway-defined biology missed by morphology and provides clinically meaningful prognostic stratification.