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ICGC PedBrain: Deep-sequencing of childhood brain tumors.

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.

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 Illumina Genome Analyzer IIx Illumina HiSeq 2000 206
EGAD00001000327 Illumina Genome Analyzer IIx Illumina HiSeq 2000 70
EGAD00001000328 Illumina HiSeq 2000 28
EGAD00001000697 Illumina Genome Analyzer IIx Illumina HiSeq 2000 90
EGAD00001000699 Illumina HiSeq 2000 78
EGAD00001001620 Illumina HiSeq 2000 45
EGAD00001001621 Illumina HiSeq 2000 31
EGAD00001001624 Illumina HiSeq 2000 188
EGAD00001001625 Illumina Genome Analyzer IIx Illumina HiSeq 2000 209
EGAD00001001630 Illumina HiSeq 2000 108
EGAD00001001847 Illumina HiSeq 2000 1
EGAD00001001891 Illumina HiSeq 2000 10
EGAD00001003127 482
EGAD00001003128 35
EGAD00001003279 Illumina HiSeq 2000 171
Publications Citations
Dissecting the genomic complexity underlying medulloblastoma.
Nature 488: 2012 100-105
567
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.
Nature 511: 2014 428-434
369
A cell-based model system links chromothripsis with hyperploidy.
Mol Syst Biol 11: 2015 828
67
Active medulloblastoma enhancers reveal subgroup-specific cellular origins.
Nature 530: 2016 57-62
223
NRL and CRX Define Photoreceptor Identity and Reveal Subgroup-Specific Dependencies in Medulloblastoma.
Cancer Cell 33: 2018 435-449.e6
37
Proteomic analysis of Medulloblastoma reveals functional biology with translational potential.
Acta Neuropathol Commun 6: 2018 48
25
TelomereHunter - in silico estimation of telomere content and composition from cancer genomes.
BMC Bioinformatics 20: 2019 272
43
Germline microsatellite genotypes differentiate children with medulloblastoma.
Neuro Oncol 22: 2020 152-162
2
The long noncoding RNA lnc-HLX-2-7 is oncogenic in Group 3 medulloblastomas.
Neuro Oncol 23: 2021 572-585
19
The long non-coding RNA <i>SPRIGHTLY</i> and its binding partner PTBP1 regulate exon 5 skipping of <i>SMYD3</i> transcripts in group 4 medulloblastomas.
Neurooncol Adv 4: 2022 vdac120
4
The oncogenic circular RNA circ_63706 is a potential therapeutic target in sonic hedgehog-subtype childhood medulloblastomas.
Acta Neuropathol Commun 11: 2023 38
1
Group-specific cellular metabolism in Medulloblastoma.
J Transl Med 21: 2023 363
1
Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN.
Nat Commun 14: 2023 3936
4
The Role of the Dysregulation of Long Non-Coding and Circular RNA Expression in Medulloblastoma: A Systematic Review.
Cancers (Basel) 15: 2023 4686
0
Childhood cancer mutagenesis caused by transposase-derived PGBD5.
Sci Adv 10: 2024 eadn4649
0