Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes

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dc.citation.articleNumber101446en_US
dc.citation.issueNumber3en_US
dc.citation.journalTitleCell Reports Medicineen_US
dc.citation.volumeNumber5en_US
dc.contributor.authorChen, Fengjuen_US
dc.contributor.authorZhang, Yiqunen_US
dc.contributor.authorSedlazeck, Fritz J.en_US
dc.contributor.authorCreighton, Chad J.en_US
dc.date.accessioned2024-08-09T16:25:24Zen_US
dc.date.available2024-08-09T16:25:24Zen_US
dc.date.issued2024en_US
dc.description.abstractGermline variation and somatic alterations contribute to the molecular profile of cancers. We combine RNA with whole genome sequencing across 1,218 cancer patients to determine the extent germline structural variants (SVs) impact expression of nearby genes. For hundreds of genes, recurrent and common germline SV breakpoints within 100 kb associate with increased or decreased expression in tumors spanning various tissues of origin. A significant fraction of germline SV expression associations involves duplication of intergenic enhancers or 3′ UTR disruption. Genes altered by both somatic and germline SVs include ATRX and CEBPA. Genes essential in cancer cell lines include BARD1 and IRS2. Genes with both expression and germline SV breakpoint patterns associated with patient survival include GCLM. Our results capture a class of phenotypic variation at work in the disease setting, including genes with cancer roles. Specific germline SVs represent potential cancer risk variants for genetic testing, including those involving genes with targeting implications.en_US
dc.identifier.citationChen, F., Zhang, Y., Sedlazeck, F. J., & Creighton, C. J. (2024). Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes. Cell Reports Medicine, 5(3). https://doi.org/10.1016/j.xcrm.2024.101446en_US
dc.identifier.digitalPIIS2666379124000697en_US
dc.identifier.doihttps://doi.org/10.1016/j.xcrm.2024.101446en_US
dc.identifier.urihttps://hdl.handle.net/1911/117628en_US
dc.language.isoengen_US
dc.publisherElsevieren_US
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution (CC BY) license.  Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleGermline structural variation globally impacts the cancer transcriptome including disease-relevant genesen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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