Genomic Rearrangements in Pediatric Cancer - EGA European Genome-Phenome Archive

Dataset ID	Description	Technology	Samples
EGAD00001007701	None		-
EGAD00001008152	RNA-Seq data for systematic gene fusion detection in Pediatric Cancer		-
EGAD00001008272	None		-
EGAD00001008466	None		-
EGAD00001008467	None		-
EGAD00001008709	None		-
EGAD00001009297	Whole genome sequencing of paired tumor-normal samples of pediatric Wilms tumors		-
EGAD00001009298	Bulk RNA-seq data of pediatric Wilms tumors		-
EGAD00001009793	We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles	Illumina NovaSeq 6000	8
EGAD00001009794	We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles	Illumina NovaSeq 6000	4
EGAD00001010042	Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations WGS		1
EGAD00001010179	iTHER is a prospective national precision oncology program aiming to define tumor molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory pediatric tumors in order to identify relevant aberrations to inform treatment.		1
EGAD00001011378	Paired tumor-normal whole genome sequencing data from primary tumors of patients diagnosed with neuroblastoma, Ewing sarcoma, Wilms tumor, hepatoblastoma and rhabdomyosarcoma		1
EGAD00001015418	Creation of living organoid biobank for ewing and ewing-like sarcomas	Illumina NovaSeq 6000	11

Publications	Citations
Improved Gene Fusion Detection in Childhood Cancer Diagnostics Using RNA Sequencing. Hehir-Kwa JY, Koudijs MJ, Verwiel ETP, Kester LA, van Tuil M, Strengman E, Buijs A, Kranendonk MEG, Hiemcke-Jiwa LS, de Haas V, van de Geer E, de Leng W, van der Lugt J, Lijnzaad P, Holstege FCP, Kemmeren P, Tops BBJ. JCO Precis Oncol 6: 2022 e2000504	11
Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes. Meister MT, Groot Koerkamp MJA, de Souza T, Breunis WB, Frazer-Mendelewska E, Brok M, DeMartino J, Manders F, Calandrini C, Kerstens HHD, Janse A, Dolman MEM, Eising S, Langenberg KPS, van Tuil M, Knops RRG, van Scheltinga ST, Hiemcke-Jiwa LS, Flucke U, Merks JHM, van Noesel MM, Tops BBJ, Hehir-Kwa JY, Kemmeren P, Molenaar JJ, van de Wetering M, van Boxtel R, Drost J, Holstege FCP. EMBO Mol Med 14: 2022 e16001	22
Molecular Characterization Reveals Subclasses of 1q Gain in Intermediate Risk Wilms Tumors. van Belzen IAEM, van Tuil M, Badloe S, Strengman E, Janse A, Verwiel ETP, van der Leest DFM, de Vos S, Baker-Hernandez J, Groenendijk A, de Krijger R, Kerstens HHD, Drost J, van den Heuvel-Eibrink MM, Tops BBJ, Holstege FCP, Kemmeren P, Hehir-Kwa JY. Cancers (Basel) 14: 2022 4872	1
Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma. DeMartino J, Meister MT, Visser LL, Brok M, Groot Koerkamp MJA, Wezenaar AKL, Hiemcke-Jiwa LS, de Souza T, Merks JHM, Rios AC, Holstege FCP, Margaritis T, Drost J. Nat Commun 14: 2023 3074	11
Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS. van Belzen IAEM, Cai C, van Tuil M, Badloe S, Strengman E, Janse A, Verwiel ETP, van der Leest DFM, Kester L, Molenaar JJ, Meijerink J, Drost J, Peng WC, Kerstens HHD, Tops BBJ, Holstege FCP, Kemmeren P, Hehir-Kwa JY. BMC Cancer 23: 2023 618	9