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Updated: Jun 4, 2026
Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
Clinical implementation of targeted panel sequencing for paediatric tumours: findings and outcomes in a Southeast
Yingting Mok1, Jian Yuan Goh2, Chik Hong Kuick3
1Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Republic of Singapore; Department of Pathology, National University Health System, Singapore, Republic of Singapore; Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Republic of Singapore.
Insights
Targeted sequencing panels are useful for paediatric tumour profiling, especially for central nervous system (CNS) cancers. This molecular profiling identified clinically significant variants in over half of young patients, aiding precision oncology efforts.
Area of Science:
- Oncology
- Genomics
- Molecular Diagnostics
Background:
- Comprehensive genomic profiling (CGP) shows promise for paediatric precision oncology.
- The clinical utility of targeted sequencing panels in routine paediatric cancer care is not well-established.
- Limited data exists on targeted sequencing panel utility in Southeast Asia.
Purpose of the Study:
- To assess the feasibility and clinical utility of the AmpliSeq Childhood Cancer Panel for paediatric tumour profiling.
- To evaluate the yield of clinically significant variants and their impact on diagnosis, therapy, and prognosis.
- To determine the utility of targeted sequencing in guiding precision oncology for paediatric solid tumours in Southeast Asia.
Main Methods:
- Prospective molecular profiling of 130 paediatric patients with solid tumours using the AmpliSeq Childhood Cancer Panel.
- The panel detected single nucleotide variants, gene fusions, and amplifications.
- Clinical impact was assessed via a molecular tumour board.
Main Results:
- Clinically significant variants were identified in 52.8% of patients.
- Variants had diagnostic (52%), therapeutic (30%), and prognostic (18%) relevance.
- Central nervous system (CNS) tumours showed the highest detection rate (70%).
- Seven patients (5.7%) received targeted therapy based on sequencing results.
- The panel was particularly useful for CNS tumours, fusion-driven sarcomas, neuroblastomas, and DICER1-associated tumours.
Conclusions:
- Targeted panel sequencing is a feasible and clinically useful tool for paediatric tumour profiling.
- The highest yield of actionable variants was observed in CNS tumours.
- While direct targeted therapy was limited, the genetic information supports biomarker-directed trials and advancing paediatric precision oncology.
Abstract:
Comprehensive genomic profiling of paediatric tumours has shown promise in guiding precision oncology approaches. However, the clinical utility of targeted sequencing panels in routine practice remains unclear. The results of such testing have not been reported in Southeast Asia. We implemented the AmpliSeq Childhood Cancer Panel for prospective molecular profiling of 130 paediatric patients with various solid tumours. The panel detects single nucleotide variants, gene fusions and amplifications. Clinical impact was assessed through a molecular tumour board. Clinically significant variants were identified in 52.8% of patients, with diagnostic, therapeutic and prognostic relevance in 52%, 30% and 18% of cases, respectively. Central nervous system (CNS) tumours showed the highest yield (70%). Seven patients (5.7%) received targeted therapy based on the sequencing results. The panel was particularly useful for CNS tumours, fusion-driven sarcomas, neuroblastomas and DICER1-associated tumours. Limitations included the need for additional testing in some cases and the inability to distinguish germline from somatic variants. In conclusion, targeted panel sequencing is feasible and clinically useful for paediatric tumour profiling, with the highest yield in CNS tumours. While the proportion of patients receiving targeted therapy was relatively low, the genetic information obtained is valuable for biomarker-directed trials and advancing precision oncology in paediatric cancers.
