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The Swedish childhood tumor biobank : systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden

Díaz de Ståhl, Teresita ; Shamikh, Alia ; Mayrhofer, Markus ; Juhos, Szilvester ; Basmaci, Elisa ; Prochazka, Gabriela ; Garcia, Maxime ; Somarajan, Praveen Raj ; Zielinska-Chomej, Katarzyna and Illies, Christopher , et al. (2023) In Journal of Translational Medicine 21(1).
Abstract

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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Biobank, Bioinformatics, Childhood cancer, Genomic, Methylation, Mutation, Next generation sequence
in
Journal of Translational Medicine
volume
21
issue
1
article number
342
publisher
BioMed Central (BMC)
external identifiers
  • pmid:37221626
  • scopus:85159966886
ISSN
1479-5876
DOI
10.1186/s12967-023-04178-4
language
English
LU publication?
yes
id
74d36791-53c9-434d-a95b-45417711cba9
date added to LUP
2023-08-15 12:09:56
date last changed
2024-04-20 00:37:39
@article{74d36791-53c9-434d-a95b-45417711cba9,
  abstract     = {{<p>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.</p>}},
  author       = {{Díaz de Ståhl, Teresita and Shamikh, Alia and Mayrhofer, Markus and Juhos, Szilvester and Basmaci, Elisa and Prochazka, Gabriela and Garcia, Maxime and Somarajan, Praveen Raj and Zielinska-Chomej, Katarzyna and Illies, Christopher and Øra, Ingrid and Siesjö, Peter and Sandström, Per Erik and Stenman, Jakob and Sabel, Magnus and Gustavsson, Bengt and Kogner, Per and Pfeifer, Susan and Ljungman, Gustaf and Sandgren, Johanna and Nistér, Monica}},
  issn         = {{1479-5876}},
  keywords     = {{Biobank; Bioinformatics; Childhood cancer; Genomic; Methylation; Mutation; Next generation sequence}},
  language     = {{eng}},
  number       = {{1}},
  publisher    = {{BioMed Central (BMC)}},
  series       = {{Journal of Translational Medicine}},
  title        = {{The Swedish childhood tumor biobank : systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden}},
  url          = {{http://dx.doi.org/10.1186/s12967-023-04178-4}},
  doi          = {{10.1186/s12967-023-04178-4}},
  volume       = {{21}},
  year         = {{2023}},
}