ICGC PedBrain: Deep-sequencing of childhood brain tumors.

Study ID	Alternative Stable ID	Type
EGAS00001000215		Whole Genome Sequencing

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.

Dataset ID	Description	Technology	Samples
EGAD00001000122	DATA_SET_ICGC_PedBrainTumor_Medulloblastoma DATA_SET_ICGC_PedBrainTumor_Medulloblastoma	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	206
EGAD00001000327	release_2: ICGC PedBrain: whole genome mate-pair sequencing release_2: ICGC PedBrain: whole genome mate-pair sequencing	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	70
EGAD00001000328	ICGC PedBrain: RNA sequencing 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 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 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 release_2: ICGC PedBrain: RNA sequencing	Illumina HiSeq 2000	45
EGAD00001001621	release_2: ICGC PedBrain: ChIP-Seq release_2: ICGC PedBrain: ChIP-Seq	Illumina HiSeq 2000	31
EGAD00001001624	release_2: ICGC PedBrain: whole exome sequencing and Target-Seq release_2: ICGC PedBrain: whole exome sequencing and Target-Seq	Illumina HiSeq 2000	188
EGAD00001001625	release_2: ICGC PedBrain: whole genome sequencing release_2: ICGC PedBrain: whole genome sequencing	Illumina Genome Analyzer IIx,Illumina HiSeq 2000	209
EGAD00001001630	release_2: ICGC PedBrain: whole genome bisulfite sequencing 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 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 Whole genome bisulfite sequencing of pedbrain - medulloblastoma	Illumina HiSeq 2000	10
EGAD00001003127	WGS data of medulloblastoma tumor/control pairs. WGS data of medulloblastoma tumor/control pairs.		482
EGAD00001003128	Exome sequencing data for medulloblastoma tumor/control pairs Exome sequencing data for medulloblastoma tumor/control pairs		35
EGAD00001003279	RNA sequencing data for 170 medulloblastoma tumor samples RNA sequencing data for 170 medulloblastoma tumor samples	Illumina HiSeq 2000	171

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

EGAD00001000328

ICGC PedBrain: RNA sequencing

Illumina HiSeq 2000

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

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

EGAD00001001620

release_2: ICGC PedBrain: RNA sequencing

Illumina HiSeq 2000

EGAD00001001621

release_2: ICGC PedBrain: ChIP-Seq

Illumina HiSeq 2000

EGAD00001001624

release_2: ICGC PedBrain: whole exome sequencing and Target-Seq

Illumina HiSeq 2000

188

EGAD00001001625