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High-coverage whole...
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
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- Zhang, Yiqun (författare)
- Baylor College of Medicine
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- Chen, Fengju (författare)
- Baylor College of Medicine
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- Fonseca, Nuno A (författare)
- European Bioinformatics Institute
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- He, Yao (författare)
- Peking University
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- Fujita, Masashi (författare)
- RIKEN Center for Integrative Medical Sciences
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- Nakagawa, Hidewaki (författare)
- RIKEN Center for Integrative Medical Sciences
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- Zhang, Zemin (författare)
- Peking University
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- Brazma, Alvis (författare)
- European Bioinformatics Institute
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- Creighton, Chad J (författare)
- Baylor College of Medicine
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- Borg, Åke (creator_code:cre_t)
- Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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- Ringnér, Markus (creator_code:cre_t)
- Lund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Molecular Cell Biology,Department of Biology,Faculty of Science
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- Staaf, Johan (creator_code:cre_t)
- Lund University,Lunds universitet,Forskningsgrupp Lungcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Bröst/lungcancer,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Research Group Lung Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Breast/lungcancer,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine
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(creator_code:org_t)
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- 2020-02-05
- 2020
- Engelska 14 s.
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
- Relaterad länk:
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http://dx.doi.org/10... (free)
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https://www.nature.c...
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- The 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.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Nyckelord
- DNA Methylation
- Databases, Genetic
- Enhancer Elements, Genetic
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- Genomic Structural Variation
- Humans
- Neoplasms/genetics
- Oncogenes
- Regulatory Sequences, Nucleic Acid
- Whole Genome Sequencing
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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Till lärosätets databas
- Av författaren/redakt...
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Zhang, Yiqun
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Chen, Fengju
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Fonseca, Nuno A
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He, Yao
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Fujita, Masashi
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Nakagawa, Hidewa ...
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visa fler...
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Zhang, Zemin
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Brazma, Alvis
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Creighton, Chad ...
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Borg, Åke
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Ringnér, Markus
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Staaf, Johan
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- Om ämnet
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- MEDICIN OCH HÄLSOVETENSKAP
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MEDICIN OCH HÄLS ...
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och Medicinska och f ...
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och Medicinsk geneti ...
- Artiklar i publikationen
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Nature Communica ...
- Av lärosätet
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Lunds universitet
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Karolinska Institutet