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    Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas

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    Authors
    Ng, A. W. T.
    Contino, G.
    Killcoyne, S.
    Devonshire, G.
    Hsu, R.
    Abbas, S.
    Su, J.
    Redmond, A. M.
    Weaver, Jamie M
    Eldridge, M. D.
    Tavaré, S.
    Edwards, P. A. W.
    Fitzgerald, R. C.
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    Affiliation
    Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge
    Issue Date
    2022
    
    Metadata
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    Abstract
    Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed structural variations (SV) with a predominance of deletions, tandem duplications and inter-chromosome junctions that could be identified as LINE-1 mobile element (ME) insertions. Complex clusters of rearrangements resembling breakage-fusion-bridge cycles or extrachromosomal circular DNA accounted for 22% of complex SVs affecting known oncogenes. Counting SV events affecting known driver genes substantially increased the recurrence rates of these drivers. After excluding fragile sites, we identified 51 candidate new drivers in genomic regions disrupted by SVs, including ETV5, KAT6B and CLTC. RUNX1 was the most recurrently altered gene (24%), with many deletions inactivating the RUNT domain but preserved the reading frame, suggesting an altered protein product. These findings underscore the importance of identification of SV events in OAC with implications for targeted therapies.
    Citation
    Ng AWT, Contino G, Killcoyne S, Devonshire G, Hsu R, Abbas S, et al. Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Vol. 5, Communications Biology. Springer Science and Business Media LLC; 2022.
    Journal
    Communications Biology
    URI
    http://hdl.handle.net/10541/625271
    DOI
    10.1038/s42003-022-03238-7
    PubMed ID
    35396535
    Additional Links
    https://dx.doi.org/10.1038/s42003-022-03238-7
    Type
    Article
    Language
    en
    ae974a485f413a2113503eed53cd6c53
    10.1038/s42003-022-03238-7
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