guest ::
| Home > User submitted records > Disentangling oncogenic amplicons in esophageal adenocarcinoma. > print |
| Home > User submitted records > Disentangling oncogenic amplicons in esophageal adenocarcinoma. > print |
| 001 | 295835 | ||
| 005 | 20241212160254.0 | ||
| 024 | 7 | _ | |a 10.1038/s41467-024-47619-4 |2 doi |
| 024 | 7 | _ | |a pmid:38744814 |2 pmid |
| 024 | 7 | _ | |a pmc:PMC11094127 |2 pmc |
| 037 | _ | _ | |a DKFZ-2024-02655 |
| 041 | _ | _ | |a English |
| 082 | _ | _ | |a 500 |
| 100 | 1 | _ | |a Ng, Alvin Wei Tian |0 P:(DE-HGF)0 |b 0 |
| 245 | _ | _ | |a Disentangling oncogenic amplicons in esophageal adenocarcinoma. |
| 260 | _ | _ | |a [London] |c 2024 |b Nature Publishing Group UK |
| 336 | 7 | _ | |a article |2 DRIVER |
| 336 | 7 | _ | |a Output Types/Journal article |2 DataCite |
| 336 | 7 | _ | |a Journal Article |b journal |m journal |0 PUB:(DE-HGF)16 |s 1734015345_6794 |2 PUB:(DE-HGF) |
| 336 | 7 | _ | |a ARTICLE |2 BibTeX |
| 336 | 7 | _ | |a JOURNAL_ARTICLE |2 ORCID |
| 336 | 7 | _ | |a Journal Article |0 0 |2 EndNote |
| 520 | _ | _ | |a Esophageal adenocarcinoma is a prominent example of cancer characterized by frequent amplifications in oncogenes. However, the mechanisms leading to amplicons that involve breakage-fusion-bridge cycles and extrachromosomal DNA are poorly understood. Here, we use 710 esophageal adenocarcinoma cases with matched samples and patient-derived organoids to disentangle complex amplicons and their associated mechanisms. Short-read sequencing identifies ERBB2, MYC, MDM2, and HMGA2 as the most frequent oncogenes amplified in extrachromosomal DNAs. We resolve complex extrachromosomal DNA and breakage-fusion-bridge cycles amplicons by integrating of de-novo assemblies and DNA methylation in nine long-read sequenced cases. Complex amplicons shared between precancerous biopsy and late-stage tumor, an enrichment of putative enhancer elements and mobile element insertions are potential drivers of complex amplicons' origin. We find that patient-derived organoids recapitulate extrachromosomal DNA observed in the primary tumors and single-cell DNA sequencing capture extrachromosomal DNA-driven clonal dynamics across passages. Prospectively, long-read and single-cell DNA sequencing technologies can lead to better prediction of clonal evolution in esophageal adenocarcinoma. |
| 536 | _ | _ | |a 313 - Krebsrisikofaktoren und Prävention (POF4-313) |0 G:(DE-HGF)POF4-313 |c POF4-313 |f POF IV |x 0 |
| 588 | _ | _ | |a Dataset connected to CrossRef, PubMed, , Journals: inrepo02.dkfz.de |
| 650 | _ | 2 | |a Humans |2 MeSH |
| 650 | _ | 2 | |a Esophageal Neoplasms: genetics |2 MeSH |
| 650 | _ | 2 | |a Esophageal Neoplasms: pathology |2 MeSH |
| 650 | _ | 2 | |a Adenocarcinoma: genetics |2 MeSH |
| 650 | _ | 2 | |a Adenocarcinoma: pathology |2 MeSH |
| 650 | _ | 2 | |a Organoids: pathology |2 MeSH |
| 650 | _ | 2 | |a Gene Amplification |2 MeSH |
| 650 | _ | 2 | |a DNA Methylation |2 MeSH |
| 650 | _ | 2 | |a Oncogenes: genetics |2 MeSH |
| 650 | _ | 2 | |a Male |2 MeSH |
| 650 | _ | 2 | |a Sequence Analysis, DNA: methods |2 MeSH |
| 650 | _ | 2 | |a Clonal Evolution: genetics |2 MeSH |
| 650 | _ | 2 | |a Female |2 MeSH |
| 700 | 1 | _ | |a McClurg, Dylan Peter |0 P:(DE-HGF)0 |b 1 |
| 700 | 1 | _ | |a Wesley, Ben |0 0009-0003-2550-9380 |b 2 |
| 700 | 1 | _ | |a Zamani, Shahriar A |0 0000-0001-8622-5013 |b 3 |
| 700 | 1 | _ | |a Black, Emily |0 0000-0001-9929-8043 |b 4 |
| 700 | 1 | _ | |a Miremadi, Ahmad |0 P:(DE-HGF)0 |b 5 |
| 700 | 1 | _ | |a Giger, Olivier |0 P:(DE-HGF)0 |b 6 |
| 700 | 1 | _ | |a Hoopen, Rogier Ten |0 P:(DE-HGF)0 |b 7 |
| 700 | 1 | _ | |a Devonshire, Ginny |0 0000-0002-1408-8176 |b 8 |
| 700 | 1 | _ | |a Redmond, Aisling M |0 P:(DE-HGF)0 |b 9 |
| 700 | 1 | _ | |a Grehan, Nicola |0 P:(DE-HGF)0 |b 10 |
| 700 | 1 | _ | |a Jammula, Sriganesh |0 P:(DE-HGF)0 |b 11 |
| 700 | 1 | _ | |a Blasko, Adrienn |0 P:(DE-HGF)0 |b 12 |
| 700 | 1 | _ | |a Li, Xiaodun |0 P:(DE-HGF)0 |b 13 |
| 700 | 1 | _ | |a Aparicio, Samuel |0 0000-0002-0487-9599 |b 14 |
| 700 | 1 | _ | |a Tavaré, Simon |0 0000-0002-3716-4952 |b 15 |
| 700 | 1 | _ | |a Clinical, Oesophageal Cancer |0 P:(DE-HGF)0 |b 16 |
| 700 | 1 | _ | |a Stratification, Molecular |0 P:(DE-HGF)0 |b 17 |e Collaboration Author |
| 700 | 1 | _ | |a Nowicki-Osuch, Karol |b 18 |
| 700 | 1 | _ | |a Fitzgerald, Rebecca C |0 0000-0002-3434-3568 |b 19 |
| 700 | 1 | _ | |a Edwards, Paul A W |0 P:(DE-HGF)0 |b 20 |e Contributor |
| 700 | 1 | _ | |a Grehan, Nicola |0 P:(DE-HGF)0 |b 21 |e Contributor |
| 700 | 1 | _ | |a Nutzinger, Barbara |0 P:(DE-HGF)0 |b 22 |e Contributor |
| 700 | 1 | _ | |a Loreno, Christine |0 P:(DE-HGF)0 |b 23 |e Contributor |
| 700 | 1 | _ | |a Abbas, Sujath |0 P:(DE-HGF)0 |b 24 |e Contributor |
| 700 | 1 | _ | |a Freeman, Adam |0 P:(DE-HGF)0 |b 25 |e Contributor |
| 700 | 1 | _ | |a Smyth, Elizabeth C |0 P:(DE-HGF)0 |b 26 |e Contributor |
| 700 | 1 | _ | |a O'Donovan, Maria |0 P:(DE-HGF)0 |b 27 |e Contributor |
| 700 | 1 | _ | |a Miremadi, Ahmad |0 P:(DE-HGF)0 |b 28 |e Contributor |
| 700 | 1 | _ | |a Malhotra, Shalini |0 P:(DE-HGF)0 |b 29 |e Contributor |
| 700 | 1 | _ | |a Tripathi, Monika |0 P:(DE-HGF)0 |b 30 |e Contributor |
| 700 | 1 | _ | |a Cheah, Calvin |0 P:(DE-HGF)0 |b 31 |e Contributor |
| 700 | 1 | _ | |a Coles, Hannah |0 P:(DE-HGF)0 |b 32 |e Contributor |
| 700 | 1 | _ | |a Millington, Curtis |0 P:(DE-HGF)0 |b 33 |e Contributor |
| 700 | 1 | _ | |a Eldridge, Matthew |0 P:(DE-HGF)0 |b 34 |e Contributor |
| 700 | 1 | _ | |a Secrier, Maria |0 P:(DE-HGF)0 |b 35 |e Contributor |
| 700 | 1 | _ | |a Jammula, Sriganesh |0 P:(DE-HGF)0 |b 36 |e Contributor |
| 700 | 1 | _ | |a Davies, Jim |0 P:(DE-HGF)0 |b 37 |e Contributor |
| 700 | 1 | _ | |a Crichton, Charles |0 P:(DE-HGF)0 |b 38 |e Contributor |
| 700 | 1 | _ | |a Carroll, Nick |0 P:(DE-HGF)0 |b 39 |e Contributor |
| 700 | 1 | _ | |a Hardwick, Richard H |0 P:(DE-HGF)0 |b 40 |e Contributor |
| 700 | 1 | _ | |a Safranek, Peter |0 P:(DE-HGF)0 |b 41 |e Contributor |
| 700 | 1 | _ | |a Hindmarsh, Andrew |0 P:(DE-HGF)0 |b 42 |e Contributor |
| 700 | 1 | _ | |a Sujendran, Vijayendran |0 P:(DE-HGF)0 |b 43 |e Contributor |
| 700 | 1 | _ | |a Hayes, Stephen J |0 P:(DE-HGF)0 |b 44 |e Contributor |
| 700 | 1 | _ | |a Ang, Yeng |0 P:(DE-HGF)0 |b 45 |e Contributor |
| 700 | 1 | _ | |a Sharrocks, Andrew |0 P:(DE-HGF)0 |b 46 |e Contributor |
| 700 | 1 | _ | |a Preston, Shaun R |0 P:(DE-HGF)0 |b 47 |e Contributor |
| 700 | 1 | _ | |a Bagwan, Izhar |0 P:(DE-HGF)0 |b 48 |e Contributor |
| 700 | 1 | _ | |a Save, Vicki |0 P:(DE-HGF)0 |b 49 |e Contributor |
| 700 | 1 | _ | |a Skipworth, Richard J E |0 P:(DE-HGF)0 |b 50 |e Contributor |
| 700 | 1 | _ | |a Hupp, Ted R |0 P:(DE-HGF)0 |b 51 |e Contributor |
| 700 | 1 | _ | |a O'Neill, J Robert |0 P:(DE-HGF)0 |b 52 |e Contributor |
| 700 | 1 | _ | |a Tucker, Olga |0 P:(DE-HGF)0 |b 53 |e Contributor |
| 700 | 1 | _ | |a Beggs, Andrew |0 P:(DE-HGF)0 |b 54 |e Contributor |
| 700 | 1 | _ | |a Taniere, Philippe |0 P:(DE-HGF)0 |b 55 |e Contributor |
| 700 | 1 | _ | |a Puig, Sonia |0 P:(DE-HGF)0 |b 56 |e Contributor |
| 700 | 1 | _ | |a Contino, Gianmarco |0 P:(DE-HGF)0 |b 57 |e Contributor |
| 700 | 1 | _ | |a Underwood, Timothy J |0 P:(DE-HGF)0 |b 58 |e Contributor |
| 700 | 1 | _ | |a Walker, Robert C |0 P:(DE-HGF)0 |b 59 |e Contributor |
| 700 | 1 | _ | |a Grace, Ben L |0 P:(DE-HGF)0 |b 60 |e Contributor |
| 700 | 1 | _ | |a Lagergren, Jesper |0 P:(DE-HGF)0 |b 61 |e Contributor |
| 700 | 1 | _ | |a Gossage, James |0 P:(DE-HGF)0 |b 62 |e Contributor |
| 700 | 1 | _ | |a Davies, Andrew |0 P:(DE-HGF)0 |b 63 |e Contributor |
| 700 | 1 | _ | |a Chang, Fuju |0 P:(DE-HGF)0 |b 64 |e Contributor |
| 700 | 1 | _ | |a Mahadeva, Ula |0 P:(DE-HGF)0 |b 65 |e Contributor |
| 700 | 1 | _ | |a Goh, Vicky |0 P:(DE-HGF)0 |b 66 |e Contributor |
| 700 | 1 | _ | |a Ciccarelli, Francesca D |0 P:(DE-HGF)0 |b 67 |e Contributor |
| 700 | 1 | _ | |a Sanders, Grant |0 P:(DE-HGF)0 |b 68 |e Contributor |
| 700 | 1 | _ | |a Berrisford, Richard |0 P:(DE-HGF)0 |b 69 |e Contributor |
| 700 | 1 | _ | |a Chan, David |0 P:(DE-HGF)0 |b 70 |e Contributor |
| 700 | 1 | _ | |a Cheong, Ed |0 P:(DE-HGF)0 |b 71 |e Contributor |
| 700 | 1 | _ | |a Kumar, Bhaskar |0 P:(DE-HGF)0 |b 72 |e Contributor |
| 700 | 1 | _ | |a Sreedharan, L. |0 P:(DE-HGF)0 |b 73 |e Contributor |
| 700 | 1 | _ | |a Parsons, Simon L |0 P:(DE-HGF)0 |b 74 |e Contributor |
| 700 | 1 | _ | |a Soomro, Irshad |0 P:(DE-HGF)0 |b 75 |e Contributor |
| 700 | 1 | _ | |a Kaye, Philip |0 P:(DE-HGF)0 |b 76 |e Contributor |
| 700 | 1 | _ | |a Saunders, John |0 P:(DE-HGF)0 |b 77 |e Contributor |
| 700 | 1 | _ | |a Lovat, Laurence |0 P:(DE-HGF)0 |b 78 |e Contributor |
| 700 | 1 | _ | |a Haidry, Rehan |0 P:(DE-HGF)0 |b 79 |e Contributor |
| 700 | 1 | _ | |a Scott, Michael |0 P:(DE-HGF)0 |b 80 |e Contributor |
| 700 | 1 | _ | |a Sothi, Sharmila |0 P:(DE-HGF)0 |b 81 |e Contributor |
| 700 | 1 | _ | |a Lishman, Suzy |0 P:(DE-HGF)0 |b 82 |e Contributor |
| 700 | 1 | _ | |a Hanna, George B |0 P:(DE-HGF)0 |b 83 |e Contributor |
| 700 | 1 | _ | |a Peters, Christopher J |0 P:(DE-HGF)0 |b 84 |e Contributor |
| 700 | 1 | _ | |a Moorthy, Krishna |0 P:(DE-HGF)0 |b 85 |e Contributor |
| 700 | 1 | _ | |a Grabowska, Anna |0 P:(DE-HGF)0 |b 86 |e Contributor |
| 700 | 1 | _ | |a Turkington, Richard |0 P:(DE-HGF)0 |b 87 |e Contributor |
| 700 | 1 | _ | |a McManus, Damian |0 P:(DE-HGF)0 |b 88 |e Contributor |
| 700 | 1 | _ | |a Coleman, Helen |0 P:(DE-HGF)0 |b 89 |e Contributor |
| 700 | 1 | _ | |a Petty, Russell D |0 P:(DE-HGF)0 |b 90 |e Contributor |
| 700 | 1 | _ | |a Bartlet, Freddie |0 P:(DE-HGF)0 |b 91 |e Contributor |
| 773 | _ | _ | |a 10.1038/s41467-024-47619-4 |g Vol. 15, no. 1, p. 4074 |0 PERI:(DE-600)2553671-0 |n 1 |p 4074 |t Nature Communications |v 15 |y 2024 |x 2041-1723 |
| 913 | 1 | _ | |a DE-HGF |b Gesundheit |l Krebsforschung |1 G:(DE-HGF)POF4-310 |0 G:(DE-HGF)POF4-313 |3 G:(DE-HGF)POF4 |2 G:(DE-HGF)POF4-300 |4 G:(DE-HGF)POF |v Krebsrisikofaktoren und Prävention |x 0 |
| 915 | _ | _ | |a JCR |0 StatID:(DE-HGF)0100 |2 StatID |b NAT COMMUN : 2022 |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0200 |2 StatID |b SCOPUS |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0300 |2 StatID |b Medline |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0320 |2 StatID |b PubMed Central |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0501 |2 StatID |b DOAJ Seal |d 2023-05-02T09:09:09Z |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0500 |2 StatID |b DOAJ |d 2023-05-02T09:09:09Z |
| 915 | _ | _ | |a Peer Review |0 StatID:(DE-HGF)0030 |2 StatID |b DOAJ : Peer review |d 2023-05-02T09:09:09Z |
| 915 | _ | _ | |a Creative Commons Attribution CC BY (No Version) |0 LIC:(DE-HGF)CCBYNV |2 V:(DE-HGF) |b DOAJ |d 2023-05-02T09:09:09Z |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0199 |2 StatID |b Clarivate Analytics Master Journal List |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1050 |2 StatID |b BIOSIS Previews |d 2023-08-29 |
| 915 | _ | _ | |a WoS |0 StatID:(DE-HGF)0113 |2 StatID |b Science Citation Index Expanded |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0150 |2 StatID |b Web of Science Core Collection |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1030 |2 StatID |b Current Contents - Life Sciences |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1190 |2 StatID |b Biological Abstracts |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1060 |2 StatID |b Current Contents - Agriculture, Biology and Environmental Sciences |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1040 |2 StatID |b Zoological Record |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0160 |2 StatID |b Essential Science Indicators |d 2023-08-29 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1150 |2 StatID |b Current Contents - Physical, Chemical and Earth Sciences |d 2023-08-29 |
| 915 | _ | _ | |a IF >= 15 |0 StatID:(DE-HGF)9915 |2 StatID |b NAT COMMUN : 2022 |d 2023-08-29 |
| 915 | _ | _ | |a Article Processing Charges |0 StatID:(DE-HGF)0561 |2 StatID |d 2023-08-29 |
| 915 | _ | _ | |a Fees |0 StatID:(DE-HGF)0700 |2 StatID |d 2023-08-29 |
| 920 | 2 | _ | |0 I:(DE-He78)C150-20160331 |k C150 |l NWG Tumorgenese und molekulare Krebsprävention |x 0 |
| 920 | 0 | _ | |0 I:(DE-He78)C150-20160331 |k C150 |l NWG Tumorgenese und molekulare Krebsprävention |x 0 |
| 920 | 1 | _ | |0 I:(DE-He78)C150-20160331 |k C150 |l NWG Tumorgenese und molekulare Krebsprävention |x 0 |
| 980 | _ | _ | |a journal |
| 980 | _ | _ | |a USER |
| 980 | _ | _ | |a VDBRELEVANT |
| 980 | _ | _ | |a I:(DE-He78)C150-20160331 |
| Library | Collection | CLSMajor | CLSMinor | Language | Author |
|---|