Genetic landscape of pediatric Rhabdomyosarcoma

We performed whole-genome sequencing of 13 paired tumor/normal Rhabdomyosarcoma genomes and analyzed somatically acquired single nucleotide variations SNVs, insertion/deletions, structural variations and copy number variations in the cancer genomes

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

6 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
EGAD00001000164	Whole Genome Sequencing accompanying Genetic landscape of pediatric Rhabdomyosarcoma.	Illumina HiSeq 2000	29
EGAD00001000878	RNA-Seq files accompanying Genetic landscape of pediatric Rhabdomyosarcoma	Illumina HiSeq 2000	42
EGAD00001001059	Whole Exome Sequencing files accompanying Genetic landscape of pediatric Rhabdomyosarcoma	Illumina HiSeq 2000	56
EGAD00001001432	PCGP Germline Study Whole Genome Sequencing	Illumina HiSeq 2000	1337
EGAD00001001433	PCGP Germline Study Whole Exome Sequencing	Illumina HiSeq 2000	906
EGAD00010001596	DNA methylation data from patient RMS tumor samples from Illumina 450 K arays	Illlimuna EPIC 450 K	32

Publications	Citations
Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data. Parker M, Chen X, Bahrami A, Dalton J, Rusch M, Wu G, Easton J, Cheung NK, Dyer M, Mardis ER, Wilson RK, Mullighan C, Gilbertson R, Baker SJ, Zambetti G, Ellison DW, Downing JR, Zhang J, Pediatric Cancer Genome Project. Genome Biol 13: 2012 R113	22
Targeting oxidative stress in embryonal rhabdomyosarcoma. Chen X, Stewart E, Shelat AA, Qu C, Bahrami A, Hatley M, Wu G, Bradley C, McEvoy J, Pappo A, Spunt S, Valentine MB, Valentine V, Krafcik F, Lang WH, Wierdl M, Tsurkan L, Tolleman V, Federico SM, Morton C, Lu C, Ding L, Easton J, Rusch M, Nagahawatte P, Wang J, Parker M, Wei L, Hedlund E, Finkelstein D, Edmonson M, Shurtleff S, Boggs K, Mulder H, Yergeau D, Skapek S, Hawkins DS, Ramirez N, Potter PM, Sandoval JA, Davidoff AM, Mardis ER, Wilson RK, Zhang J, Downing JR, Dyer MA, St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project. Cancer Cell 24: 2013 710-724	186
Development and characterization of a human orthotopic neuroblastoma xenograft. Stewart E, Shelat A, Bradley C, Chen X, Federico S, Thiagarajan S, Shirinifard A, Bahrami A, Pappo A, Qu C, Finkelstein D, Sablauer A, Dyer MA. Dev Biol 407: 2015 344-355	21
The Childhood Solid Tumor Network: A new resource for the developmental biology and oncology research communities. Stewart E, Federico S, Karlstrom A, Shelat A, Sablauer A, Pappo A, Dyer MA. Dev Biol 411: 2016 287-293	45
PAX3-FOXO1 transgenic zebrafish models identify HES3 as a mediator of rhabdomyosarcoma tumorigenesis. Kendall GC, Watson S, Xu L, LaVigne CA, Murchison W, Rakheja D, Skapek SX, Tirode F, Delattre O, Amatruda JF. Elife 7: 2018 e33800	23
Barriers to accessing public cancer genomic data. Learned K, Durbin A, Currie R, Kephart ET, Beale HC, Sanders LM, Pfeil J, Goldstein TC, Salama SR, Haussler D, Vaske OM, Bjork IM. Sci Data 6: 2019 98	17
Bayesian Modeling Identifies PLAG1 as a Key Regulator of Proliferation and Survival in Rhabdomyosarcoma Cells. Zheng Y, Xu L, Hassan M, Zhou X, Zhou Q, Rakheja D, Skapek SX. Mol Cancer Res 18: 2020 364-374	6
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data. Tian L, Li Y, Edmonson MN, Zhou X, Newman S, McLeod C, Thrasher A, Liu Y, Tang B, Rusch MC, Easton J, Ma J, Davis E, Trull A, Michael JR, Szlachta K, Mullighan C, Baker SJ, Downing JR, Ellison DW, Zhang J. Genome Biol 21: 2020 126	50
Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q. Neggers JE, Paolella BR, Asfaw A, Rothberg MV, Skipper TA, Yang A, Kalekar RL, Krill-Burger JM, Dharia NV, Kugener G, Kalfon J, Yuan C, Dumont N, Gonzalez A, Abdusamad M, Li YY, Spurr LF, Wu WW, Durbin AD, Wolpin BM, Piccioni F, Root DE, Boehm JS, Cherniack AD, Tsherniak A, Hong AL, Hahn WC, Stegmaier K, Golub TR, Vazquez F, Aguirre AJ. Cell Rep 33: 2020 108493	16
The landscape of coding RNA editing events in pediatric cancer. Wen J, Rusch M, Brady SW, Shao Y, Edmonson MN, Shaw TI, Powers BB, Tian L, Easton J, Mullighan CG, Gruber T, Ellison D, Zhang J. BMC Cancer 21: 2021 1233	4
Exon skipping in genes encoding lineage-defining myogenic transcription factors in rhabdomyosarcoma. Butler E, Xu L, Rakheja D, Schwettmann B, Toubbeh S, Guo L, Kim J, Skapek SX, Zheng Y. Cold Spring Harb Mol Case Stud None: 2022 mcs.a006190	0
Haploinsufficiency of the lysosomal sialidase NEU1 results in a model of pleomorphic rhabdomyosarcoma in mice. Machado ER, van de Vlekkert D, Sheppard HS, Perry S, Downing SM, Laxton J, Ashmun R, Finkelstein DB, Neale GA, Hu H, Harwood FC, Koo SC, Grosveld GC, d'Azzo A. Commun Biol 5: 2022 992	2
VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis. Watson S, LaVigne CA, Xu L, Surdez D, Cyrta J, Calderon D, Cannon MV, Kent MR, Silvius KM, Kucinski JP, Harrison EN, Murchison W, Rakheja D, Tirode F, Delattre O, Amatruda JF, Kendall GC. Cell Rep 42: 2023 112013	0
Comprehensive analysis of mutational signatures reveals distinct patterns and molecular processes across 27 pediatric cancers. Thatikonda V, Islam SMA, Autry RJ, Jones BC, Gröbner SN, Warsow G, Hutter B, Huebschmann D, Fröhling S, Kool M, Blattner-Johnson M, Jones DTW, Alexandrov LB, Pfister SM, Jäger N. Nat Cancer 4: 2023 276-289	7
Methyltransferase Inhibition Enables Tgf<b>β</b> Driven Induction of <i>CDKN2A</i> and <i>B</i> in Cancer Cells. Liu YT, Romero C, Xiao X, Guo L, Zhou X, Applebaum MA, Xu L, Skapek SX. Mol Cell Biol 43: 2023 115-129	0