StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	23796897	Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, Brennan CW, Yung WK, Weinstein JN, Aldape KD, Sulman EP, Chen K, Koul D, Verhaak RG	A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival	Genes & Development	2013 Jul 	12	Glioblastoma	Next Generation Sequencing	Homo sapiens	TCGA-06-0129			hs12:32552893-32552893,hs12:40619357-40619357;hs12:6954966-6954966,hs12:95869847-95869847;hs12:51386593-hs12:48501148-48516550;hs6:3410422-3410422,hs6:47221257-47221257;hs12:69864310-69885431,hs12:57957222-57957222;hs12:56663345-56664102,hs12:6964565-6964565;hs12:53861077-53861077,hs12:100482873-100482873;hs12:27156169-27156169,hs12:103670988-103670988;hs6:33393680-33393680,hs6:44220782-44220782;hs12:81929201-82147752,hs12:63954442-63954442;hs12:40345059-40345059,hs12:110834257-110834257;hs6:34791125-34791125,hs12:91358103-91358103;hs12:105538650-105538650,hs12:71928895-71928895;hs12:132630210-132629150,hs12:113837515-113837515;hs6:37623476-37626021,hs6:43126555-43126555;hs4:140222985-140222985,hs9:113638002-113638002;hs12:69756687-69756687,hs12:132522227-132527849	ANAPC7;C12orf42;COQ10A;DPY19L2;EP400;EPYC;FGD4;FRS2;Gene_B;GNB3;KIAA1033;KIF5A;LGR5;LRRK2;METAP2;NOC4L;PCBP2;PFKM;PPFIA2;SDS;SLC11A2;SLC2A13;TM7SF3;UHRF1BP1L;USP5;YEATS4;	Department of Bioinformatics and Computational Biology	With the advent of high-throughput sequencing technologies, much progress has been made in the identification of somatic structural rearrangements in cancer genomes. However, characterization of the complex alterations and their associated mechanisms remains inadequate. Here, we report a comprehensive analysis of whole-genome sequencing and DNA copy number data sets from The Cancer Genome Atlas to relate chromosomal alterations to imbalances in DNA dosage and describe the landscape of intragenic breakpoints in glioblastoma multiforme (GBM). Gene length, guanine-cytosine (GC) content, and local presence of a copy number alteration were closely associated with breakpoint susceptibility. A dense pattern of repeated focal amplifications involving the murine double minute 2 (MDM2)/cyclin-dependent kinase 4 (CDK4) oncogenes and associated with poor survival was identified in 5% of GBMs. Gene fusions and rearrangements were detected concomitant within the breakpoint-enriched region. At the gene level, we noted recurrent breakpoints in genes such as apoptosis regulator FAF1. Structural alterations of the FAF1 gene disrupted expression and led to protein depletion. Restoration of the FAF1 protein in glioma cell lines significantly increased the FAS-mediated apoptosis response. Our study uncovered a previously underappreciated genomic mechanism of gene deregulation that can confer growth advantages on tumor cells and may generate cancer-specific vulnerabilities in subsets of GBM. 	NCBI 36/hg18				Yes	COQ10A,USP5;FGD4,LRRK2;FRS2,KIF5A;GNB3,METAP2;KIAA1033,LGR5;NOC4L,SDS;PCBP2,UHRF1BP1L;PPFIA2,DPY19L2;SLC11A2,PFKM;SLC2A13,ANAPC7;TM7SF3,C12orf42;UHRF1BP1,EPYC;YEATS4,EP400