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Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity.
Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, Li B, Arden K, Ren B, Nathanson DA, Kornblum HI, Taylor MD, Kaushal S, Cavenee WK, Wechsler-Reya R, Furnari FB, Vandenberg SR, Rao PN, Wahl GM, Bafna V, Mischel PS. Turner KM, et al. Among authors: deshpande v. Nature. 2017 Mar 2;543(7643):122-125. doi: 10.1038/nature21356. Epub 2017 Feb 8. Nature. 2017. PMID: 28178237 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: deshpande v. 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.
REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats.
Dolzhenko E, Weisburd B, Ibañez K, Rajan-Babu IS, Anyansi C, Bennett MF, Billingsley K, Carroll A, Clamons S, Danzi MC, Deshpande V, Ding J, Fazal S, Halman A, Jadhav B, Qiu Y, Richmond PA, Saunders CT, Scheffler K, van Vugt JJFA, Zwamborn RRAJ; Genomics England Research Consortium; Chong SS, Friedman JM, Tucci A, Rehm HL, Eberle MA. Dolzhenko E, et al. Among authors: deshpande v. Genome Med. 2022 Aug 11;14(1):84. doi: 10.1186/s13073-022-01085-z. Genome Med. 2022. PMID: 35948990 Free PMC article.
Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study.
Ibañez K, Polke J, Hagelstrom RT, Dolzhenko E, Pasko D, Thomas ERA, Daugherty LC, Kasperaviciute D, Smith KR; WGS for Neurological Diseases Group; Deans ZC, Hill S, Fowler T, Scott RH, Hardy J, Chinnery PF, Houlden H, Rendon A, Caulfield MJ, Eberle MA, Taft RJ, Tucci A; Genomics England Research Consortium. Ibañez K, et al. Lancet Neurol. 2022 Mar;21(3):234-245. doi: 10.1016/S1474-4422(21)00462-2. Lancet Neurol. 2022. PMID: 35182509 Free PMC article.
ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.
Dolzhenko E, Deshpande V, Schlesinger F, Krusche P, Petrovski R, Chen S, Emig-Agius D, Gross A, Narzisi G, Bowman B, Scheffler K, van Vugt JJFA, French C, Sanchis-Juan A, Ibáñez K, Tucci A, Lajoie BR, Veldink JH, Raymond FL, Taft RJ, Bentley DR, Eberle MA. Dolzhenko E, et al. Among authors: deshpande v. Bioinformatics. 2019 Nov 1;35(22):4754-4756. doi: 10.1093/bioinformatics/btz431. Bioinformatics. 2019. PMID: 31134279 Free PMC article.
807 results