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.

Type: Whole Genome Sequencing
Archiver: European Genome-Phenome Archive (EGA)

15 Datasets 15 Publications

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

Publications	Citations
Dissecting the genomic complexity underlying medulloblastoma. Jones DT, Jäger N, Kool M, Zichner T, Hutter B, Sultan M, Cho YJ, Pugh TJ, Hovestadt V, Stütz AM, Rausch T, Warnatz HJ, Ryzhova M, Bender S, Sturm D, Pleier S, Cin H, Pfaff E, Sieber L, Wittmann A, Remke M, Witt H, Hutter S, Tzaridis T, Weischenfeldt J, Raeder B, Avci M, Amstislavskiy V, Zapatka M, Weber UD, Wang Q, Lasitschka B, Bartholomae CC, Schmidt M, von Kalle C, Ast V, Lawerenz C, Eils J, Kabbe R, Benes V, van Sluis P, Koster J, Volckmann R, Shih D, Betts MJ, Russell RB, Russell RB, Coco S, Tonini GP, Schüller U, Hans V, Graf N, Kim YJ, Monoranu C, Roggendorf W, Unterberg A, Herold-Mende C, Milde T, Kulozik AE, von Deimling A, Witt O, Maass E, Rössler J, Ebinger M, Schuhmann MU, Frühwald MC, Hasselblatt M, Jabado N, Rutkowski S, von Bueren AO, Williamson D, Clifford SC, McCabe MG, Collins VP, Wolf S, Wiemann S, Lehrach H, Brors B, Scheurlen W, Felsberg J, Reifenberger G, Northcott PA, Taylor MD, Meyerson M, Pomeroy SL, Yaspo ML, Korbel JO, Korshunov A, Eils R, Pfister SM, Lichter P. Nature 488: 2012 100-105	577
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM. Nature 511: 2014 428-434	386
A cell-based model system links chromothripsis with hyperploidy. Mardin BR, Drainas AP, Waszak SM, Weischenfeldt J, Isokane M, Stütz AM, Raeder B, Efthymiopoulos T, Buccitelli C, Segura-Wang M, Northcott P, Pfister SM, Lichter P, Ellenberg J, Korbel JO. Mol Syst Biol 11: 2015 828	71
Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Lin CY, Erkek S, Tong Y, Yin L, Federation AJ, Zapatka M, Haldipur P, Kawauchi D, Risch T, Warnatz HJ, Worst BC, Ju B, Orr BA, Zeid R, Polaski DR, Segura-Wang M, Waszak SM, Jones DT, Kool M, Hovestadt V, Buchhalter I, Sieber L, Johann P, Chavez L, Gröschel S, Ryzhova M, Korshunov A, Chen W, Chizhikov VV, Millen KJ, Amstislavskiy V, Lehrach H, Yaspo ML, Eils R, Lichter P, Korbel JO, Pfister SM, Bradner JE, Northcott PA. Nature 530: 2016 57-62	230
NRL and CRX Define Photoreceptor Identity and Reveal Subgroup-Specific Dependencies in Medulloblastoma. Garancher A, Lin CY, Morabito M, Richer W, Rocques N, Larcher M, Bihannic L, Smith K, Miquel C, Leboucher S, Herath NI, Dupuy F, Varlet P, Haberler C, Walczak C, El Tayara N, Volk A, Puget S, Doz F, Delattre O, Druillennec S, Ayrault O, Wechsler-Reya RJ, Eychène A, Bourdeaut F, Northcott PA, Pouponnot C. Cancer Cell 33: 2018 435-449.e6	39
Proteomic analysis of Medulloblastoma reveals functional biology with translational potential. Rivero-Hinojosa S, Lau LS, Stampar M, Staal J, Zhang H, Gordish-Dressman H, Northcott PA, Pfister SM, Taylor MD, Brown KJ, Rood BR. Acta Neuropathol Commun 6: 2018 48	25
TelomereHunter - in silico estimation of telomere content and composition from cancer genomes. Feuerbach L, Sieverling L, Deeg KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Mughal SS, Chudasama P, Glimm H, Scholl C, Lichter P, Fröhling S, Pfister SM, Jones DTW, Rippe K, Brors B. BMC Bioinformatics 20: 2019 272	49
Germline microsatellite genotypes differentiate children with medulloblastoma. Rivero-Hinojosa S, Kinney N, Garner HR, Rood BR. Neuro Oncol 22: 2020 152-162	2
The long noncoding RNA lnc-HLX-2-7 is oncogenic in Group 3 medulloblastomas. Katsushima K, Lee B, Kunhiraman H, Zhong C, Murad R, Yin J, Liu B, Garancher A, Gonzalez-Gomez I, Monforte HL, Stapleton S, Vibhakar R, Bettegowda C, Wechsler-Reya RJ, Jallo G, Raabe E, Eberhart CG, Perera RJ. Neuro Oncol 23: 2021 572-585	24
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. Lee B, Katsushima K, Pokhrel R, Yuan M, Stapleton S, Jallo G, Wechsler-Reya RJ, Eberhart CG, Ray A, Perera RJ. Neurooncol Adv 4: 2022 vdac120	7
The oncogenic circular RNA circ_63706 is a potential therapeutic target in sonic hedgehog-subtype childhood medulloblastomas. Katsushima K, Pokhrel R, Mahmud I, Yuan M, Murad R, Baral P, Zhou R, Chapagain P, Garrett T, Stapleton S, Jallo G, Bettegowda C, Raabe E, Wechsler-Reya RJ, Eberhart CG, Perera RJ. Acta Neuropathol Commun 11: 2023 38	3
Group-specific cellular metabolism in Medulloblastoma. Funke VLE, Walter C, Melcher V, Wei L, Sandmann S, Hotfilder M, Varghese J, Jäger N, Kool M, Jones DTW, Pfister SM, Milde T, Mynarek M, Rutkowski S, Seggewiss J, Jeising D, de Faria FW, Marquardt T, Albert TK, Schüller U, Kerl K. J Transl Med 21: 2023 363	2
Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN. Fuchs S, Danßmann C, Klironomos F, Winkler A, Fallmann J, Kruetzfeldt LM, Szymansky A, Naderi J, Bernhart SH, Grunewald L, Helmsauer K, Rodriguez-Fos E, Kirchner M, Mertins P, Astrahantseff K, Suenkel C, Toedling J, Meggetto F, Remke M, Stadler PF, Hundsdoerfer P, Deubzer HE, Künkele A, Lang P, Fuchs J, Henssen AG, Eggert A, Rajewsky N, Hertwig F, Schulte JH. Nat Commun 14: 2023 3936	4
The Role of the Dysregulation of Long Non-Coding and Circular RNA Expression in Medulloblastoma: A Systematic Review. Martinez de Estibariz I, Jakjimovska A, Illarregi U, Martin-Guerrero I, Gutiérrez-Camino A, Lopez-Lopez E, Bilbao-Aldaiturriaga N. Cancers (Basel) 15: 2023 4686	2
Childhood cancer mutagenesis caused by transposase-derived PGBD5. Yamada M, Keller RR, Gutierrez RL, Cameron D, Suzuki H, Sanghrajka R, Vaynshteyn J, Gerwin J, Maura F, Hooper W, Shah M, Robine N, Demarest P, Bayin NS, Zapater LJ, Reed C, Hébert S, Masilionis I, Chaligne R, Socci ND, Taylor MD, Kleinman CL, Joyner AL, Raju GP, Kentsis A. Sci Adv 10: 2024 eadn4649	2