The DOI matches its Crossref record; 76 of the 76 references it cites were found in a registry or an index.
Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs
Open accessAbstract
Summary Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g. deletion) or complex (e.g. chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are “towers” of low-JCN duplications associated with early replicating regions and superenhancers, enriched in breast and ovarian cancers. Rigma comprise “chasms” of low-JCN deletions at late-replicating fragile sites, enriched in gastrointestinal carcinomas. Tyfonas are “typhoons” of high-JCN junctions and fold-back inversions enriched in expressed protein-coding fusions and breakend hypermutation, frequently found in acral, but not cutaneous, melanomas. Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis.
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Metadata
- Authors
- Hadi, K., Yao, X., Behr, J. M., Deshpande, A., Xanthopoulakis, C., Tian, H., Kudman, S., Rosiene, J., Darmofal, M., DeRose, J., Mortensen, R., Adney, E. M., Shaiber, A., Gajic, Z., Sigouros, M., Eng, K., Wala, J. A., Wrzeszczyński, K. O., Arora, K., Shah, M., Emde, A.-K., Felice, V., Frank, M. O., Darnell, R. B., Ghandi, M., Huang, F., Dewhurst, S., Maciejowski, J., de Lange, T., Setton, J., Riaz, N., Reis-Filho, J. S., Powell, S., Knowles, D. A., Reznik, E., Mishra, B., Beroukhim, R., Zody, M. C., Robine, N., Oman, K. M., Sanchez, C. A., Kuhner, M. K., Smith, L. P., Galipeau, P. C., Paulson, T. G., Reid, B. J., Li, X., Wilkes, D., Sboner, A., Mosquera, J. M., Elemento, O., & Imielinski, M.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-10
- Volume
- 183
- Issue
- 1
- Pages
- 197-210.e32
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W3091245808
- Cited by
- 269
- References
- 76
- FWCI
- 11.29
- Type
- journal article
- Language
- en
- Open access
- bronze
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 365 d)
- Funders
- Doris Duke Charitable Foundation
- Starr Foundation
- Burroughs Wellcome Fund
- Melanoma Research Alliance
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- Hadi, K., Yao, X., Behr, J. M., Deshpande, A., Xanthopoulakis, C., Tian, H., Kudman, S., Rosiene, J., Darmofal, M., DeRose, J., Mortensen, R., Adney, E. M., Shaiber, A., Gajic, Z., Sigouros, M., Eng, K., Wala, J. A., Wrzeszczyński, K. O., Arora, K., . . . Imielinski, M. (2020). Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. https://doi.org/10.1016/j.cell.2020.08.006
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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