Abstract：
:A systematic cataloging of genes affected by genomic rearrangement, using multiple patient cohorts and cancer types, can provide insight into cancer-relevant alterations outside of exomes. By integrative analysis of whole-genome sequencing (predominantly low pass) and gene expression data from 1,448 cancers involving 18 histopathological types in The Cancer Genome Atlas, we identified hundreds of genes for which the nearby presence (within 100 kb) of a somatic structural variant (SV) breakpoint is associated with altered expression. While genomic rearrangements are associated with widespread copy-number alteration (CNA) patterns, approximately 1,100 genes-including overexpressed cancer driver genes (e.g., TERT, ERBB2, CDK12, CDK4) and underexpressed tumor suppressors (e.g., TP53, RB1, PTEN, STK11)-show SV-associated deregulation independent of CNA. SVs associated with the disruption of topologically associated domains, enhancer hijacking, or fusion transcripts are implicated in gene upregulation. For cancer-relevant pathways, SVs considerably expand our understanding of how genes are affected beyond point mutation or CNA.
journal_name
Cell Repjournal_title
Cell reportsauthors
Zhang Y,Yang L,Kucherlapati M,Chen F,Hadjipanayis A,Pantazi A,Bristow CA,Lee EA,Mahadeshwar HS,Tang J,Zhang J,Seth S,Lee S,Ren X,Song X,Sun H,Seidman J,Luquette LJ,Xi R,Chin L,Protopopov A,Li W,Park PJ,Kuchedoi
10.1016/j.celrep.2018.06.025subject
Has Abstractpub_date
2018-07-10 00:00:00pages
515-527issue
2issn
2211-1247pii
S2211-1247(18)30920-3journal_volume
24pub_type
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