Retinoblastoma was one of the first malignant tumors to be described as a genetic disease and its development occurs from the loss of function of the retinoblastoma gene (RB1). The difficulty in accessing the tumor during diagnosis highlights the need for non-invasive diagnostic methods. Studies have shown that liquid biopsy, obtained from any fluid material in the body, for example blood, contains free tumor cells and free and circulating DNA or RNA, making it a convenient tool for diagnosis and prognosis during cancer treatment without the need for invasive procedures. Taking advantage of these events, given this situation, we investigated molecular alterations in samples from retinoblastoma cases, using the NGS strategy as a powerful tool for characterization and aid in diagnosis and prognosis. Genomic data from 76 patients diagnosed with retinoblastoma, comprising 162 samples, tumor (TU), aqueous humor (AH), and peripheral blood (PB), were analyzed using the Oncomine Childhood Cancer Research Panel (OCCRA^®). A total of 22 altered genes were detected, and 54 variants. Of the 76 cases, 29 included paired tumor (TU), aqueous humor (AH), and peripheral blood (PB) samples from the same patient. Alterations in the RB1 gene were detected in 16 of these 29 cases, with concordant alterations identified across all three sample types in three patients. In 12 out of 29 patients, the same genetic alteration was found in both TU and AH. In conclusion, the OCCRA panel enabled the detection, in different samples, of molecular alterations in the RB1 gene, as well as CNAs in the MYCN, ABL2, and MDM4 genes. Limitations of AH were observed, primarily due to the small volume of material available and the consequently low concentration of cell-free DNA (cfDNA). However, as AH provides a viable alternative for analyzing tumors, inaccessible to traditional biopsy methods, liquid biopsy holds significant potential to improve diagnostic accuracy and guide treatment strategies in retinoblastoma cases.

Retinoblastoma (RB) is the most common intraocular malignancy of childhood, yet molecular assessment of disease dissemination and minimal residual disease (MRD) remains challenging due to the contraindication of intraocular biopsy. Here, we evaluate the feasibility of cell-free RNA (cfRNA)- and circulating tumor cell RNA (ctcRNA)-based liquid biopsy for the sensitive detection of disseminated retinoblastoma using digital PCR (dPCR) targeting the retina-specific markers CRX and RBP3. We analyzed 433 bone marrow (BM), peripheral blood (PB) and cerebrospinal fluid (CSF) samples collected longitudinally from 50 patients with RB. dPCR assays demonstrated high analytical sensitivity. cfRNA detection showed complete sensitivity and negative predictive value in bone marrow compared with myelogram analysis, frequently identifying molecular positivity in cytologically negative samples. In cerebrospinal fluid, cfRNA detection was highly specific but less sensitive, reflecting compartment-specific biological constraints. Longitudinal analysis revealed that changes in CRX and RBP3 ctcRNA levels closely tracked treatment response, preceded cytological evidence of bone marrow involvement in several cases, and identified molecular persistence or re-emergence during follow-up, including after hematopoietic stem cell transplantation. Together, these findings demonstrate that cfRNA- and ctcRNA-based liquid biopsy using CRX and RBP3 enables sensitive and dynamic detection of disseminated retinoblastoma, particularly in bone marrow, and supports its potential utility for MRD monitoring. Longitudinal patient analyses will be required to define prognostic thresholds and establish the clinical role of this approach in risk stratification and long-term surveillance.

Soft tissue sarcomas (STSs) are a heterogeneous group of rare mesenchymal malignancies with overlapping morphological and immunohistochemical features, often making definitive diagnosis challenging. Recent advances in next-generation sequencing (NGS) have enabled the identification of recurrent molecular alterations that contribute to tumor classification, prognostic stratification, and precision oncology approaches. This retrospective study aimed to evaluate the diagnostic and clinical impact of molecular profiling in pediatric soft tissue sarcomas using the Oncomine Childhood Cancer Research Assay (OCCRA) panel. Fifty-five frozen tumor samples representing 24 distinct soft tissue sarcoma subtypes were obtained from the Pediatric Oncology Institute -IOP/GRAACC/UNIFESP Biobank (B-053). Molecular analysis was performed using NGS to identify gene fusions, single nucleotide variants (SNVs), copy number variations (CNVs), and insertions/deletions (InDels). Clinically relevant molecular alterations were identified in 70% (37/55) of cases, including 18 fusion transcripts, 13 SNVs, 8 CNVs, and 6 InDels. Recurrent and diagnostically relevant alterations included BCOR::CCNB3, ASPSCR1::TFE3, NFR1::BRAF, FUS::DDIT3, EML4::NTRK3, ETV6::NTRK3, CIC::DUX4, NAB2::STAT6 and SS18::SSX1/2 fusions, as well as amplifications involving PDGFRA, FGFR1, GLI1, CDK4, ERBB3, and KIT. Pathogenic variants affecting genes involved in tumor suppression and chromatin remodeling, including TP53, NF1, DICER1, SMARCA4, PTEN, and PIK3CA, were also detected. Importantly, molecular profiling had significant diagnostic impact in several histologically ambiguous tumors, enabling molecular reclassification and refinement of previously inconclusive or inaccurate pathological diagnoses. In multiple cases, NGS transformed descriptive histopathological interpretations into genetically defined sarcoma entities, including NTRK-rearranged spindle cell neoplasms, CIC-rearranged sarcomas, synovial sarcoma, low-grade fibromyxoid sarcoma, and clear cell sarcoma. Furthermore, the identification of actionable alterations highlighted potential opportunities for targeted therapies and precision medicine approaches. Our findings demonstrate that comprehensive molecular profiling significantly enhances diagnostic accuracy in pediatric soft tissue sarcomas, particularly in morphologically challenging cases. The integration of NGS into routine sarcoma diagnostics enables biologically informed tumor classification and supports personalized therapeutic strategies.

Oncocytic thyroid carcinomas are characterized by a unique chromosomal landscape and frequent resistance to radioactive iodine therapy, underscoring the need for improved molecular characterization. Although ALK rearrangements, particularly STRN::ALK fusions, have been described in thyroid carcinomas, their biological and clinical significance in oncocytic thyroid neoplasms remains unclear. This study investigated STRN exon 3- ALK exon 20-derived transcripts in 56 oncocytic thyroid neoplasms using RT-PCR, followed by cloning and Sanger sequencing of positive cases. Transcript-positive cases were further evaluated by fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and in silico structural modeling. STRN :: ALK -derived transcripts were detected in 9 of 56 tumors; however, their frequency reflected the combined detection of distinct transcript architectures. Only 2 of 56 tumors (3.6%) harbored canonical in-frame STRN :: ALK fusions, whereas 7 of 56 tumors (12.5%) contained noncanonical out-of-frame variants. Although ALK rearrangement by FISH was confirmed in all transcript-positive tumors irrespective of transcript architecture, detectable ALK protein expression by IHC was observed only in tumors harboring canonical in-frame fusions, whereas all noncanonical variants lacked detectable ALK protein expression. Structural modeling was concordant with these observations, suggesting preservation of kinase-domain features in canonical fusions and predicted disruption in noncanonical variants. Overall, STRN::ALK transcripts in oncocytic thyroid neoplasms exhibit marked architectural heterogeneity with distinct ALK protein expression patterns. ALK FISH-positive/IHC-negative cases should be interpreted cautiously, as they may not represent biologically equivalent ALK-driven neoplasia, with uncertain therapeutic relevance. Integrated molecular and protein-level assessment may support interpretation of ALK alterations in oncocytic thyroid neoplasms.