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Orphan_Tumour_Study___familial_neuroblastoma

The aim of this study is to study the genomes of ultra rare childhood tumours

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

7 Datasets 17 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
EGAD00001003884	The genetic basis of many rare childhood cancers remains unknown. These include a spectrum of infant soft tissue tumors without canonical gene fusions, encompassing congenital mesoblastic nephroma (CMN) of the kidney and infantile fibrosarcoma (IFS). Here, we integrated whole genome and transcriptome sequencing and identified diagnostic markers and novel therapeutic strategies.	HiSeq X Ten	37
EGAD00001004774	We investigated the somatic genetic basis of Wilms’ tumour and found complex phylogenetic relations between tumours.	HiSeq X Ten	203
EGAD00001005770	The aim of this study is to reconstruct the phylogenetic development of childhood tumours	HiSeq X Ten	8
EGAD00001006423	Leukaemia and related blood cancers occur due to genetic changes that typically accumulate over many years. This study will employ targeted next-generation sequencing to retrace the preclinical evolution of several types of haematological malignancy. Investigating the progression of the earliest pre-malignant ancestral clones promises to offer valuable insights into early leukaemia evolution and therapeutic vulnerabilities of leukaemia stem cells.	HiSeq X Ten Illumina NovaSeq 6000	137
EGAD00001007853	We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.	HiSeq X Ten	3
EGAD00001008345	Using the chromium 3' expression assay, we generated an atlas of neuroblastoma and the human fetal adrenal gland. These data were complemented with whole genome sequencing of normal and tumour DNA from the neuroblastoma samples.	Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina MiSeq Illumina NovaSeq 6000	32
EGAD00001009005	Single cell transcriptomes, generated using chromium 10X 3' sequencing, for two tumour types (AT/RT, and Ewing's sarcoma). For each individual, tumour and normal whole genome sequencing was also obtained using Illumina short read sequencing to an average depth of 30X. These data were used to validate the accuracy of a method for identifying cancer cell transcriptomes based on the allelic shift produced by copy number changes.	HiSeq X Ten Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NovaSeq 6000	15

Publications	Citations
Recurrent intragenic rearrangements of EGFR and BRAF in soft tissue tumors of infants. Wegert J, Vokuhl C, Collord G, Del Castillo Velasco-Herrera M, Farndon SJ, Guzzo C, Jorgensen M, Anderson J, Slater O, Duncan C, Bausenwein S, Streitenberger H, Ziegler B, Furtwängler R, Graf N, Stratton MR, Campbell PJ, Jones DT, Koelsche C, Pfister SM, Mifsud W, Sebire N, Sparber-Sauer M, Koscielniak E, Rosenwald A, Gessler M, Behjati S. Nat Commun 9: 2018 2378	36
Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S. Science 361: 2018 594-599	387
Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation. Subramanian A, Sidhom EH, Emani M, Vernon K, Sahakian N, Zhou Y, Kost-Alimova M, Slyper M, Waldman J, Dionne D, Nguyen LT, Weins A, Marshall JL, Rosenblatt-Rosen O, Regev A, Greka A. Nat Commun 10: 2019 5462	99
Single cell derived mRNA signals across human kidney tumors. Young MD, Mitchell TJ, Custers L, Margaritis T, Morales-Rodriguez F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR, van den Heuvel-Eibrink MM, Comitani F, Piapi A, Bugallo-Blanco E, Thevanesan C, Burke C, Prigmore E, Ambridge K, Roberts K, Braga FAV, Coorens THH, Del Valle I, Wilbrey-Clark A, Mamanova L, Stewart GD, Gnanapragasam VJ, Rampling D, Sebire N, Coleman N, Hook L, Warren A, Haniffa M, Kool M, Pfister SM, Achermann JC, He X, Barker RA, Shlien A, Bayraktar OA, Teichmann SA, Holstege FC, Meyer KB, Drost J, Straathof K, Behjati S. Nat Commun 12: 2021 3896	21
The Extracellular Matrix Environment of Clear Cell Renal Cell Carcinoma Determines Cancer Associated Fibroblast Growth. Bond KH, Chiba T, Wynne KPH, Vary CPH, Sims-Lucas S, Coburn JM, Oxburgh L. Cancers (Basel) 13: 2021 5873	19
Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia. Khabirova E, Jardine L, Coorens THH, Webb S, Treger TD, Engelbert J, Porter T, Prigmore E, Collord G, Piapi A, Teichmann SA, Inglott S, Williams O, Heidenreich O, Young MD, Straathof K, Bomken S, Bartram J, Haniffa M, Behjati S. Nat Med 28: 2022 743-751	29
Erratum for the Research Article: "Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell". None Sci Adv 8: 2022 eabq6127	0
Genetic association and single-cell transcriptome analyses reveal distinct features connecting autoimmunity with cancers. Li S, Lu C, Zhang Y, Zhao X, Lin K, Kong X, Fox D, Xue L, Sun L, Liu Y, Mao F. iScience 25: 2022 104631	2
Precise identification of cancer cells from allelic imbalances in single cell transcriptomes. Trinh MK, Pacyna CN, Kildisiute G, Thevanesan C, Piapi A, Ambridge K, Anderson ND, Khabirova E, Prigmore E, Straathof K, Behjati S, Young MD. Commun Biol 5: 2022 884	3
A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma. Alchahin AM, Mei S, Tsea I, Hirz T, Kfoury Y, Dahl D, Wu CL, Subtelny AO, Wu S, Scadden DT, Shin JH, Saylor PJ, Sykes DB, Kharchenko PV, Baryawno N. Nat Commun 13: 2022 5747	20
Topological identification and interpretation for single-cell gene regulation elucidation across multiple platforms using scMGCA. Yu Z, Su Y, Lu Y, Yang Y, Wang F, Zhang S, Chang Y, Wong KC, Li X. Nat Commun 14: 2023 400	15
New insights into fibrotic signaling in renal cell carcinoma. Chen JY, Yiu WH, Tang PM, Tang SC. Front Cell Dev Biol 11: 2023 1056964	2
The GPCR-Gα<sub>s</sub>-PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure. Wu VH, Yung BS, Faraji F, Saddawi-Konefka R, Wang Z, Wenzel AT, Song MJ, Pagadala MS, Clubb LM, Chiou J, Sinha S, Matic M, Raimondi F, Hoang TS, Berdeaux R, Vignali DAA, Iglesias-Bartolome R, Carter H, Ruppin E, Mesirov JP, Gutkind JS. Nat Immunol 24: 2023 1318-1330	15
An integrated single-cell analysis of human adrenal cortex development. Del Valle I, Young MD, Kildisiute G, Ogunbiyi OK, Buonocore F, Simcock IC, Khabirova E, Crespo B, Moreno N, Brooks T, Niola P, Swarbrick K, Suntharalingham JP, McGlacken-Byrne SM, Arthurs OJ, Behjati S, Achermann JC. JCI Insight 8: 2023 e168177	4
Transcriptional repression of the oncofetal LIN28B gene by the transcription factor SOX6. Pastori V, Zambanini G, Citterio E, Weiss T, Nakamura Y, Cantù C, Ronchi AE. Sci Rep 14: 2024 10287	0
An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs. Chapple RH, Liu X, Natarajan S, Alexander MIM, Kim Y, Patel AG, LaFlamme CW, Pan M, Wright WC, Lee HM, Zhang Y, Lu M, Koo SC, Long C, Harper J, Savage C, Johnson MD, Confer T, Akers WJ, Dyer MA, Sheppard H, Easton J, Geeleher P. Genome Biol 25: 2024 161	1
Neuroblastoma plasticity during metastatic progression stems from the dynamics of an early sympathetic transcriptomic trajectory. Villalard B, Boltjes A, Reynaud F, Imbaud O, Thoinet K, Timmerman I, Croze S, Theoulle E, Atzeni G, Lachuer J, Molenaar JJ, Tytgat GAM, Delloye-Bourgeois C, Castellani V. Nat Commun 15: 2024 9570	1