{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Affymetrix_U133v2"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000462"],"sample_count":["75"],"description":["EGA dataset EGAD00010000462"],"repository":["EGA"],"title":["Title not provided"],"pubmed_abstract":["Epigenetic dysregulation is an emerging hallmark of cancers. We developed a high-information-content mass spectrometry approach to profile global histone modifications in human cancers. When applied to 115 lines from the Cancer Cell Line Encyclopedia, this approach identified distinct molecular chromatin signatures. One signature was characterized by increased histone 3 lysine 36 (H3K36) dimethylation, exhibited by several lines harboring translocations in NSD2, which encodes a methyltransferase. A previously unknown NSD2 p.Glu1099Lys (p.E1099K) variant was identified in nontranslocated acute lymphoblastic leukemia (ALL) cell lines sharing this signature. Ectopic expression of the variant induced a chromatin signature characteristic of NSD2 hyperactivation and promoted transformation. NSD2 knockdown selectively inhibited the proliferation of NSD2-mutant lines and impaired the in vivo growth of an NSD2-mutant ALL xenograft. Sequencing analysis of >1,000 pediatric cancer genomes identified the NSD2 p.E1099K alteration in 14% of t(12;21) ETV6-RUNX1-containing ALLs. These findings identify NSD2 as a potential therapeutic target for pediatric ALL and provide a general framework for the functional annotation of cancer epigenomes.","We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), an algorithm for detecting somatic copy-number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation on the basis of changes in read depth and the detection of localized structural variations, with high accuracy and sensitivity. Analysis of 43 cancer genomes from both pediatric and adult patients revealed novel oncogenic CNAs, complex rearrangements and subclonal CNAs missed by alternative approaches."],"pubmed_title":["Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia.","CONSERTING: integrating copy-number analysis with structural-variation detection."],"pubmed_authors":["Chen Xiang X, Gupta Pankaj P, Wang Jianmin J, Nakitandwe Joy J, Roberts Kathryn K, Dalton James D JD, Parker Matthew M, Patel Samir S, Holmfeldt Linda L, Payne Debbie D, Easton John J, Ma Jing J, Rusch Michael M, Wu Gang G, Patel Aman A, Baker Suzanne J SJ, Dyer Michael A MA, Shurtleff Sheila S, Espy Stephen S, Pounds Stanley S, Downing James R JR, Ellison David W DW, Mullighan Charles G CG, Zhang Jinghui J","Jaffe Jacob D JD, Wang Yan Y, Chan Ho Man HM, Zhang Jinghui J, Huether Robert R, Kryukov Gregory V GV, Bhang Hyo-eun C HE, Taylor Jordan E JE, Hu Min M, Englund Nathan P NP, Yan Feng F, Wang Zhaofu Z, Robert McDonald E E, Wei Lei L, Ma Jing J, Easton John J, Yu Zhengtian Z, deBeaumount Rosalie R, Gibaja Veronica V, Venkatesan Kavitha K, Schlegel Robert R, Sellers William R WR, Keen Nicholas N, Liu Jun J, Caponigro Giordano G, Barretina Jordi J, Cooke Vesselina G VG, Mullighan Charles C, Carr Steven A SA, Downing James R JR, Garraway Levi A LA, Stegmeier Frank F"],"additional_accession":[]},"is_claimable":false,"name":"PCGP_SJLGG_Array_dataset - samples","description":"SJLGG Case samples using Gene Expression Array","dates":{"updated":"2017-07-26 15:39:24"},"accession":"EGAD00010000462","cross_references":{"TAXONOMY":["9606"],"pubmed":["25938371","24076604"],"EGA":["EGAC00001000044","EGAS00001000255"]}}