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Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.
Chapman OS, Luebeck J, Sridhar S, Wong IT, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. Chapman OS, et al. Among authors: rajkumar u. Nat Genet. 2023 Dec;55(12):2189-2199. doi: 10.1038/s41588-023-01551-3. Epub 2023 Nov 9. Nat Genet. 2023. PMID: 37945900 Free PMC article.
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers.
Kim H, Nguyen NP, Turner K, Wu S, Gujar AD, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin SB, Yi E, Menghi F, Schulte JH, Henssen AG, Chang HY, Beck CR, Mischel PS, Bafna V, Verhaak RGW. Kim H, et al. Among authors: rajkumar u. Nat Genet. 2020 Sep;52(9):891-897. doi: 10.1038/s41588-020-0678-2. Epub 2020 Aug 17. Nat Genet. 2020. PMID: 32807987 Free PMC article.
The evolutionary dynamics of extrachromosomal DNA in human cancers.
Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, Liu Z, Huang W, Chang HY, Bafna V, Henssen AG, Werner B, Mischel PS. Lange JT, et al. Among authors: rajkumar u. Nat Genet. 2022 Oct;54(10):1527-1533. doi: 10.1038/s41588-022-01177-x. Epub 2022 Sep 19. Nat Genet. 2022. PMID: 36123406 Free PMC article.
Circular ecDNA promotes accessible chromatin and high oncogene expression.
Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. Wu S, et al. Among authors: rajkumar u. Nature. 2019 Nov;575(7784):699-703. doi: 10.1038/s41586-019-1763-5. Epub 2019 Nov 20. Nature. 2019. PMID: 31748743 Free PMC article.
ecDNA hubs drive cooperative intermolecular oncogene expression.
Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong IT, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. Hung KL, et al. Among authors: rajkumar u. Nature. 2021 Dec;600(7890):731-736. doi: 10.1038/s41586-021-04116-8. Epub 2021 Nov 24. Nature. 2021. PMID: 34819668 Free PMC article.
FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.
Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. Javadzadeh S, et al. Among authors: rajkumar u. NAR Genom Bioinform. 2022 Apr 26;4(2):lqac032. doi: 10.1093/nargab/lqac032. eCollection 2022 Jun. NAR Genom Bioinform. 2022. PMID: 35493723 Free PMC article.
Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change.
Dehkordi SR, Wong IT, Ni J, Luebeck J, Zhu K, Prasad G, Krockenberger L, Xu G, Chowdhury B, Rajkumar U, Caplin A, Muliaditan D, Coruh C, Jin Q, Turner K, Teo SX, Pang AWC, Alexandrov LB, Chua CEL, Furnari FB, Paulson TG, Law JA, Chang HY, Yue F, DasGupta R, Zhao J, Mischel PS, Bafna V. Dehkordi SR, et al. Among authors: rajkumar u. bioRxiv [Preprint]. 2023 Dec 13:2023.12.12.571349. doi: 10.1101/2023.12.12.571349. bioRxiv. 2023. PMID: 38168210 Free PMC article. Preprint.
37 results