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Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.
Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P; PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium. Dentro SC, et al. Among authors: deshwar ag. Cell. 2021 Apr 15;184(8):2239-2254.e39. doi: 10.1016/j.cell.2021.03.009. Epub 2021 Apr 7. Cell. 2021. PMID: 33831375 Free PMC article.
Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.
Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar AG; PCAWG Evolution and Heterogeneity Working Group; Morris QD; PCAWG Consortium. Rubanova Y, et al. Among authors: deshwar ag. Nat Commun. 2022 Dec 8;13(1):7567. doi: 10.1038/s41467-022-32336-7. Nat Commun. 2022. PMID: 36482170 Free PMC article. No abstract available.
A practical guide to cancer subclonal reconstruction from DNA sequencing.
Tarabichi M, Salcedo A, Deshwar AG, Ni Leathlobhair M, Wintersinger J, Wedge DC, Van Loo P, Morris QD, Boutros PC. Tarabichi M, et al. Among authors: deshwar ag. Nat Methods. 2021 Feb;18(2):144-155. doi: 10.1038/s41592-020-01013-2. Epub 2021 Jan 4. Nat Methods. 2021. PMID: 33398189 Free PMC article. Review.
Transcriptome-Wide Off-Target Effects of Steric-Blocking Oligonucleotides.
Holgersen EM, Gandhi S, Zhou Y, Kim J, Vaz B, Bogojeski J, Bugno M, Shalev Z, Cheung-Ong K, Gonçalves J, O'Hara M, Kron K, Verby M, Sun M, Kakaradov B, Delong A, Merico D, Deshwar AG. Holgersen EM, et al. Among authors: deshwar ag. Nucleic Acid Ther. 2021 Dec;31(6):392-403. doi: 10.1089/nat.2020.0921. Epub 2021 Aug 13. Nucleic Acid Ther. 2021. PMID: 34388351 Free PMC article.
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.
Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M; PCAWG Evolution and Heterogeneity Working Group; SMC-Het Participants; Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Salcedo A, et al. Among authors: deshwar ag. Nat Biotechnol. 2024 Jun 11. doi: 10.1038/s41587-024-02250-y. Online ahead of print. Nat Biotechnol. 2024. PMID: 38862616
A community effort to create standards for evaluating tumor subclonal reconstruction.
Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, Buchanan A, Lalansingh CM, P'ng C, Anghel CV, Umar I, Lo B, Zou W; DREAM SMC-Het Participants; Simpson JT, Stuart JM, Anastassiou D, Guan Y, Ewing AD, Ellrott K, Wedge DC, Morris Q, Van Loo P, Boutros PC. Salcedo A, et al. Among authors: deshwar ag. Nat Biotechnol. 2020 Jan;38(1):97-107. doi: 10.1038/s41587-019-0364-z. Epub 2020 Jan 9. Nat Biotechnol. 2020. PMID: 31919445 Free PMC article.
ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping.
Merico D, Spickett C, O'Hara M, Kakaradov B, Deshwar AG, Fradkin P, Gandhi S, Gao J, Grant S, Kron K, Schmitges FW, Shalev Z, Sun M, Verby M, Cahill M, Dowling JJ, Fransson J, Wienholds E, Frey BJ. Merico D, et al. Among authors: deshwar ag. NPJ Genom Med. 2020 Apr 8;5:16. doi: 10.1038/s41525-020-0123-6. eCollection 2020. NPJ Genom Med. 2020. PMID: 32284880 Free PMC article.
16 results