Study

ICGC PedBrain: Deep-sequencing of childhood brain tumors.

Study ID Alternative Stable ID Type
EGAS00001000215 Whole Genome Sequencing

Study Description

Brain tumors constitute the childhood tumors with the highest mortality rates and survival is often associated with severe long-term sequelae due to intensive multimodal treatment regimens. Thus, the PedBrainTumor network aims at the identification of robust biomarkers for clinical management and novel molecular targets for therapeutic interventions. Using massively parallel whole-genome sequencing, and transcriptome and methylome sequencing for subsets of cases, we aim to decipher the molecular causes of medulloblastoma as well as low-grade astrocytoma, and to identify markers to stratify patients for specialized treatment. As the PedBrain network is affiliated with clinical trials in medulloblastoma and pilocytic astrocytoma, validation cohorts for the translation of key findings into clinical settings are readily available.

Study Datasets 15 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001000122
DATA_SET_ICGC_PedBrainTumor_Medulloblastoma
Illumina Genome Analyzer IIx,Illumina HiSeq 2000 206
EGAD00001000327
release_2: ICGC PedBrain: whole genome mate-pair sequencing
Illumina Genome Analyzer IIx,Illumina HiSeq 2000 70
EGAD00001000328
ICGC PedBrain: RNA sequencing
Illumina HiSeq 2000 28
EGAD00001000697
Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.
Illumina Genome Analyzer IIx,Illumina HiSeq 2000 90
EGAD00001000699
Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.
Illumina HiSeq 2000 78
EGAD00001001620
release_2: ICGC PedBrain: RNA sequencing
Illumina HiSeq 2000 45
EGAD00001001621
release_2: ICGC PedBrain: ChIP-Seq
Illumina HiSeq 2000 31
EGAD00001001624
release_2: ICGC PedBrain: whole exome sequencing and Target-Seq
Illumina HiSeq 2000 188
EGAD00001001625
release_2: ICGC PedBrain: whole genome sequencing
Illumina Genome Analyzer IIx,Illumina HiSeq 2000 209
EGAD00001001630
release_2: ICGC PedBrain: whole genome bisulfite sequencing
Illumina HiSeq 2000 108
EGAD00001001847
4C-seq data was generated for regions of interest to confirm enhancer-gene promoter interactions
Illumina HiSeq 2000 1
EGAD00001001891
Whole genome bisulfite sequencing of pedbrain - medulloblastoma
Illumina HiSeq 2000 10
EGAD00001003127
WGS data of medulloblastoma tumor/control pairs.
482
EGAD00001003128
Exome sequencing data for medulloblastoma tumor/control pairs
35
EGAD00001003279
RNA sequencing data for 170 medulloblastoma tumor samples
Illumina HiSeq 2000 171

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Publications

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