Browsing by Author "MacConaill, Laura"

Now showing items 1-13 of 13

    • BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers 

      Abo, Ryan P.; Ducar, Matthew; Garcia, Elizabeth P.; Thorner, Aaron R.; Rojas-Rudilla, Vanesa; Lin, Ling; Sholl, Lynette M.; Hahn, William C.; Meyerson, Matthew; Lindeman, Neal I.; Van Hummelen, Paul; MacConaill, Laura E. (Oxford University Press, 2015)
      Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially ...

    • Colorectal Cancers from Distinct Ancestral Populations Show Variations in BRAF Mutation Frequency 

      Hanna, Megan C.; Go, Christina; Roden, Christine; Jones, Robert T.; Pochanard, Panisa; Javed, Ahmed Yasir; Javed, Awais; Mondal, Chandrani; Palescandolo, Emanuele; Van Hummelen, Paul; Hatton, Charles; Bass, Adam J.; Chun, Sung Min; Na, Deuk Chae; Kim, Tae-Im; Jang, Se Jin; Osarogiagbon, Raymond U.; Hahn, William C.; Meyerson, Matthew; Garraway, Levi A.; MacConaill, Laura E. (Public Library of Science, 2013)
      It has been demonstrated for some cancers that the frequency of somatic oncogenic mutations may vary in ancestral populations. To determine whether key driver alterations might occur at different frequencies in colorectal ...

    • Comparison of Prevalence and Types of Mutations in Lung Cancers Among Black and White Populations 

      Campbell, Joshua David; Lathan, Christopher Scott; Sholl, Lynette Marie; Ducar, Matthew; Vega, Mikenah; Sunkavalli, Ashwini; Lin, Ling; Hanna, Megan; Schubert, Laura; Thorner, Aaron; Faris, Nicholas; Williams, David; Osarogiagbon, Raymond U.; van Hummelen, Paul; Meyerson, Matthew Langer; MacConaill, Laura Eleanor (American Medical Association (AMA), 2017)
      Importance Lung cancer is the leading cause of cancer death in the United States in all ethnic and racial groups. The overall death rate from lung cancer is higher in black patients than in white patients. Objective ...

    • Differential Sensitivity of Melanoma Cell Lines with BRAFV600E Mutation to the Specific Raf Inhibitor PLX4032 

      Søndergaard, Jonas N; Nazarian, Ramin; Guo, Deliang; Hsueh, Teli; Mok, Stephen; Sazegar, Hooman; Barretina, Jordi G; Kehoe, Sarah M; Attar, Narsis; von Euw, Erika; Zuckerman, Jonathan E; Chmielowski, Bartosz; Comin-Anduix, Begoña; Koya, Richard C; Mischel, Paul S; Lo, Roger S; Ribas, Antoni; Wang, Qi; MacConaill, Laura Eleanor (BioMed Central, 2010)
      Blocking oncogenic signaling induced by the BRAFV600E mutation is a promising approach for melanoma treatment. We tested the anti-tumor effects of a specific inhibitor of Raf protein kinases, PLX4032/RG7204, in melanoma ...

    • Genotyping Cancer-Associated Genes in Chordoma Identifies Mutations in Oncogenes and Areas of Chromosomal Loss Involving CDKN2A, PTEN, and SMARCB1 

      Choy, Edwin; MacConaill, Laura E.; Cote, Gregory M.; Le, Long P.; Shen, Jacson K.; Nielsen, Gunnlaugur P.; Iafrate, Anthony J.; Garraway, Levi A.; Hornicek, Francis J.; Duan, Zhenfeng (Public Library of Science, 2014)
      The molecular mechanisms underlying chordoma pathogenesis are unknown. We therefore sought to identify novel mutations to better understand chordoma biology and to potentially identify therapeutic targets. Given the ...

    • High-Throughput Genotyping in Metastatic Esophageal Squamous Cell Carcinoma Identifies Phosphoinositide-3-Kinase and BRAF Mutations 

      Maeng, Chi Hoon; Lee, Jeeyun; van Hummelen, Paul; Jang, Jiryeon; Kim, Kyoung-Mee; Shim, Young-Mog; Park, Se Hoon; Palescandolo, Emanuele; Park, Ha Young; Kang, So Young; MacConaill, Laura Eleanor (Public Library of Science, 2012)
      Background: Given the high incidence of metastatic esophageal squamous cell carcinoma, especially in Asia, we screened for the presence of somatic mutations using OncoMap platform with the aim of defining subsets of patients ...

    • High-Throughput Mutation Profiling Identifies Frequent Somatic Mutations in Advanced Gastric Adenocarcinoma 

      Lee, Jeeyun; van Hummelen, Paul; Go, Christina; Jang, Jiryeon; Park, Joon Oh; Kim, Kyoung-Mee; Palescandolo, Emanuele; Park, Ha Young; Kang, So Young; Kang, Won Ki; MacConaill, Laura Eleanor (Public Library of Science, 2012)
      Background: Gastric cancer is one of the leading cancer types in incidence and mortality, especially in Asia. In order to improve survival, identification of a catalogue of molecular alterations underlying gastric cancer ...

    • The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine 

      Garofalo, Andrea; Sholl, Lynette; Reardon, Brendan; Taylor-Weiner, Amaro; Amin-Mansour, Ali; Miao, Diana; Liu, David; Oliver, Nelly; MacConaill, Laura; Ducar, Matthew; Rojas-Rudilla, Vanesa; Giannakis, Marios; Ghazani, Arezou; Gray, Stacy; Janne, Pasi; Garber, Judy; Joffe, Steve; Lindeman, Neal; Wagle, Nikhil; Garraway, Levi A.; Van Allen, Eliezer M. (BioMed Central, 2016)
      Background: The diversity of clinical tumor profiling approaches (small panels to whole exomes with matched or unmatched germline analysis) may engender uncertainty about their benefits and liabilities, particularly in ...

    • Mutational Profiling Reveals PIK3CA Mutations in Gallbladder Carcinoma 

      Deshpande, Vikram; Nduaguba, Afamefuna Maxwell; Zimmerman, Stephanie M; Kehoe, Sarah M; MacConaill, Laura Eleanor; Lauwers, Gregory Y.; Ferrone, Cristina Rosa; Bardeesy, Nabeel; Zhu, Andrew Xiuxuan; Hezel, Aram F (Springer Science + Business Media, 2011)

    • Novel Genetic Mutations in a Sporadic Port-Wine Stain 

      Lian, Christine Guo; Sholl, Lynette Marie; Zakka, Labib; O, Teresa M.; Liu, Cynthia; Xu, Shuyun; Stanek, Ewelina; Garcia, Elizabeth; Jia, Yonghui; MacConaill, Laura Eleanor; Murphy, George Francis; Waner, Milton; Mihm, Martin Charles (American Medical Association (AMA), 2014)
      Importance Port-wine stains (PWSs) are common congenital cutaneous capillary malformations. A somatic GNAQ mutation was recently identified in patients with sporadic PWSs and Sturge-Weber syndrome. However, subsequent ...

    • Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples 

      Campbell, Catarina D.; Kehoe, Sarah M.; Hatton, Charles; Niu, Lili; Yao, Keluo; Hanna, Megan; Mondal, Chandrani; Luongo, Lauren; Baker, Alissa C.; Philips, Juliet; Goff, Deborah J.; Rubin, Mark A.; Corso, Gianni; Roviello, Franco; MacConaill, Laura Eleanor; Bass, Adam Joel; Davis, Matthew J; Emery, Caroline Margaret; Fiorentino, Michelangelo; Polyak, Kornelia; Chan, Jennifer Ang; Wang, Yufang; Fletcher, Jonathan A.; Santagata, Sandro; Shivdasani, Ramesh Arjun; Kieran, Mark W.; Ligon, Keith Lloyd; Stiles, Charles Dean; Hahn, William C.; Meyerson, Matthew Langer; Garraway, Levi Alexander; Jones, Chris (Public Library of Science, 2009)
      Background: Detection of critical cancer gene mutations in clinical tumor specimens may predict patient outcomes and inform treatment options; however, high-throughput mutation profiling remains underdeveloped as a diagnostic ...

    • Toward Accurate High-Throughput SNP Genotyping in the Presence of Inherited Copy Number Variation 

      MacConaill, Laura Eleanor; Aldred, Micheala A; Lu, Xincheng; LaFramboise, Thomas (BioMed Central, 2007)
      Background: The recent discovery of widespread copy number variation in humans has forced a shift away from the assumption of two copies per locus per cell throughout the autosomal genome. In particular, a SNP site can no ...

    • Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine 

      Allen, Eliezer M. Van; Wagle, Nikhil; Stojanov, Petar; Perrin, Danielle L.; Cibulskis, Kristian; Marlow, Sara; Jane-Valbuena, Judit; Friedrich, Dennis C.; Kryukov, Gregory; Carter, Scott L.; McKenna, Aaron; Sivachenko, Andrey; Rosenberg, Mara; Kiezun, Adam; Voet, Douglas; Lawrence, Michael; Lichtenstein, Lee T.; Gentry, Jeff G.; Huang, Franklin W.; Fostel, Jennifer; Farlow, Deborah; Barbie, David; Gandhi, Leena; Lander, Eric S.; Gray, Stacy W.; Joffe, Steven; Janne, Pasi; Garber, Judy; MacConaill, Laura; Lindeman, Neal; Rollins, Barrett; Kantoff, Philip; Fisher, Sheila A.; Gabriel, Stacey; Getz, Gad; Garraway, Levi A. (2013)
      Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES ...