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Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.
Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, Stewart C, Rosenberg M, Francis JM, Zhang CZ, Cohen O, Oh C, Ding H, Polak P, Lloyd M, Mahmud S, Helvie K, Merrill MS, Santiago RA, O'Connor EP, Jeong SH, Leeson R, Barry RM, Kramkowski JF, Zhang Z, Polacek L, Lohr JG, Schleicher M, Lipscomb E, Saltzman A, Oliver NM, Marini L, Waks AG, Harshman LC, Tolaney SM, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Johannessen CM, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Love JC, Meyerson M. Adalsteinsson VA, et al. Among authors: polak p. Nat Commun. 2017 Nov 6;8(1):1324. doi: 10.1038/s41467-017-00965-y. Nat Commun. 2017. PMID: 29109393 Free PMC article.
A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer.
Polak P, Kim J, Braunstein LZ, Karlic R, Haradhavala NJ, Tiao G, Rosebrock D, Livitz D, Kübler K, Mouw KW, Kamburov A, Maruvka YE, Leshchiner I, Lander ES, Golub TR, Zick A, Orthwein A, Lawrence MS, Batra RN, Caldas C, Haber DA, Laird PW, Shen H, Ellisen LW, D'Andrea AD, Chanock SJ, Foulkes WD, Getz G. Polak P, et al. Nat Genet. 2017 Oct;49(10):1476-1486. doi: 10.1038/ng.3934. Epub 2017 Aug 21. Nat Genet. 2017. PMID: 28825726 Free PMC article.
Analysis of somatic microsatellite indels identifies driver events in human tumors.
Maruvka YE, Mouw KW, Karlic R, Parasuraman P, Kamburov A, Polak P, Haradhvala NJ, Hess JM, Rheinbay E, Brody Y, Koren A, Braunstein LZ, D'Andrea A, Lawrence MS, Bass A, Bernards A, Michor F, Getz G. Maruvka YE, et al. Among authors: polak p. Nat Biotechnol. 2017 Oct;35(10):951-959. doi: 10.1038/nbt.3966. Epub 2017 Sep 11. Nat Biotechnol. 2017. PMID: 28892075 Free PMC article.
Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma.
Gopal RK, Kübler K, Calvo SE, Polak P, Livitz D, Rosebrock D, Sadow PM, Campbell B, Donovan SE, Amin S, Gigliotti BJ, Grabarek Z, Hess JM, Stewart C, Braunstein LZ, Arndt PF, Mordecai S, Shih AR, Chaves F, Zhan T, Lubitz CC, Kim J, Iafrate AJ, Wirth L, Parangi S, Leshchiner I, Daniels GH, Mootha VK, Dias-Santagata D, Getz G, McFadden DG. Gopal RK, et al. Among authors: polak p. Cancer Cell. 2018 Aug 13;34(2):242-255.e5. doi: 10.1016/j.ccell.2018.06.013. Cancer Cell. 2018. PMID: 30107175 Free PMC article.
Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors.
Miao D, Margolis CA, Vokes NI, Liu D, Taylor-Weiner A, Wankowicz SM, Adeegbe D, Keliher D, Schilling B, Tracy A, Manos M, Chau NG, Hanna GJ, Polak P, Rodig SJ, Signoretti S, Sholl LM, Engelman JA, Getz G, Jänne PA, Haddad RI, Choueiri TK, Barbie DA, Haq R, Awad MM, Schadendorf D, Hodi FS, Bellmunt J, Wong KK, Hammerman P, Van Allen EM. Miao D, et al. Among authors: polak p. Nat Genet. 2018 Sep;50(9):1271-1281. doi: 10.1038/s41588-018-0200-2. Epub 2018 Aug 27. Nat Genet. 2018. PMID: 30150660 Free PMC article.
RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues.
Yizhak K, Aguet F, Kim J, Hess JM, Kübler K, Grimsby J, Frazer R, Zhang H, Haradhvala NJ, Rosebrock D, Livitz D, Li X, Arich-Landkof E, Shoresh N, Stewart C, Segrè AV, Branton PA, Polak P, Ardlie KG, Getz G. Yizhak K, et al. Among authors: polak p. Science. 2019 Jun 7;364(6444):eaaw0726. doi: 10.1126/science.aaw0726. Science. 2019. PMID: 31171663 Free PMC article.
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.
Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group; Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris QD, Stein LD; PCAWG Consortium. Jiao W, et al. Among authors: polak p. Nat Commun. 2020 Feb 5;11(1):728. doi: 10.1038/s41467-019-13825-8. Nat Commun. 2020. PMID: 32024849 Free PMC article.
Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Nature. 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5. Nature. 2020. PMID: 32025007 Free PMC article.
The repertoire of mutational signatures in human cancer.
Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V; PCAWG Mutational Signatures Working Group; Getz G, Rozen SG, Stratton MR; PCAWG Consortium. Alexandrov LB, et al. Nature. 2020 Feb;578(7793):94-101. doi: 10.1038/s41586-020-1943-3. Epub 2020 Feb 5. Nature. 2020. PMID: 32025018 Free PMC article.
357 results