Abstract
The development of Next-Generation Sequencing (NGS) has provided useful diagnostic, prognostic, and therapeutic strategies for individualized management of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Consequently, NGS is rapidly being established in clinical practice. However, the technology’s complexity, bioinformatics analysis, and the different available options difficult a broad consensus between different laboratories in its daily routine introduction. This collaborative study among Spanish centers was aimed to assess the feasibility, pros, and cons of our customized panel and other commercial alternatives of NGS-targeted approaches. The custom panel was tested in three different sequencing centers. We used the same samples to assess other commercial panels (OncomineTM Childhood Cancer Research Assay; Archer®FusionPlex® ALL, and Human Comprehensive Cancer Panel GeneRead Panel v2®). Overall, the panels showed a good performance in different centers and platforms, but each NGS approach presented some issues, as well as pros and cons. Moreover, a previous consensus on the analysis and reporting following international guidelines would be preferable to improve the concordance in results among centers. Our study shows the challenges posed by NGS methodology and the need to consider several aspects of the chosen NGS-targeted approach and reach a consensus before implementing it in daily practice.
Highlights
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer and the primary cause of death related to cancer in childhood [1,2,3]
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Genome-wide NGS approaches provide a high amount of information and are progressively cheaper, but the complexity in their analysis hampers their use in daily routine
Summary
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer and the primary cause of death related to cancer in childhood [1,2,3]. Global analyses of the entire genome (Whole-Genome Sequencing, WGS) or exome (Whole-Exome Sequencing, WES) are available in research. Still, few of these approaches are offered by clinical laboratories to guide routine clinical practice: they remain expensive, time-consuming, and laborious [7]. We need to incorporate easier and cost-effective targeted sequencing approaches into clinical practice [8]. Library preparation protocols, and enrichment assays to achieve accurate variant calling that enables us to define relevant causative variants, but they offer better base-pair coverage, running times, costs, and easier dataset handling than WGS and WES [9]. There are a plethora of different custom-NGS panels developed by research groups and commercially available panels
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