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000177477 037__ $$aDKFZ-2021-02564
000177477 041__ $$aEnglish
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000177477 1001_ $$aZhang, Yiqun$$b0
000177477 245__ $$aHigh-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
000177477 260__ $$a[London]$$bNature Publishing Group UK$$c2020
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000177477 500__ $$asiehe Correction: DKFZ Autoren affiliiert im PCAWG Consortium: https://inrepo02.dkfz.de/record/212439   /https://doi.org/10.1038/s41467-022-32333-w
000177477 520__ $$aThe impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered expression. For the majority of these genes, expression increases rather than decreases with corresponding breakpoint events. Up-regulated cancer-associated genes impacted by this phenomenon include TERT, MDM2, CDK4, ERBB2, CD274, PDCD1LG2, and IGF2. TERT-associated breakpoints involve ~3% of cases, most frequently in liver biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involve ~1% of non-amplified cases. For many genes, SVs are significantly associated with increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the promoter is often increased with nearby SV breakpoint, which may involve inactivation of repressor elements.
000177477 536__ $$0G:(DE-HGF)POF3-312$$a312 - Functional and structural genomics (POF3-312)$$cPOF3-312$$fPOF III$$x0
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000177477 650_2 $$2MeSH$$aDNA Methylation
000177477 650_2 $$2MeSH$$aDatabases, Genetic
000177477 650_2 $$2MeSH$$aEnhancer Elements, Genetic
000177477 650_2 $$2MeSH$$aGene Expression Regulation, Neoplastic
000177477 650_2 $$2MeSH$$aGenes, Tumor Suppressor
000177477 650_2 $$2MeSH$$aGenomic Structural Variation
000177477 650_2 $$2MeSH$$aHumans
000177477 650_2 $$2MeSH$$aNeoplasms: genetics
000177477 650_2 $$2MeSH$$aOncogenes
000177477 650_2 $$2MeSH$$aRegulatory Sequences, Nucleic Acid
000177477 650_2 $$2MeSH$$aWhole Genome Sequencing
000177477 7001_ $$aChen, Fengju$$b1
000177477 7001_ $$aFonseca, Nuno A$$b2
000177477 7001_ $$aHe, Yao$$b3
000177477 7001_ $$aFujita, Masashi$$b4
000177477 7001_ $$aNakagawa, Hidewaki$$b5
000177477 7001_ $$aZhang, Zemin$$b6
000177477 7001_ $$aBrazma, Alvis$$b7
000177477 7001_ $$aPCAWGTranscriptomeWorkingGroup$$b8
000177477 7001_ $$aPCAWGStructuralVariationWorkingGroup$$b9
000177477 7001_ $$aCreighton, Chad J$$b10
000177477 7001_ $$aPCAWGConsortium$$b11
000177477 773__ $$0PERI:(DE-600)2553671-0$$a10.1038/s41467-019-13885-w$$gVol. 11, no. 1, p. 736$$n1$$p736$$tNature Communications$$v11$$x2041-1723$$y2020
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000177477 9141_ $$y2020
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