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Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk paediatric cancer

Zero Childhood Cancer is a precision medicine program to benefit children with poor-outcome, rare, relapsed or refractory cancer. Utilising tumour and germline whole genome sequencing (WGS) and RNA sequencing (RNAseq) across 252 tumours from high-risk paediatric cancer patients, we identified 968 reportable molecular aberrations (39.9% in WGS and RNAseq, 35.1% WGS-only, 25.0% RNAseq-only). 93.7% of patients had at least one germline or somatic aberration, 71.4% had therapeutic targets and 5.2% had a change in diagnosis. WGS identified pathogenic cancer-predisposing variants in 16.2% of patients. In 76 CNS tumours, methylome analysis confirmed diagnosis in 71.1% and contributed to a change of diagnosis in two cases (2.6%). To date 43 patients have received a recommended therapy, 38 of whom could be evaluated. A small but encouraging proportion of 31% showed some evidence of clinical benefit. Comprehensive molecular profiling resolved the molecular basis of virtually all high-risk cancers, which in some cases has significant clinical impact.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001006876 NextSeq 500 226
EGAD00001006902 HiSeq X Ten 480
EGAD00001006906 500
EGAD00001006907 500
EGAD00001006908 252
EGAD00001006909 76
EGAD00001006910 247
EGAD00001008358 HiSeq X Ten NextSeq 500 94
Publications Citations
Diffuse leptomeningeal glioneuronal tumour (DLGNT) in children: the emerging role of genomic analysis.
Acta Neuropathol Commun 9: 2021 147
In vitro and in vivo drug screens of tumor cells identify novel therapies for high-risk child cancer.
EMBO Mol Med 14: 2022 e14608
Diagnostic classification of childhood cancer using multiscale transcriptomics.
Nat Med 29: 2023 656-666
A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer.
Genome Med 15: 2023 20
High-Throughput Drug Screening of Primary Tumor Cells Identifies Therapeutic Strategies for Treating Children with High-Risk Cancer.
Cancer Res 83: 2023 2716-2732