Despite substantial progress in treating primary childhood malignancies, accurate classification of some entities at the time of diagnosis and relapses from high-risk entities remain major clinical challenges. To this end, we have developed two programs on a national level addressing these topics, namely Molecular Neuropathology 2.0 (MNP2.0) for the accurate classification of CNS tumors and the INFORM registry study (INdividualized therapy FOr Relapsed Malignancies in Childhood), which attempts to rapidly generate personalized tumor profiles and identify therapeutic targets in a clinical diagnostic environment for relapse patients.
In MNP2.0, DNA methylation fingerprints, which are thought to closely reflect the cell of origin, are used to accurately classify brain tumors into biologically and clinically meaningful subgroups. Amongst a total of 9000 analyzed CNS tumor specimens, we have established a reference set of 2200 samples with very good histopathological and clinical annotation covering 70 different entities and subgroups. This reference is now used for an individual sample as a comparison to identify the class with the best fit. A web interface to make this reference dataset available to the community is currently being built. First evidence from ~800 diagnostic cases within the MNP2.0 study suggests that in about 10% of cases the histopathological diagnosis will be changed in a way that affects clinical management of the patient. In about an additional 20% of cases, the diagnosis is refined by revealing a meaningful subgroup that cannot be established by conventional neuropathology alone (e.g., molecular subgroup of medulloblastoma or ependymoma). Ongoing round robin experiments with other centers indicate that the methodology is very robust and it is very well feasible to establish this diagnostic pipeline at other centers. In 2015, a pilot study is starting, which will enable all pediatric brain tumor patients across Germany to benefit from this new diagnostic aid.
The INFORM pilot phase assessed the feasibility of integrating rapid molecular profiling in the clinical management of pediatric cancer patients with progressive or relapsed high-risk malignancies. Whole-exome and low-coverage whole-genome sequencing was performed on tumor and normal DNA, complemented with matched tumor RNA sequencing (Illumina HiSeq2500, ‘rapid’ mode). 57 pilot patients (average age 13 years) were enrolled from 20 centers throughout Germany in the INFORM pilot phase. Tumor tissue was sufficient for DNA analysis of 52 cases and RNA-seq of 47. The average turnaround time from tissue arrival to molecular results was 25 days. Actionable targets with at least ‘borderline’ evidence (according to a prioritization score harmonized with the other major pediatric precision oncology programs across Europe) were identified in 28 patients (49%). Based on the findings, targeted therapeutics were incorporated in the treatment regime of several patients, with anecdotal reports of marked responses.