Search Results - "Stewart, Chip"

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues by Yizhak, Keren, Aguet, François, Kim, Jaegil, Hess, Julian M, Kübler, Kirsten, Grimsby, Jonna, Frazer, Ruslana, Zhang, Hailei, Haradhvala, Nicholas J, Rosebrock, Daniel, Livitz, Dimitri, Li, Xiao, Arich-Landkof, Eila, Shoresh, Noam, Stewart, Chip, Segrè, Ayellet V, Branton, Philip A, Polak, Paz, Ardlie, Kristin G, Getz, Gad

“…How somatic mutations accumulate in normal cells is poorly understood. A comprehensive analysis of RNA sequencing data from ~6700 samples across 29 normal…”
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SvABA: genome-wide detection of structural variants and indels by local assembly by Wala, Jeremiah A, Bandopadhayay, Pratiti, Greenwald, Noah F, O'Rourke, Ryan, Sharpe, Ted, Stewart, Chip, Schumacher, Steve, Li, Yilong, Weischenfeldt, Joachim, Yao, Xiaotong, Nusbaum, Chad, Campbell, Peter, Getz, Gad, Meyerson, Matthew, Zhang, Cheng-Zhong, Imielinski, Marcin, Beroukhim, Rameen

“…Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling…”
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Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing by Helman, Elena, Lawrence, Michael S, Stewart, Chip, Sougnez, Carrie, Getz, Gad, Meyerson, Matthew

“…Retrotransposons constitute a major source of genetic variation, and somatic retrotransposon insertions have been reported in cancer. Here, we applied…”
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MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping by Lee, Wan-Ping, Stromberg, Michael P, Ward, Alistair, Stewart, Chip, Garrison, Erik P, Marth, Gabor T

“…MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current…”
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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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Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition by Burger, Jan A., Landau, Dan A., Taylor-Weiner, Amaro, Bozic, Ivana, Zhang, Huidan, Sarosiek, Kristopher, Wang, Lili, Stewart, Chip, Fan, Jean, Hoellenriegel, Julia, Sivina, Mariela, Dubuc, Adrian M., Fraser, Cameron, Han, Yulong, Li, Shuqiang, Livak, Kenneth J., Zou, Lihua, Wan, Youzhong, Konoplev, Sergej, Sougnez, Carrie, Brown, Jennifer R., Abruzzo, Lynne V., Carter, Scott L., Keating, Michael J., Davids, Matthew S., Wierda, William G., Cibulskis, Kristian, Zenz, Thorsten, Werner, Lillian, Cin, Paola Dal, Kharchencko, Peter, Neuberg, Donna, Kantarjian, Hagop, Lander, Eric, Gabriel, Stacey, O’Brien, Susan, Letai, Anthony, Weitz, David A., Nowak, Martin A., Getz, Gad, Wu, Catherine J.

“…Resistance to the Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib has been attributed solely to mutations in BTK and related pathway molecules. Using…”
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Targetable genetic features of primary testicular and primary central nervous system lymphomas by Chapuy, Bjoern, Roemer, Margaretha G.M., Stewart, Chip, Tan, Yuxiang, Abo, Ryan P., Zhang, Liye, Dunford, Andrew J., Meredith, David M., Thorner, Aaron R., Jordanova, Ekaterina S., Liu, Gang, Feuerhake, Friedrich, Ducar, Matthew D., Illerhaus, Gerald, Gusenleitner, Daniel, Linden, Erica A., Sun, Heather H., Homer, Heather, Aono, Miyuki, Pinkus, Geraldine S., Ligon, Azra H., Ligon, Keith L., Ferry, Judith A., Freeman, Gordon J., van Hummelen, Paul, Golub, Todd R., Getz, Gad, Rodig, Scott J., de Jong, Daphne, Monti, Stefano, Shipp, Margaret A.

“…Primary central nervous system lymphomas (PCNSLs) and primary testicular lymphomas (PTLs) are extranodal large B-cell lymphomas (LBCLs) with inferior responses…”
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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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Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma by Gopal, Raj K., Kübler, Kirsten, Calvo, Sarah E., Polak, Paz, Livitz, Dimitri, Rosebrock, Daniel, Sadow, Peter M., Campbell, Braidie, Donovan, Samuel E., Amin, Salma, Gigliotti, Benjamin J., Grabarek, Zenon, Hess, Julian M., Stewart, Chip, Braunstein, Lior Z., Arndt, Peter F., Mordecai, Scott, Shih, Angela R., Chaves, Frances, Zhan, Tiannan, Lubitz, Carrie C., Kim, Jiwoong, Iafrate, A. John, Wirth, Lori, Parangi, Sareh, Leshchiner, Ignaty, Daniels, Gilbert H., Mootha, Vamsi K., Dias-Santagata, Dora, Getz, Gad, McFadden, David G.

“…Hürthle cell carcinoma of the thyroid (HCC) is a form of thyroid cancer recalcitrant to radioiodine therapy that exhibits an accumulation of mitochondria. We…”
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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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Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia by Landau, Dan A., Carter, Scott L., Stojanov, Petar, McKenna, Aaron, Stevenson, Kristen, Lawrence, Michael S., Sougnez, Carrie, Stewart, Chip, Sivachenko, Andrey, Wang, Lili, Wan, Youzhong, Zhang, Wandi, Shukla, Sachet A., Vartanov, Alexander, Fernandes, Stacey M., Saksena, Gordon, Cibulskis, Kristian, Tesar, Bethany, Gabriel, Stacey, Hacohen, Nir, Meyerson, Matthew, Lander, Eric S., Neuberg, Donna, Brown, Jennifer R., Getz, Gad, Wu, Catherine J.

“…Clonal evolution is a key feature of cancer progression and relapse. We studied intratumoral heterogeneity in 149 chronic lymphocytic leukemia (CLL) cases by…”
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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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Genetic and Clonal Dissection of Murine Small Cell Lung Carcinoma Progression by Genome Sequencing by McFadden, David G., Papagiannakopoulos, Thales, Taylor-Weiner, Amaro, Stewart, Chip, Carter, Scott L., Cibulskis, Kristian, Bhutkar, Arjun, McKenna, Aaron, Dooley, Alison, Vernon, Amanda, Sougnez, Carrie, Malstrom, Scott, Heimann, Megan, Park, Jennifer, Chen, Frances, Farago, Anna F., Dayton, Talya, Shefler, Erica, Gabriel, Stacey, Getz, Gad, Jacks, Tyler

“…Small cell lung carcinoma (SCLC) is a highly lethal, smoking-associated cancer with few known targetable genetic alterations. Using genome sequencing, we…”
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The genomic landscape of pediatric Ewing sarcoma by Crompton, Brian D, Stewart, Chip, Taylor-Weiner, Amaro, Alexe, Gabriela, Kurek, Kyle C, Calicchio, Monica L, Kiezun, Adam, Carter, Scott L, Shukla, Sachet A, Mehta, Swapnil S, Thorner, Aaron R, de Torres, Carmen, Lavarino, Cinzia, Suñol, Mariona, McKenna, Aaron, Sivachenko, Andrey, Cibulskis, Kristian, Lawrence, Michael S, Stojanov, Petar, Rosenberg, Mara, Ambrogio, Lauren, Auclair, Daniel, Seepo, Sara, Blumenstiel, Brendan, DeFelice, Matthew, Imaz-Rosshandler, Ivan, Schwarz-Cruz Y Celis, Angela, Rivera, Miguel N, Rodriguez-Galindo, Carlos, Fleming, Mark D, Golub, Todd R, Getz, Gad, Mora, Jaume, Stegmaier, Kimberly

“…Pediatric Ewing sarcoma is characterized by the expression of chimeric fusions of EWS and ETS family transcription factors, representing a paradigm for…”
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Lack of transgenerational effects of ionizing radiation exposure from the Chernobyl accident by Yeager, Meredith, Machiela, Mitchell J, Kothiyal, Prachi, Dean, Michael, Bodelon, Clara, Suman, Shalabh, Wang, Mingyi, Mirabello, Lisa, Nelson, Chase W, Zhou, Weiyin, Palmer, Cameron, Ballew, Bari, Colli, Leandro M, Freedman, Neal D, Dagnall, Casey, Hutchinson, Amy, Vij, Vibha, Maruvka, Yosi, Hatch, Maureen, Illienko, Iryna, Belayev, Yuri, Nakamura, Nori, Chumak, Vadim, Bakhanova, Elena, Belyi, David, Kryuchkov, Victor, Golovanov, Ivan, Gudzenko, Natalia, Cahoon, Elizabeth K, Albert, Paul, Drozdovitch, Vladimir, Little, Mark P, Mabuchi, Kiyohiko, Stewart, Chip, Getz, Gad, Bazyka, Dimitry, Berrington de Gonzalez, Amy, Chanock, Stephen J

“…Effects of radiation exposure from the Chernobyl nuclear accident remain a topic of interest. We investigated germline de novo mutations (DNMs) in children…”
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DeTiN: overcoming tumor-in-normal contamination by Taylor-Weiner, Amaro, Stewart, Chip, Giordano, Thomas, Miller, Mendy, Rosenberg, Mara, Macbeth, Alyssa, Lennon, Niall, Rheinbay, Esther, Landau, Dan-Avi, Wu, Catherine J., Getz, Gad

“…Comparison of sequencing data from a tumor sample with data from a matched germline control is a key step for accurate detection of somatic mutations…”
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Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background by Elvers, Ingegerd, Turner-Maier, Jason, Swofford, Ross, Koltookian, Michele, Johnson, Jeremy, Stewart, Chip, Zhang, Cheng-Zhong, Schumacher, Steven E, Beroukhim, Rameen, Rosenberg, Mara, Thomas, Rachael, Mauceli, Evan, Getz, Gad, Palma, Federica Di, Modiano, Jaime F, Breen, Matthew, Lindblad-Toh, Kerstin, Alföldi, Jessica

“…Lymphoma is the most common hematological malignancy in developed countries. Outcome is strongly determined by molecular subtype, reflecting a need for new and…”
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Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma by Bao, Chunyang, Tourdot, Richard W., Brunette, Gregory J., Stewart, Chip, Sun, Lili, Baba, Hideo, Watanabe, Masayuki, Agoston, Agoston T., Jajoo, Kunal, Davison, Jon M., Nason, Katie S., Getz, Gad, Wang, Kenneth K., Imamura, Yu, Odze, Robert, Bass, Adam J., Stachler, Matthew D., Zhang, Cheng-Zhong

“…The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise…”
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Integrative and Comparative Genomic Analysis of Lung Squamous Cell Carcinomas in East Asian Patients by YOUNGWOOK KIM, HAMMERMAN, Peter S, LAWRENCE, Michael S, STOJANOV, Petar, CARTER, Scott L, McKENNA, Aaron, STEWART, Chip, SIVACHENKO, Andrey Y, OH, In-Jae, HONG KWAN KIM, YONG SOO CHOI, KWHANMIEN KIM, JAEGIL KIM, YOUNG MOG SHIM, KIM, Kyu-Sik, SONG, Sang-Yun, NA, Kook-Joo, CHOI, Yoon-La, HAYES, D. Neil, JHINGOOK KIM, SUKKI CHO, KIM, Young-Chul, JIN SEOK AHN, YOON, Ji-Ae, AHN, Myung-Ju, GETZ, Gad, MEYERSON, Matthew, KEUNCHIL PARK, YOOMI LEE, SUN, Jong-Mu, WILKERSON, Matthew D, CHANDRA SEKHAR PEDAMALLU, CIBULSKIS, Kristian, YEONG KYUNG YOO

“…Lung squamous cell carcinoma (SCC) is the second most prevalent type of lung cancer. Currently, no targeted therapeutics are approved for treatment of this…”
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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.

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