Genomic Rearrangements in Pediatric Cancer

This study contains a collection of samples used to determine the role and impact of genomic rearrangements in a pan cancer pediatric cohort.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

20 Datasets 8 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
EGAD00001007701	None		1
EGAD00001008152	RNA-Seq data for systematic gene fusion detection in Pediatric Cancer		1
EGAD00001008272	None		1
EGAD00001008466	None		1
EGAD00001008467	None		1
EGAD00001008709	None		1
EGAD00001009297	Whole genome sequencing of paired tumor-normal samples of pediatric Wilms tumors		1
EGAD00001009298	Bulk RNA-seq data of pediatric Wilms tumors		1
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
EGAD00001015450	Our study utilizes two novel techniques, cyclical immunofluorescence imaging and single-cell spatial transcriptomics, to spatially map the tumor microenvironment of a large sample set of pediatric high-grade gliomas (pHGG). Using these methods, we have identified an abundant immunosuppressive myeloid cell population that has not been described in the context of pediatric high-grade gliomas. We validate our findings using an in vitro assay, spatial analysis on additional pHGG biopsies, independent spatial transcriptomic data, bulk RNA sequencing data of an expanded cohort of in-house patients, and publicly available bulk RNA sequencing data of an even larger cohort of pHGG patients.		1
EGAD00001015502	Key objective Are the prognostic transcriptomic G1/G2 gene expression signature, MYC overexpression, and MYC amplification replicable stratifying biomarkers for future clinical trials in high-grade osteosarcoma? Knowledge gathered In an unselected cohort, the G2 gene expression signature and MYC overexpression, but not MYC amplification, were independently associated with poor event-free and overall survival. Relevance Transcriptomic biomarkers may serve as stratifying factors that guide the management of patients with high-grade osteosarcoma. Current data underlines the importance of prospective validation of the G1/G2 signature and MYC overexpression in an international, multicenter, study.		1
EGAD00001015598	Extensive characterization of mutational signature SBS7a in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) samples. We aimed to describe the presentation of SBS7a in BCP-ALL, identify other pediatric cancers presenting with SBS7a, look into the link of SBS7a and UV-light in the context of BCP-ALL and cancers with provable UV exposure, and pinpoint when SBS7a was acquired.		1
EGAD00001015599	Extensive characterization of mutational signature SBS7a in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) samples. We aimed to describe the presentation of SBS7a in BCP-ALL, identify other pediatric cancers presenting with SBS7a, look into the link of SBS7a and UV-light in the context of BCP-ALL and cancers with provable UV exposure, and pinpoint when SBS7a was acquired.		1
EGAD00001015647	RNA-seq dataset of Neoantigen Peptides derived from V(D)J-recombined Immunoglobulins Drive Outgrowth of Cytolytic CD8+ T-cells		1
EGAD00001015705	Aim: to comprehensively characterize the cellular and transcriptional landscape of pediatric pilocytic astrocytomas across anatomical tumor locations	Illumina NovaSeq 6000	6

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	30
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	42
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	3
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	38
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	16
Complex structural variation is prevalent and highly pathogenic in pediatric solid tumors. van Belzen IAEM, van Tuil M, Badloe S, Janse A, Verwiel ETP, Santoso M, de Vos S, Baker-Hernandez J, Kerstens HHD, Solleveld-Westerink N, Meister MT, Drost J, van den Heuvel-Eibrink MM, Merks JHM, Molenaar JJ, Peng WC, Tops BBJ, Holstege FCP, Kemmeren P, Hehir-Kwa JY. Cell Genom 4: 2024 100675	4
Corrigendum to "Implementation of paediatric precision oncology into clinical practice: The individualized therapies for children with cancer program 'iTHER'" [Eur J Cancer 175 (2022) 311-325]. Langenberg KPS, Meister MT, Bakhuizen JJ, Boer JM, van Eijkelenburg NKA, Hulleman E, Ilan U, Looze EJ, Dierselhuis MP, Lugt JV, Breunis W, Schild LG, Ober K, van Hooff SR, Scheijde-Vermeulen MA, Hiemcke-Jiwa LS, Flucke UE, Kranendonk MEG, Wesseling P, Sonneveld E, Punt S, Boltjes A, van Dijk F, Verwiel ETP, Volckmann R, Hehir-Kwa JY, Kester LA, Koudijs MMJ, Waanders E, Holstege FCP, Vormoor HJ, Hoving EW, Noesel MMV, Pieters R, Kool M, Stumpf M, Blattner-Johnson M, Balasubramanian GP, Van Tilburg CM, Jones BC, Jones DTW, Witt O, Pfister SM, Jongmans MCJ, Kuiper RP, de Krijger RR, Wijnen MHW, den Boer ML, Zwaan CM, Kemmeren P, Koster J, Tops BBJ, Goemans BF, Molenaar JJ. Eur J Cancer 221: 2025 115423	0
Small round cell sarcoma tumoroid biobank reveals CIC::DUX4 sarcoma vulnerability to MCL-1 inhibition. Ringnalda FCAS, van Son GJF, Verweij LHG, Kim SY, Amo-Addae V, Flucke UE, Hiemcke-Jiwa LS, Langenberg KPS, Bramer JAM, Heimans L, van de Sande MAJ, van Houdt WJ, van Noesel MM, Kerstens HHD, Santoso M, Seifert G, Delattre O, Scotlandi K, Geoerger B, Merks JHM, Molenaar JJ, van Boxtel R, van de Wetering M, Sanders K, Clevers H. Nat Commun 16: 2025 7689	0