Genetic landscape of pediatric Osteosarcoma

We performed whole-genome sequencing of 37 paired tumor/normal OS genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

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

5 Datasets 10 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
EGAD00001000159	DATA FILES FOR SJOS	Illumina HiSeq 2000	37
EGAD00001001053	DATA FILES FOR SJOS-WGS-2ndBatch	Illumina HiSeq 2000	27
EGAD00001001432	PCGP Germline Study Whole Genome Sequencing	Illumina HiSeq 2000	1337
EGAD00001001433	PCGP Germline Study Whole Exome Sequencing	Illumina HiSeq 2000	906
EGAD00001003154	RNA-Seq files for SJOS study	Illumina HiSeq 2000	14

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	23
Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Chen X, Bahrami A, Pappo A, Easton J, Dalton J, Hedlund E, Ellison D, Shurtleff S, Wu G, Wei L, Parker M, Rusch M, Nagahawatte P, Wu J, Mao S, Boggs K, Mulder H, Yergeau D, Lu C, Ding L, Edmonson M, Qu C, Wang J, Li Y, Navid F, Daw NC, Mardis ER, Wilson RK, Downing JR, Zhang J, Dyer MA, St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project. Cell Rep 7: 2014 104-112	447
Computel: computation of mean telomere length from whole-genome next-generation sequencing data. Nersisyan L, Arakelyan A. PLoS One 10: 2015 e0125201	39
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	47
Activation of PTHrP-cAMP-CREB1 signaling following p53 loss is essential for osteosarcoma initiation and maintenance. Walia MK, Ho PM, Taylor S, Ng AJ, Gupte A, Chalk AM, Zannettino AC, Martin TJ, Walkley CR. Elife 5: 2016 e13446	23
Genome-Informed Targeted Therapy for Osteosarcoma. Sayles LC, Breese MR, Koehne AL, Leung SG, Lee AG, Liu HY, Spillinger A, Shah AT, Tanasa B, Straessler K, Hazard FK, Spunt SL, Marina N, Kim GE, Cho SJ, Avedian RS, Mohler DG, Kim MO, DuBois SG, Hawkins DS, Sweet-Cordero EA. Cancer Discov 9: 2019 46-63	213
The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment. Brady SW, Ma X, Bahrami A, Satas G, Wu G, Newman S, Rusch M, Putnam DK, Mulder HL, Yergeau DA, Edmonson MN, Easton J, Alexandrov LB, Chen X, Mardis ER, Wilson RK, Downing JR, Pappo AS, Raphael BJ, Dyer MA, Zhang J. Mol Cancer Res 17: 2019 895-906	24
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	6
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	15
Evolving copy number gains promote tumor expansion and bolster mutational diversification. Wang Z, Xia Y, Mills L, Nikolakopoulos AN, Maeser N, Dehm SM, Sheltzer JM, Sun R. Nat Commun 15: 2024 2025	7