CNS Embryonal tumors
type: Dataset
description: The dataset represents a total of 58 DNA samples from 16 male and 12 female pediatric patients affected with embryonal central nervous system tumors. The samples were subject to whole genome sequencing, WGS, [48 samples, (representing 12 male and 11 female individuals)] and whole exome sequencing, WES, [10 samples, (representing 4 male and 1 female individuals)]. One tumor tissue sample and one peripheral blood sample were analyzed from each of 26 patients, whereas two tumor tissue samples and one peripheral blood sample were analyzed from two patients. The WGS samples were sequenced 2x150 bp paired-end on an Illumina HiSeqX v2.5 instrument, and the WES samples were sequenced 2x100 bp paired-end on an Illumina HiSeq 2500 instrument. The FASTQ files generated were aligned to the human reference genome sequence GRCh38/hg38 using bwa-mem, with the ALT-aware option turned on. Sorting of reads and marking of PCR duplicates was performed with GATK. Base quality score recalibration and joint realignment of reads around insertions and deletions (indels) were conducted using GATK tools. The dataset consists of 58 files in the CRAM format (lossless compression) with a total file size of ~8,8 TB. All CRAM files but one, are derived from one sequence run and one sample. P4551_227N_P4552_112N is a CRAM file where 2 sequence runs (P4551_227N and P4552_112N) from peripheral blood samples from the same individual, P019, were aligned into one single CRAM file. Additional genomic and molecular data (FASTQ, BAM, IDAT, and VCF files) and limited clinical data can be requested by ethically approved projects conducting research in the field of pediatric cancer. This dataset is one of 3 datasets included in the study "A Combined Omics and Tissue Biobank for Paediatric Cancers" (http://identifiers.org/ega.study:EGAS50000000209).
conditions of access: https://publications.europa.eu/resource/authority/access-right/NON_PUBLIC
conditions of access: info:eu-repo/semantics/restrictedAccess
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: The Swedish Childhood Tumour Biobank
creator: Karolinska Institutet
date modified: 2024-02-22
date published: 2024-02-22
language: English
is part of: http://identifiers.org/ega.study:EGAS50000000209
keywords: Genetics and Genomics
  type: DefinedTerm
  term code: 10609
keywords: health
keywords: genomics
keywords: cancer
keywords: biobank
keywords: children
keywords: tumour
publisher: Karolinska Institutet
version: 0

PropertyValue
property ID: PURL
value: http://identifiers.org/ega.dataset:EGAD50000000298

English
type: Language
alternate name: eng

Karolinska Institutet
type: Organization