Search Results - "Gabriel, Stacey"

Advances in understanding cancer genomes through second-generation sequencing by Meyerson, Matthew, Gabriel, Stacey, Getz, Gad

“…Key Points Analyses of cancer genome sequences and structures provide insights for understanding cancer biology, diagnosis and therapy. The application of…”
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Estimating epidemiologic dynamics from cross-sectional viral load distributions by Hay, James A, Kennedy-Shaffer, Lee, Kanjilal, Sanjat, Lennon, Niall J, Gabriel, Stacey B, Lipsitch, Marc, Mina, Michael J

“…Estimating an epidemic's trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are…”
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Pacific biosciences sequencing technology for genotyping and variation discovery in human data by Carneiro, Mauricio O, Russ, Carsten, Ross, Michael G, Gabriel, Stacey B, Nusbaum, Chad, DePristo, Mark A

“…Pacific Biosciences technology provides a fundamentally new data type that provides the potential to overcome some limitations of current next generation…”
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A Dominant Mutation in Human RAD51 Reveals Its Function in DNA Interstrand Crosslink Repair Independent of Homologous Recombination by Wang, Anderson T., Kim, Taeho, Wagner, John E., Conti, Brooke A., Lach, Francis P., Huang, Athena L., Molina, Henrik, Sanborn, Erica M., Zierhut, Heather, Cornes, Belinda K., Abhyankar, Avinash, Sougnez, Carrie, Gabriel, Stacey B., Auerbach, Arleen D., Kowalczykowski, Stephen C., Smogorzewska, Agata

“…Repair of DNA interstrand crosslinks requires action of multiple DNA repair pathways, including homologous recombination. Here, we report a de novo…”
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Genetic Interleukin 6 Signaling Deficiency Attenuates Cardiovascular Risk in Clonal Hematopoiesis by Bick, Alexander G., Pirruccello, James P., Griffin, Gabriel K., Gupta, Namrata, Gabriel, Stacey, Saleheen, Danish, Libby, Peter, Kathiresan, Sekar, Natarajan, Pradeep

“…BACKGROUND:Clonal hematopoiesis of indeterminate potential (CHIP) refers to clonal expansion of hematopoietic stem cells attributable to acquired leukemic…”
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Discovery and saturation analysis of cancer genes across 21 tumour types by Lawrence, Michael S., Stojanov, Petar, Mermel, Craig H., Robinson, James T., Garraway, Levi A., Golub, Todd R., Meyerson, Matthew, Gabriel, Stacey B., Lander, Eric S., Getz, Gad

“…Although a few cancer genes are mutated in a high proportion of tumours of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To…”
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Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples by Cibulskis, Kristian, Lawrence, Michael S, Carter, Scott L, Sivachenko, Andrey, Jaffe, David, Sougnez, Carrie, Gabriel, Stacey, Meyerson, Matthew, Lander, Eric S, Getz, Gad

“…The MuTect algorithm for calling somatic point mutations enables subclonal analysis of the whole-genome or whole-exome sequencing data being generated in…”
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Pan-cancer patterns of somatic copy number alteration by Zack, Travis I, Schumacher, Steven E, Carter, Scott L, Cherniack, Andrew D, Saksena, Gordon, Tabak, Barbara, Lawrence, Michael S, Zhang, Cheng-Zhong, Wala, Jeremiah, Mermel, Craig H, Sougnez, Carrie, Gabriel, Stacey B, Hernandez, Bryan, Shen, Hui, Laird, Peter W, Getz, Gad, Meyerson, Matthew, Beroukhim, Rameen

“…Rameen Beroukhim and colleagues analyzed somatic structural alterations in 12 tumor types. Whole-genome doubling was found in over a third of all cancers,…”
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Recurrent and functional regulatory mutations in breast cancer by Rheinbay, Esther, Parasuraman, Prasanna, Grimsby, Jonna, Tiao, Grace, Engreitz, Jesse M., Kim, Jaegil, Lawrence, Michael S., Taylor-Weiner, Amaro, Rodriguez-Cuevas, Sergio, Rosenberg, Mara, Hess, Julian, Stewart, Chip, Maruvka, Yosef E., Stojanov, Petar, Cortes, Maria L., Seepo, Sara, Cibulskis, Carrie, Tracy, Adam, Pugh, Trevor J., Lee, Jesse, Zheng, Zongli, Ellisen, Leif W., Iafrate, A. John, Boehm, Jesse S., Gabriel, Stacey B., Meyerson, Matthew, Golub, Todd R., Baselga, Jose, Hidalgo-Miranda, Alfredo, Shioda, Toshi, Bernards, Andre, Lander, Eric S., Getz, Gad

“…Genomic analysis of tumours has led to the identification of hundreds of cancer genes on the basis of the presence of mutations in protein-coding regions. By…”
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A framework for variation discovery and genotyping using next-generation DNA sequencing data by DePristo, Mark A, Banks, Eric, Poplin, Ryan, Garimella, Kiran V, Maguire, Jared R, Hartl, Christopher, Philippakis, Anthony A, del Angel, Guillermo, Rivas, Manuel A, Hanna, Matt, McKenna, Aaron, Fennell, Tim J, Kernytsky, Andrew M, Sivachenko, Andrey Y, Cibulskis, Kristian, Gabriel, Stacey B, Altshuler, David, Daly, Mark J

“…Mark DePristo and colleagues report an analytical framework to discover and genotype variation using whole exome and genome resequencing data from…”
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Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease by Jaiswal, Siddhartha, Natarajan, Pradeep, Silver, Alexander J, Gibson, Christopher J, Bick, Alexander G, Shvartz, Eugenia, McConkey, Marie, Gupta, Namrata, Gabriel, Stacey, Ardissino, Diego, Baber, Usman, Mehran, Roxana, Fuster, Valentin, Danesh, John, Frossard, Philippe, Saleheen, Danish, Melander, Olle, Sukhova, Galina K, Neuberg, Donna, Libby, Peter, Kathiresan, Sekar, Ebert, Benjamin L

“…The development of clonal hematopoiesis with increasing age was associated with nearly a doubling in the risk of coronary heart disease, along with an increase…”
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De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly by Lee, Jeong Ho, Huynh, My, Silhavy, Jennifer L, Kim, Sangwoo, Dixon-Salazar, Tracy, Heiberg, Andrew, Scott, Eric, Bafna, Vineet, Hill, Kiley J, Collazo, Adrienne, Funari, Vincent, Russ, Carsten, Gabriel, Stacey B, Mathern, Gary W, Gleeson, Joseph G

“…Joseph Gleeson and colleagues report exome sequencing of 20 individuals with hemimegalencephaly (HME), identifying de novo somatic mutations in the PIK3CA ,…”
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A framework for the interpretation of de novo mutation in human disease by Samocha, Kaitlin E, Robinson, Elise B, Sanders, Stephan J, Stevens, Christine, Sabo, Aniko, McGrath, Lauren M, Kosmicki, Jack A, Rehnström, Karola, Mallick, Swapan, Kirby, Andrew, Wall, Dennis P, MacArthur, Daniel G, Gabriel, Stacey B, DePristo, Mark, Purcell, Shaun M, Palotie, Aarno, Boerwinkle, Eric, Buxbaum, Joseph D, Cook, Edwin H, Gibbs, Richard A, Schellenberg, Gerard D, Sutcliffe, James S, Devlin, Bernie, Roeder, Kathryn, Neale, Benjamin M, Daly, Mark J

“…Mark Daly and colleagues present a statistical framework to evaluate the role of de novo mutations in human disease by calibrating a model of de novo mutation…”
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Whole-exome sequencing and homozygosity analysis implicate depolarization-regulated neuronal genes in autism by Chahrour, Maria H, Yu, Timothy W, Lim, Elaine T, Ataman, Bulent, Coulter, Michael E, Hill, R Sean, Stevens, Christine R, Schubert, Christian R, Greenberg, Michael E, Gabriel, Stacey B, Walsh, Christopher A

“…Although autism has a clear genetic component, the high genetic heterogeneity of the disorder has been a challenge for the identification of causative genes…”
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Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel by Mitt, Mario, Kals, Mart, Pärn, Kalle, Gabriel, Stacey B, Lander, Eric S, Palotie, Aarno, Ripatti, Samuli, Morris, Andrew P, Metspalu, Andres, Esko, Tõnu, Mägi, Reedik, Palta, Priit

“…Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation…”
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The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data by McKenna, Aaron, Hanna, Matthew, Banks, Eric, Sivachenko, Andrey, Cibulskis, Kristian, Kernytsky, Andrew, Garimella, Kiran, Altshuler, David, Gabriel, Stacey, Daly, Mark, DePristo, Mark A

“…Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among…”
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Paired exome analysis of Barrett's esophagus and adenocarcinoma by Stachler, Matthew D, Taylor-Weiner, Amaro, Peng, Shouyong, McKenna, Aaron, Agoston, Agoston T, Odze, Robert D, Davison, Jon M, Nason, Katie S, Loda, Massimo, Leshchiner, Ignaty, Stewart, Chip, Stojanov, Petar, Seepo, Sara, Lawrence, Michael S, Ferrer-Torres, Daysha, Lin, Jules, Chang, Andrew C, Gabriel, Stacey B, Lander, Eric S, Beer, David G, Getz, Gad, Carter, Scott L, Bass, Adam J

“…Adam Bass, Gad Getz, Scott Carter and colleagues report the whole-exome sequences of 25 pairs of esophageal adenocarcinoma and Barrett's esophagus. They…”
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A Functional Landscape of Resistance to ALK Inhibition in Lung Cancer by Wilson, Frederick H., Johannessen, Cory M., Piccioni, Federica, Tamayo, Pablo, Kim, Jong Wook, Van Allen, Eliezer M., Corsello, Steven M., Capelletti, Marzia, Calles, Antonio, Butaney, Mohit, Sharifnia, Tanaz, Gabriel, Stacey B., Mesirov, Jill P., Hahn, William C., Engelman, Jeffrey A., Meyerson, Matthew, Root, David E., Jänne, Pasi A., Garraway, Levi A.

“…We conducted a large-scale functional genetic study to characterize mechanisms of resistance to ALK inhibition in ALK-dependent lung cancer cells. We identify…”
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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 by Costello, Maura, Pugh, Trevor J, Fennell, Timothy J, Stewart, Chip, Lichtenstein, Lee, Meldrim, James C, Fostel, Jennifer L, Friedrich, Dennis C, Perrin, Danielle, Dionne, Danielle, Kim, Sharon, Gabriel, Stacey B, Lander, Eric S, Fisher, Sheila, Getz, Gad

“…As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing…”
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Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma by Giannakis, Marios, Mu, Xinmeng Jasmine, Shukla, Sachet A., Qian, Zhi Rong, Cohen, Ofir, Nishihara, Reiko, Bahl, Samira, Cao, Yin, Amin-Mansour, Ali, Yamauchi, Mai, Sukawa, Yasutaka, Stewart, Chip, Rosenberg, Mara, Mima, Kosuke, Inamura, Kentaro, Nosho, Katsuhiko, Nowak, Jonathan A., Lawrence, Michael S., Giovannucci, Edward L., Chan, Andrew T., Ng, Kimmie, Meyerhardt, Jeffrey A., Van Allen, Eliezer M., Getz, Gad, Gabriel, Stacey B., Lander, Eric S., Wu, Catherine J., Fuchs, Charles S., Ogino, Shuji, Garraway, Levi A.

“…Large-scale genomic characterization of tumors from prospective cohort studies may yield new insights into cancer pathogenesis. We performed whole-exome…”
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