Browsing by Author "Weir, Barbara Ann"

Now showing items 1-7 of 7

    • Absolute quantification of somatic DNA alterations in human cancer 

      Carter, Scott L.; Cibulskis, Kristian; Helman, Elena; McKenna, Aaron; Shen, Hui; Zack, Travis; Laird, Peter W.; Onofrio, Robert C.; Winckler, Wendy; Weir, Barbara A.; Beroukhim, Rameen; Pellman, David; Levine, Douglas A.; Lander, Eric S.; Meyerson, Matthew; Getz, Gad (2015)
      We developed a computational method (ABSOLUTE) that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations. ABSOLUTE can detect subclonal heterogeneity, somatic homozygosity, and ...

    • Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis 

      LaFramboise, Thomas; Weir, Barbara Ann; Zhao, Xiaojun; Beroukhim, Rameen; Li, Cheng; Harrington, David Paul; Sellers, William R; Meyerson, Matthew Langer (Public Library of Science, 2005)
      Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. Similarly, ...

    • An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer 

      Sulahian, R; Casey, F; Shen, J; Qian, Zhirong; Shin, H; Ogino, Shuji; Weir, Barbara Ann; Vazquez, F; Liu, Xiaole (Shirley) Shirley; Hahn, William Chun; Bass, Adam Joel; Chan, Vivian; Shivdasani, Ramesh Arjun (Springer Nature, 2013)
      Lineage-restricted transcription factors (TFs) are frequently mutated or overexpressed in cancer and contribute toward malignant behaviors, but the molecular bases of their oncogenic properties are largely unknown. Because ...

    • Major Copy Proportion Analysis of Tumor Samples Using SNP Arrays 

      Li, Cheng; Beroukhim, Rameen; Weir, Barbara Ann; Winckler, Wendy; Garraway, Levi Alexander; Sellers, William R; Meyerson, Matthew Langer (BioMed Central, 2008)
      Background: Single nucleotide polymorphisms (SNPs) are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been developed for high-throughput ...

    • PAK1 is a Breast Cancer Oncogene that Coordinately Activates MAPK and MET Signaling 

      Shrestha, Yashaswi; Schafer, Eric J.; Boehm, Jesse S.; He, Frank; Wang, Shumei; Barretina, Jordi; Thomas, Sapana Rachael; Du, Jinyan; Weir, Barbara Ann; Zhao, Jean J.; Golub, Todd R.; Beroukhim, Rameen; Hahn, William C.; Polyak, Kornelia (Nature Publishing Group, 2012)
      Activating mutations in the RAS family or BRAF frequently occur in many types of human cancers but are rarely detected in breast tumors. However, activation of the RAS-RAF-MEK-ERK Mitogen-Activated Protein Kinase (MAPK) ...

    • Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies 

      Cowley, Glenn S; Weir, Barbara A; Vazquez, Francisca; Tamayo, Pablo; Scott, Justine A; Rusin, Scott; East-Seletsky, Alexandra; Ali, Levi D; Gerath, William FJ; Pantel, Sarah E; Lizotte, Patrick H; Jiang, Guozhi; Hsiao, Jessica; Tsherniak, Aviad; Dwinell, Elizabeth; Aoyama, Simon; Okamoto, Michael; Harrington, William; Gelfand, Ellen; Green, Thomas M; Tomko, Mark J; Gopal, Shuba; Wong, Terence C; Li, Hubo; Howell, Sara; Stransky, Nicolas; Liefeld, Ted; Jang, Dongkeun; Bistline, Jonathan; Hill Meyers, Barbara; Armstrong, Scott A; Anderson, Ken C; Stegmaier, Kimberly; Reich, Michael; Pellman, David; Boehm, Jesse S; Mesirov, Jill P; Golub, Todd R; Root, David E; Hahn, William C (Nature Publishing Group, 2014)
      Using a genome-scale, lentivirally delivered shRNA library, we performed massively parallel pooled shRNA screens in 216 cancer cell lines to identify genes that are required for cell proliferation and/or viability. Cell ...

    • SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas 

      Bass, Adam Joel; Watanabe, Hideo; Mermel, Craig; Yu, Soyoung; Perner, Sven; Verhaak, Roel; Kim, So Jeong; Wardwell, Leslie; Tamayo, Pablo; Gat-Viks, Irit; Ramos, Alex H; Woo, Michele S; Weir, Barbara Ann; Getz, Gad A; Beroukhim, Rameen; O, Michael; Dutt, Amit; Rozenblatt-Rosen, Orit; Dziunycz, Piotr; Komisarof, Justin; Chirieac, Lucian Radu; LaFargue, Christopher J; Scheble, Veit; Wilbertz, Theresia; Ma, Changqing; Rao, Shilpa; Nakagawa, Hiroshi; Stairs, Douglas B; Lin, Lin; Giordano, Thomas J; Wagner, Patrick; Minna, John D; Gazdar, Adi F; Zhu, Chang Qi; Brose, Marcia S; Cecconello, Ivan; Jr, Ulysses Ribeiro; Marie, Suely K; Dahl, Olav; Shivdasani, Ramesh Arjun; Tsao, Ming-Sound; Rubin, Mark A; Wong, Kwok-Kin; Regev, Aviv; Hahn, William Chun; Beer, David G; Rustgi, Anil K; Meyerson, Matthew Langer (Springer Nature, 2009)
      Lineage survival oncogenes are activated by somatic DNA alterations in cancers arising from the cell lineages in which these genes play a role in normal development.1,2 Here we show that a peak of genomic amplification on ...