Implementation of a Comprehensive Multi-level Molecular Strategy for the Identification of Genetic Alterations in Pediatric Solid Tumors Aimed at Achieving a Personalized Approach to the Patient

Background: In Argentina, central nervous system (CNS) solid tumors (19%) and non-CNS solid tumors (25%) account for 44% of pediatric tumors. The new World Health organization (WHO) 2016 classification, which includes genomic characterization, comprises more than 100 CNS tumor entities and subclasses. In children, glial lineage tumors (gliomas) are the most frequent and comprise astrocytomas, ependymomas and oligodendroglioma, while embryonal CNS tumors are a heterogeneous group of WHO grade IV tumors. Pediatric soft tissue tumors (STT) present difficulties for accurate diagnosis since their morphological and immunophenotypic features overlap among the different histological patterns.

The emergence of new molecular techniques has generated a great advance in the field of solid tumors, particularly in the molecular definition of groups of patients. This fact makes tailor-made treatment feasible, according to the biology of the tumor.

In particular, in children, the identification of treatment targets is especially important since it may avoid unnecessary sequel in a growing child. This project allows the articulation between basic and clinical research groups, thus consolidating the objective of basic translational research and generating both clinical and basic knowledge about the pathogenesis of pediatric solid tumors in our country.

Aim: To standardize and implement a comprehensive multi-level molecular strategy, using medium and high complexity techniques, for the detection of molecular alterations in primary pediatric solid tumors (neuroblastoma, rhabdomyosarcoma, Ewing sarcoma family tumors, soft tissue sarcomas and CNS tumors (gliomas and embryonal)), that can be applied to the diagnosis, prognosis and/or use of targeted therapies against molecular targets in order to provide a tailored therapeutic opportunity.

Material and methods: Pediatric cases of solid tumors will be enrolled prospectively. Based on the statistics of the participating centers, 100 samples will be included. From each case, a formalin fixed biopsy will be available and when possible, a fragment will also be preserved at -70ºC. Clinical and follow-up data will be obtained from the clinical records.

The methodological approaches include: 1) Immunohistochemical detection of tumor lineage determinant markers, some of them with predictive value. 2) FISH (fluorescence in situ hybridization) with break-apart strategy for genes involved in recurrent chromosomal translocations and locus-specific design probes for other unbalanced structural chromosomal structural alterations (amplifications and deletions of genes or chromosomal segments). 3) Real time (RT)-polymerase chain reaction (PCR) detection of fusion transcripts resulting from chromosomal translocations. 4) Quantitative polymerase chain reaction (qPCR) and Sanger sequencing analysis of single nucleotide polymorphisms (SNPs) as targets for therapy. 5) Sanger sequencing analysis of fusions, ins/del as a complement to RT-PCR or FISH (fluorescence in situ hybridization), 6) Next Generation Sequencing (NGS) with a specific and customized panel containing all necessary genes to define a tumor´s genomic mutation profile for diagnosis, risk stratification and prognosis of pediatric tumors. However, NGS sequencing will only be applied in those cases which could not be resolved with the previous strategies or cases with poor evolution

Based on the above analyses, an integrated analysis algorithm will be developed according to WHO recommendations, but adapted to the facilities of the institution. Molecular findings will be correlated with clinical and histological data