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Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation.
Costello M, Pugh TJ, Fennell TJ, Stewart C, Lichtenstein L, Meldrim JC, Fostel JL, Friedrich DC, Perrin D, Dionne D, Kim S, Gabriel SB, Lander ES, Fisher S, Getz G. Costello M, et al. Among authors: fennell tj. Nucleic Acids Res. 2013 Apr 1;41(6):e67. doi: 10.1093/nar/gks1443. Epub 2013 Jan 8. Nucleic Acids Res. 2013. PMID: 23303777 Free PMC article.
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries.
Fisher S, Barry A, Abreu J, Minie B, Nolan J, Delorey TM, Young G, Fennell TJ, Allen A, Ambrogio L, Berlin AM, Blumenstiel B, Cibulskis K, Friedrich D, Johnson R, Juhn F, Reilly B, Shammas R, Stalker J, Sykes SM, Thompson J, Walsh J, Zimmer A, Zwirko Z, Gabriel S, Nicol R, Nusbaum C. Fisher S, et al. Among authors: fennell tj. Genome Biol. 2011;12(1):R1. doi: 10.1186/gb-2011-12-1-r1. Epub 2011 Jan 4. Genome Biol. 2011. PMID: 21205303 Free PMC article.
Targeted exon sequencing by in-solution hybrid selection.
Blumenstiel B, Cibulskis K, Fisher S, DeFelice M, Barry A, Fennell T, Abreu J, Minie B, Costello M, Young G, Maquire J, Kernytsky A, Melnikov A, Rogov P, Gnirke A, Gabriel S. Blumenstiel B, et al. Curr Protoc Hum Genet. 2010 Jul;Chapter 18:Unit 18.4. doi: 10.1002/0471142905.hg1804s66. Curr Protoc Hum Genet. 2010. PMID: 20582916
Melanoma genome sequencing reveals frequent PREX2 mutations.
Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, Ramos AH, Pugh TJ, Stransky N, Parkin M, Winckler W, Mahan S, Ardlie K, Baldwin J, Wargo J, Schadendorf D, Meyerson M, Gabriel SB, Golub TR, Wagner SN, Lander ES, Getz G, Chin L, Garraway LA. Berger MF, et al. Among authors: fennell t. Nature. 2012 May 9;485(7399):502-6. doi: 10.1038/nature11071. Nature. 2012. PMID: 22622578 Free PMC article.
A framework for variation discovery and genotyping using next-generation DNA sequencing data.
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. DePristo MA, et al. Among authors: fennell tj. Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806. Epub 2011 Apr 10. Nat Genet. 2011. PMID: 21478889 Free PMC article.
RNA-SeQC: RNA-seq metrics for quality control and process optimization.
DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. DeLuca DS, et al. Bioinformatics. 2012 Jun 1;28(11):1530-2. doi: 10.1093/bioinformatics/bts196. Epub 2012 Apr 25. Bioinformatics. 2012. PMID: 22539670 Free PMC article.
Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Lawrence MS, et al. Among authors: fennell t. Nature. 2013 Jul 11;499(7457):214-218. doi: 10.1038/nature12213. Epub 2013 Jun 16. Nature. 2013. PMID: 23770567 Free PMC article.
The genomic complexity of primary human prostate cancer.
Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA. Berger MF, et al. Among authors: fennell t. Nature. 2011 Feb 10;470(7333):214-20. doi: 10.1038/nature09744. Nature. 2011. PMID: 21307934 Free PMC article.
63 results