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Reason: The sequence data presented in this publication contains sensitive information and cannot be openly shared.

The Swedish Childhood Tumor Biobank: Systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden

posted on 2023-03-16, 15:38 authored by Teresita Díaz de StåhlTeresita Díaz de Ståhl, Alia Shamikh, Markus Mayrhofer, Szilvester Juhos, Elisa Basmaci, Gabriela Prochazka, Maxime Garcia, Praveen Raj Somarajan, Katarzyna Zielinska-Chomej, Karim Katkhada, Jenny von Salomé, Christopher Illies, Ingrid Ora, Peter Siesjö, Per-Erik Sandström, Jakob Stenman, Magnus Sabel, Bengt Gustavsson, Per Kogner, Susan Pfeifer, Gustaf Ljungman, Johanna SandgrenJohanna Sandgren, Monica Nistér


Data Set Description

The dataset consists of whole genome (WGS) and whole exome sequencing (WES) data from 82 biobanked central nervous system (CNS) tumors and patient-matched peripheral blood-derived DNA from 79 affected pediatric patients. The data was generated as part of a study conducted by Díaz de Ståhl, T. et. al., mansucript to be sumitted.

The sequence data presented in this publication contains sensitive information and cannot be openly shared. However, the authors intend to share the data for use in research projects after a medicolegal review and controlled access through FEGA Sweden, which is a national node of the Federated European Genome-phenome Archive (FEGA). FEGA Sweden will be hosted by the National Bioinformatics Infrastructure Sweden (NBIS) at SciLifeLab, and the datasets will be findable through the European Genome-phenome Archive web portal.

The dataset comprises WGS from 137 samples (70 tumors and 67 blood samples) and WES from 24 samples (12 tumors and 12 blood samples) from several diagnoses, including medulloblastomas, ependymomas, glioblastomas/primitive neuroectodermal tumors/embryonal tumors, pilocytic astrocytomas, astrocytoma/glioma, atypical teratoid rhabdoid tumors, oligodendrogliomas, meningiomas, craniopharyngiomas, pineoblastoma, ganglioglioma, pituitary adenoma, choroid plexus tumor, and schwannoma.

The tumor DNA was extracted from fresh frozen tissue, and patient-matched normal DNA was extracted from peripheral blood cells. 

The WGS and WES libraries and associated next-generation sequencing (NGS) were conducted at the Genomic Production Center, SciLifeLab, Stockholm, Sweden. The WGS libraries were prepared using the TruSeq PCR-free (126 samples) or TruSeq Nano, NeoPrep (11 samples) DNA sample preparation kits, followed by paired-end 150 bp read length sequencing on a HiSeq X (Illumina Inc.) instrument. The WES libraries were prepared using the Agilent SureSelect Human All Exon V5 (22 samples) or the Twist Human Core Exome (2 samples) DNA sample preparation kits, followed by paired-end 100 bp read length sequencing on a HiSeq 2500 (Illumina Inc.) instrument.


Terms for access

Access to the pediatric cancer dataset will only be granted to authorized research projects who meet specific ethical and legal criteria and have a clear need for the data. These criteria include adherence to ethical guidelines, such as an ethical permit and obedience to the General Data Protection Regulation (GDPR) It also includes the submission of a research proposal outlining their objectives, methods, and commitment to upholding the highest ethical and legal standards.

The protected pediatric dataset is exclusively available for research projects that require access to pediatric data sets and cannot be achieved using adult data. These projects aim to deepen our understanding of the causes and mechanisms of pediatric cancer, identify new therapeutic targets, and develop more effective treatments for affected children. Our goal is to facilitate meaningful research that contributes to better outcomes for pediatric cancer patients in the future. 


The Swedish Childhood Cancer Fund



Karolinska Institutet

Access request email