The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden.
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Díaz de Ståhl T, Shamikh A, Mayrhofer M, Juhos S, Basmaci E, Prochazka G, Garcia M, Somarajan PR, Zielinska-Chomej K, Illies C, Øra I, Siesjö P, Sandström P, Stenman J, Sabel M, Gustavsson B, Kogner P, Pfeifer S, Ljungman G, Sandgren J, Nistér M
J Transl Med 21 (1) 342 [2023-05-23; online 2023-05-23]
The Swedish Childhood Tumor Biobank (BTB) is a nonprofit national infrastructure for collecting tissue samples and genomic data from pediatric patients diagnosed with central nervous system (CNS) and other solid tumors. The BTB is built on a multidisciplinary network established to provide the scientific community with standardized biospecimens and genomic data, thereby improving knowledge of the biology, treatment and outcome of childhood tumors. As of 2022, over 1100 fresh-frozen tumor samples are available for researchers. We present the workflow of the BTB from sample collection and processing to the generation of genomic data and services offered. To determine the research and clinical utility of the data, we performed bioinformatics analyses on next-generation sequencing (NGS) data obtained from a subset of 82 brain tumors and patient blood-derived DNA combined with methylation profiling to enhance the diagnostic accuracy and identified germline and somatic alterations with potential biological or clinical significance. The BTB procedures for collection, processing, sequencing, and bioinformatics deliver high-quality data. We observed that the findings could impact patient management by confirming or clarifying the diagnosis in 79 of the 82 tumors and detecting known or likely driver mutations in 68 of 79 patients. In addition to revealing known mutations in a broad spectrum of genes implicated in pediatric cancer, we discovered numerous alterations that may represent novel driver events and specific tumor entities. In summary, these examples reveal the power of NGS to identify a wide number of actionable gene alterations. Making the power of NGS available in healthcare is a challenging task requiring the integration of the work of clinical specialists and cancer biologists; this approach requires a dedicated infrastructure, as exemplified here by the BTB.
Bioinformatics Long-term Support WABI [Collaborative]
Bioinformatics Support for Computational Resources [Service]
Bioinformatics Support, Infrastructure and Training [Collaborative]
NGI Short read [Collaborative]
NGI Stockholm (Genomics Production) [Collaborative]
NGI Uppsala (SNP&SEQ Technology Platform) [Service]
National Genomics Infrastructure [Collaborative]
PubMed 37221626
DOI 10.1186/s12967-023-04178-4
Crossref 10.1186/s12967-023-04178-4
pmc: PMC10204274
pii: 10.1186/s12967-023-04178-4