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Andrew J Mungall

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https://www.readbyqxmd.com/read/27899602/the-human-phenotype-ontology-in-2017
#1
Sebastian Köhler, Nicole A Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M Bello, Cornelius F Boerkoel, Kym M Boycott, Michael Brudno, Orion J Buske, Patrick F Chinnery, Valentina Cipriani, Laureen E Connell, Hugh J S Dawkins, Laura E DeMare, Andrew D Devereau, Bert B A de Vries, Helen V Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna A Jähn, Roger James, Roland Krause, Stanley J F Laulederkind, Hanns Lochmüller, Gholson J Lyon, Soichi Ogishima, Annie Olry, Willem H Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H Scott, Michael Segal, Panagiotis I Sergouniotis, Richard Sever, Cynthia L Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W M Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O B Jacobsen, Tudor Groza, Damian Smedley, Christopher J Mungall, Melissa Haendel, Peter N Robinson
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27851968/analysis-of-normal-human-mammary-epigenomes-reveals-cell-specific-active-enhancer-states-and-associated-transcription-factor-networks
#2
Davide Pellacani, Misha Bilenky, Nagarajan Kannan, Alireza Heravi-Moussavi, David J H F Knapp, Sitanshu Gakkhar, Michelle Moksa, Annaick Carles, Richard Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones, Samuel Aparicio, Martin Hirst, Connie J Eaves
The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27824051/genomic-analyses-identify-recurrent-mef2d-fusions-in-acute-lymphoblastic-leukaemia
#3
Zhaohui Gu, Michelle Churchman, Kathryn Roberts, Yongjin Li, Yu Liu, Richard C Harvey, Kelly McCastlain, Shalini C Reshmi, Debbie Payne-Turner, Ilaria Iacobucci, Ying Shao, I-Ming Chen, Marcus Valentine, Deqing Pei, Karen L Mungall, Andrew J Mungall, Yussanne Ma, Richard Moore, Marco Marra, Eileen Stonerock, Julie M Gastier-Foster, Meenakshi Devidas, Yunfeng Dai, Brent Wood, Michael Borowitz, Eric E Larsen, Kelly Maloney, Leonard A Mattano, Anne Angiolillo, Wanda L Salzer, Michael J Burke, Francesca Gianni, Orietta Spinelli, Jerald P Radich, Mark D Minden, Anthony V Moorman, Bella Patel, Adele K Fielding, Jacob M Rowe, Selina M Luger, Ravi Bhatia, Ibrahim Aldoss, Stephen J Forman, Jessica Kohlschmidt, Krzysztof Mrózek, Guido Marcucci, Clara D Bloomfield, Wendy Stock, Steven Kornblau, Hagop M Kantarjian, Marina Konopleva, Elisabeth Paietta, Cheryl L Willman, Mignon L Loh, Stephen P Hunger, Charles G Mullighan
Chromosomal rearrangements are initiating events in acute lymphoblastic leukaemia (ALL). Here using RNA sequencing of 560 ALL cases, we identify rearrangements between MEF2D (myocyte enhancer factor 2D) and five genes (BCL9, CSF1R, DAZAP1, HNRNPUL1 and SS18) in 22 B progenitor ALL (B-ALL) cases with a distinct gene expression profile, the most common of which is MEF2D-BCL9. Examination of an extended cohort of 1,164 B-ALL cases identified 30 cases with MEF2D rearrangements, which include an additional fusion partner, FOXJ2; thus, MEF2D-rearranged cases comprise 5...
November 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27785453/distributed-cognition-and-process-management-enabling-individualized-translational-research-the-nih-undiagnosed-diseases-program-experience
#4
Amanda E Links, David Draper, Elizabeth Lee, Jessica Guzman, Zaheer Valivullah, Valerie Maduro, Vlad Lebedev, Maxim Didenko, Garrick Tomlin, Michael Brudno, Marta Girdea, Sergiu Dumitriu, Melissa A Haendel, Christopher J Mungall, Damian Smedley, Harry Hochheiser, Andrew M Arnold, Bert Coessens, Steven Verhoeven, William Bone, David Adams, Cornelius F Boerkoel, William A Gahl, Murat Sincan
The National Institutes of Health Undiagnosed Diseases Program (NIH UDP) applies translational research systematically to diagnose patients with undiagnosed diseases. The challenge is to implement an information system enabling scalable translational research. The authors hypothesized that similar complex problems are resolvable through process management and the distributed cognition of communities. The team, therefore, built the NIH UDP integrated collaboration system (UDPICS) to form virtual collaborative multidisciplinary research networks or communities...
2016: Frontiers in Medicine
https://www.readbyqxmd.com/read/27702824/significance-of-tp53-mutation-in-wilms-tumors-with-diffuse-anaplasia-a-report-from-the-children-s-oncology-group
#5
Ariadne H A G Ooms, Samantha Gadd, Daniela S Gerhard, Malcolm A Smith, Jaime M Guidry Auvil, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan, Cu Nguyen, Ying Hu, Yussanne Ma, Zusheng Zong, Andrew J Mungall, Richard A Moore, Marco A Marra, Vicki Huff, Jeffrey S Dome, Yueh-Yun Chi, Jing Tian, James I Geller, Charles G Mullighan, Jing Ma, David A Wheeler, Oliver A Hampton, Amy L Walz, Marry M van den Heuvel-Eibrink, Ronald R de Krijger, Nicole Ross, Julie M Gastier-Foster, Elizabeth J Perlman
PURPOSE: To investigate the role and significance of TP53 mutation in diffusely anaplastic Wilms tumors (DAWTs). EXPERIMENTAL DESIGN: All DAWTs registered on National Wilms Tumor Study-5 (n = 118) with available samples were analyzed for TP53 mutations and copy loss. Integrative genomic analysis was performed on 39 selected DAWTs. RESULTS: Following analysis of a single random sample, 57 DAWTs (48%) demonstrated TP53 mutations, 13 (11%) copy loss without mutation, and 48 (41%) lacked both [defined as TP53-wild-type (wt)]...
October 4, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27268263/comprehensive-characterization-of-programmed-death-ligand-structural-rearrangements-in-b-cell-non-hodgkin-lymphomas
#6
Lauren C Chong, David D W Twa, Anja Mottok, Susana Ben-Neriah, Bruce W Woolcock, Yongjun Zhao, Kerry J Savage, Marco A Marra, David W Scott, Randy D Gascoyne, Ryan D Morin, Andrew J Mungall, Christian Steidl
Programmed death ligands (PDLs) are immune-regulatory molecules that are frequently affected by chromosomal alterations in B-cell lymphomas. Although PDL copy-number variations are well characterized, a detailed and comprehensive analysis of structural rearrangements (SRs) and associated phenotypic consequences is largely lacking. Here, we used oligonucleotide capture sequencing of 67 formalin-fixed paraffin-embedded tissues derived from primary B-cell lymphomas and 1 cell line to detect and characterize, at base-pair resolution, SRs of the PDL locus (9p24...
September 1, 2016: Blood
https://www.readbyqxmd.com/read/27182968/divergent-modes-of-clonal-spread-and-intraperitoneal-mixing-in-high-grade-serous-ovarian-cancer
#7
Andrew McPherson, Andrew Roth, Emma Laks, Tehmina Masud, Ali Bashashati, Allen W Zhang, Gavin Ha, Justina Biele, Damian Yap, Adrian Wan, Leah M Prentice, Jaswinder Khattra, Maia A Smith, Cydney B Nielsen, Sarah C Mullaly, Steve Kalloger, Anthony Karnezis, Karey Shumansky, Celia Siu, Jamie Rosner, Hector Li Chan, Julie Ho, Nataliya Melnyk, Janine Senz, Winnie Yang, Richard Moore, Andrew J Mungall, Marco A Marra, Alexandre Bouchard-Côté, C Blake Gilks, David G Huntsman, Jessica N McAlpine, Samuel Aparicio, Sohrab P Shah
We performed phylogenetic analysis of high-grade serous ovarian cancers (68 samples from seven patients), identifying constituent clones and quantifying their relative abundances at multiple intraperitoneal sites. Through whole-genome and single-nucleus sequencing, we identified evolutionary features including mutation loss, convergence of the structural genome and temporal activation of mutational processes that patterned clonal progression. We then determined the precise clonal mixtures comprising each tumor sample...
July 2016: Nature Genetics
https://www.readbyqxmd.com/read/27154141/high-performance-web-services-for-querying-gene-and-variant-annotation
#8
Jiwen Xin, Adam Mark, Cyrus Afrasiabi, Ginger Tsueng, Moritz Juchler, Nikhil Gopal, Gregory S Stupp, Timothy E Putman, Benjamin J Ainscough, Obi L Griffith, Ali Torkamani, Patricia L Whetzel, Christopher J Mungall, Sean D Mooney, Andrew I Su, Chunlei Wu
Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information...
2016: Genome Biology
https://www.readbyqxmd.com/read/27148585/putative-braf-activating-fusion-in-a-medullary-thyroid-cancer
#9
Katayoon Kasaian, Sam M Wiseman, Blair A Walker, Jacqueline E Schein, Martin Hirst, Richard A Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones
Medullary thyroid cancer (MTC) is a malignancy of the calcitonin-producing parafollicular cells of the thyroid gland. Surgery is the only curative treatment for this cancer. External beam radiation therapy is reserved for adjuvant treatment of MTC with aggressive features. Targeted therapeutics vandetanib and cabozantinib are approved for the treatment of aggressive and metastatic tumors that are not amenable to surgery. The use of these multikinase inhibitors are supported by the observed overactivation of the RET oncoprotein in a large subpopulation of MTCs...
March 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27143256/csf3r-mutations-have-a-high-degree-of-overlap-with-cebpa-mutations-in-pediatric-aml
#10
LETTER
Julia E Maxson, Rhonda E Ries, Yi-Cheng Wang, Robert B Gerbing, E Anders Kolb, Sarah L Thompson, Jaime M Guidry Auvil, Marco A Marra, Yussanne Ma, Zusheng Zong, Andrew J Mungall, Richard Moore, William Long, Patee Gesuwan, Tanja M Davidsen, Leandro C Hermida, Seamus B Hughes, Jason E Farrar, Jerald P Radich, Malcolm A Smith, Daniela S Gerhard, Alan S Gamis, Todd A Alonzo, Soheil Meshinchi
No abstract text is available yet for this article.
June 16, 2016: Blood
https://www.readbyqxmd.com/read/27094764/a-somatic-reference-standard-for-cancer-genome-sequencing
#11
David W Craig, Sara Nasser, Richard Corbett, Simon K Chan, Lisa Murray, Christophe Legendre, Waibhav Tembe, Jonathan Adkins, Nancy Kim, Shukmei Wong, Angela Baker, Daniel Enriquez, Stephanie Pond, Erin Pleasance, Andrew J Mungall, Richard A Moore, Timothy McDaniel, Yussanne Ma, Steven J M Jones, Marco A Marra, John D Carpten, Winnie S Liang
Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27036018/mir-509-3p-is-clinically-significant-and-strongly-attenuates-cellular-migration-and-multi-cellular-spheroids-in-ovarian-cancer
#12
Yinghong Pan, Gordon Robertson, Lykke Pedersen, Emilia Lim, Anadulce Hernandez-Herrera, Amy C Rowat, Sagar L Patil, Clara K Chan, Yunfei Wen, Xinna Zhang, Upal Basu-Roy, Alka Mansukhani, Andy Chu, Payal Sipahimalani, Reanne Bowlby, Denise Brooks, Nina Thiessen, Cristian Coarfa, Yussanne Ma, Richard A Moore, Jacquie E Schein, Andrew J Mungall, Jinsong Liu, Chad V Pecot, Anil K Sood, Steven J M Jones, Marco A Marra, Preethi H Gunaratne
Ovarian cancer presents as an aggressive, advanced stage cancer with widespread metastases that depend primarily on multicellular spheroids in the peritoneal fluid. To identify new druggable pathways related to metastatic progression and spheroid formation, we integrated microRNA and mRNA sequencing data from 293 tumors from The Cancer Genome Atlas (TCGA) ovarian cancer cohort. We identified miR-509-3p as a clinically significant microRNA that is more abundant in patients with favorable survival in both the TCGA cohort (P = 2...
May 3, 2016: Oncotarget
https://www.readbyqxmd.com/read/26977886/genome-wide-profiles-of-extra-cranial-malignant-rhabdoid-tumors-reveal-heterogeneity-and-dysregulated-developmental-pathways
#13
Hye-Jung E Chun, Emilia L Lim, Alireza Heravi-Moussavi, Saeed Saberi, Karen L Mungall, Mikhail Bilenky, Annaick Carles, Kane Tse, Inna Shlafman, Kelsey Zhu, Jenny Q Qian, Diana L Palmquist, An He, William Long, Rodrigo Goya, Michelle Ng, Veronique G LeBlanc, Erin Pleasance, Nina Thiessen, Tina Wong, Eric Chuah, Yong-Jun Zhao, Jacquie E Schein, Daniela S Gerhard, Michael D Taylor, Andrew J Mungall, Richard A Moore, Yussanne Ma, Steven J M Jones, Elizabeth J Perlman, Martin Hirst, Marco A Marra
Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs...
March 14, 2016: Cancer Cell
https://www.readbyqxmd.com/read/26760213/divergent-clonal-selection-dominates-medulloblastoma-at-recurrence
#14
A Sorana Morrissy, Livia Garzia, David J H Shih, Scott Zuyderduyn, Xi Huang, Patryk Skowron, Marc Remke, Florence M G Cavalli, Vijay Ramaswamy, Patricia E Lindsay, Salomeh Jelveh, Laura K Donovan, Xin Wang, Betty Luu, Kory Zayne, Yisu Li, Chelsea Mayoh, Nina Thiessen, Eloi Mercier, Karen L Mungall, Yusanne Ma, Kane Tse, Thomas Zeng, Karey Shumansky, Andrew J L Roth, Sohrab Shah, Hamza Farooq, Noriyuki Kijima, Borja L Holgado, John J Y Lee, Stuart Matan-Lithwick, Jessica Liu, Stephen C Mack, Alex Manno, K A Michealraj, Carolina Nor, John Peacock, Lei Qin, Juri Reimand, Adi Rolider, Yuan Y Thompson, Xiaochong Wu, Trevor Pugh, Adrian Ally, Mikhail Bilenky, Yaron S N Butterfield, Rebecca Carlsen, Young Cheng, Eric Chuah, Richard D Corbett, Noreen Dhalla, An He, Darlene Lee, Haiyan I Li, William Long, Michael Mayo, Patrick Plettner, Jenny Q Qian, Jacqueline E Schein, Angela Tam, Tina Wong, Inanc Birol, Yongjun Zhao, Claudia C Faria, José Pimentel, Sofia Nunes, Tarek Shalaby, Michael Grotzer, Ian F Pollack, Ronald L Hamilton, Xiao-Nan Li, Anne E Bendel, Daniel W Fults, Andrew W Walter, Toshihiro Kumabe, Teiji Tominaga, V Peter Collins, Yoon-Jae Cho, Caitlin Hoffman, David Lyden, Jeffrey H Wisoff, James H Garvin, Duncan S Stearns, Luca Massimi, Ulrich Schüller, Jaroslav Sterba, Karel Zitterbart, Stephanie Puget, Olivier Ayrault, Sandra E Dunn, Daniela P C Tirapelli, Carlos G Carlotti, Helen Wheeler, Andrew R Hallahan, Wendy Ingram, Tobey J MacDonald, Jeffrey J Olson, Erwin G Van Meir, Ji-Yeoun Lee, Kyu-Chang Wang, Seung-Ki Kim, Byung-Kyu Cho, Torsten Pietsch, Gudrun Fleischhack, Stephan Tippelt, Young Shin Ra, Simon Bailey, Janet C Lindsey, Steven C Clifford, Charles G Eberhart, Michael K Cooper, Roger J Packer, Maura Massimino, Maria Luisa Garre, Ute Bartels, Uri Tabori, Cynthia E Hawkins, Peter Dirks, Eric Bouffet, James T Rutka, Robert J Wechsler-Reya, William A Weiss, Lara S Collier, Adam J Dupuy, Andrey Korshunov, David T W Jones, Marcel Kool, Paul A Northcott, Stefan M Pfister, David A Largaespada, Andrew J Mungall, Richard A Moore, Nada Jabado, Gary D Bader, Steven J M Jones, David Malkin, Marco A Marra, Michael D Taylor
The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon-driven, functional genomic mouse model of medulloblastoma with 'humanized' in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%)...
January 21, 2016: Nature
https://www.readbyqxmd.com/read/26713234/emerging-semantics-to-link-phenotype-and-environment
#15
Anne E Thessen, Daniel E Bunker, Pier Luigi Buttigieg, Laurel D Cooper, Wasila M Dahdul, Sami Domisch, Nico M Franz, Pankaj Jaiswal, Carolyn J Lawrence-Dill, Peter E Midford, Christopher J Mungall, Martín J Ramírez, Chelsea D Specht, Lars Vogt, Rutger Aldo Vos, Ramona L Walls, Jeffrey W White, Guanyang Zhang, Andrew R Deans, Eva Huala, Suzanna E Lewis, Paula M Mabee
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods...
2015: PeerJ
https://www.readbyqxmd.com/read/26680454/the-genomic-and-transcriptomic-landscape-of-anaplastic-thyroid-cancer-implications-for-therapy
#16
COMPARATIVE STUDY
Katayoon Kasaian, Sam M Wiseman, Blair A Walker, Jacqueline E Schein, Yongjun Zhao, Martin Hirst, Richard A Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones
BACKGROUND: Anaplastic thyroid carcinoma is the most undifferentiated form of thyroid cancer and one of the deadliest of all adult solid malignancies. Here we report the first genomic and transcriptomic profile of anaplastic thyroid cancer including those of several unique cell lines and outline novel potential drivers of malignancy and targets of therapy. METHODS: We describe whole genomic and transcriptomic profiles of 1 primary anaplastic thyroid tumor and 3 authenticated cell lines...
2015: BMC Cancer
https://www.readbyqxmd.com/read/26635203/mllt1-yeats-domain-mutations-in-clinically-distinctive-favourable-histology-wilms-tumours
#17
Elizabeth J Perlman, Samantha Gadd, Stefan T Arold, Anand Radhakrishnan, Daniela S Gerhard, Lawrence Jennings, Vicki Huff, Jaime M Guidry Auvil, Tanja M Davidsen, Jeffrey S Dome, Daoud Meerzaman, Chih Hao Hsu, Cu Nguyen, James Anderson, Yussanne Ma, Andrew J Mungall, Richard A Moore, Marco A Marra, Charles G Mullighan, Jing Ma, David A Wheeler, Oliver A Hampton, Julie M Gastier-Foster, Nicole Ross, Malcolm A Smith
Wilms tumour is an embryonal tumour of childhood that closely resembles the developing kidney. Genomic changes responsible for the development of the majority of Wilms tumours remain largely unknown. Here we identify recurrent mutations within Wilms tumours that involve the highly conserved YEATS domain of MLLT1 (ENL), a gene known to be involved in transcriptional elongation during early development. The mutant MLLT1 protein shows altered binding to acetylated histone tails. Moreover, MLLT1-mutant tumours show an increase in MYC gene expression and HOX dysregulation...
December 4, 2015: Nature Communications
https://www.readbyqxmd.com/read/26536169/comprehensive-molecular-characterization-of-papillary-renal-cell-carcinoma
#18
W Marston Linehan, Paul T Spellman, Christopher J Ricketts, Chad J Creighton, Suzanne S Fei, Caleb Davis, David A Wheeler, Bradley A Murray, Laura Schmidt, Cathy D Vocke, Myron Peto, Abu Amar M Al Mamun, Eve Shinbrot, Anurag Sethi, Samira Brooks, W Kimryn Rathmell, Angela N Brooks, Katherine A Hoadley, A Gordon Robertson, Denise Brooks, Reanne Bowlby, Sara Sadeghi, Hui Shen, Daniel J Weisenberger, Moiz Bootwalla, Stephen B Baylin, Peter W Laird, Andrew D Cherniack, Gordon Saksena, Scott Haake, Jun Li, Han Liang, Yiling Lu, Gordon B Mills, Rehan Akbani, Mark D M Leiserson, Benjamin J Raphael, Pavana Anur, Donald Bottaro, Laurence Albiges, Nandita Barnabas, Toni K Choueiri, Bogdan Czerniak, Andrew K Godwin, A Ari Hakimi, Thai H Ho, James Hsieh, Michael Ittmann, William Y Kim, Bhavani Krishnan, Maria J Merino, Kenna R Mills Shaw, Victor E Reuter, Ed Reznik, Carl S Shelley, Brian Shuch, Sabina Signoretti, Ramaprasad Srinivasan, Pheroze Tamboli, George Thomas, Satish Tickoo, Kenneth Burnett, Daniel Crain, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph D Paulauskis, Robert J Penny, Candace Shelton, W Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Melissa T Avedon, Jay Bowen, Julie M Gastier-Foster, Mark Gerken, Kristen M Leraas, Tara M Lichtenberg, Nilsa C Ramirez, Tracie Santos, Lisa Wise, Erik Zmuda, John A Demchok, Ina Felau, Carolyn M Hutter, Margi Sheth, Heidi J Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C Zenklusen, Jiashan Zhang, Brenda Ayala, Julien Baboud, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Adrian Ally, Miruna Balasundaram, Saianand Balu, Rameen Beroukhim, Tom Bodenheimer, Christian Buhay, Yaron S N Butterfield, Rebecca Carlsen, Scott L Carter, Hsu Chao, Eric Chuah, Amanda Clarke, Kyle R Covington, Mahmoud Dahdouli, Ninad Dewal, Noreen Dhalla, Harsha V Doddapaneni, Jennifer A Drummond, Stacey B Gabriel, Richard A Gibbs, Ranabir Guin, Walker Hale, Alicia Hawes, D Neil Hayes, Robert A Holt, Alan P Hoyle, Stuart R Jefferys, Steven J M Jones, Corbin D Jones, Divya Kalra, Christie Kovar, Lora Lewis, Jie Li, Yussanne Ma, Marco A Marra, Michael Mayo, Shaowu Meng, Matthew Meyerson, Piotr A Mieczkowski, Richard A Moore, Donna Morton, Lisle E Mose, Andrew J Mungall, Donna Muzny, Joel S Parker, Charles M Perou, Jeffrey Roach, Jacqueline E Schein, Steven E Schumacher, Yan Shi, Janae V Simons, Payal Sipahimalani, Tara Skelly, Matthew G Soloway, Carrie Sougnez, Angela Tam, Donghui Tan, Nina Thiessen, Umadevi Veluvolu, Min Wang, Matthew D Wilkerson, Tina Wong, Junyuan Wu, Liu Xi, Jane Zhou, Jason Bedford, Fengju Chen, Yao Fu, Mark Gerstein, David Haussler, Katayoon Kasaian, Phillip Lai, Shiyun Ling, Amie Radenbaugh, David Van Den Berg, John N Weinstein, Jingchun Zhu, Monique Albert, Iakovina Alexopoulou, Jeremiah J Andersen, J Todd Auman, John Bartlett, Sheldon Bastacky, Julie Bergsten, Michael L Blute, Lori Boice, Roni J Bollag, Jeff Boyd, Erik Castle, Ying-Bei Chen, John C Cheville, Erin Curley, Benjamin Davies, April DeVolk, Rajiv Dhir, Laura Dike, John Eckman, Jay Engel, Jodi Harr, Ronald Hrebinko, Mei Huang, Lori Huelsenbeck-Dill, Mary Iacocca, Bruce Jacobs, Michael Lobis, Jodi K Maranchie, Scott McMeekin, Jerome Myers, Joel Nelson, Jeremy Parfitt, Anil Parwani, Nicholas Petrelli, Brenda Rabeno, Somak Roy, Andrew L Salner, Joel Slaton, Melissa Stanton, R Houston Thompson, Leigh Thorne, Kelinda Tucker, Paul M Weinberger, Cynthia Winemiller, Leigh Anne Zach, Rosemary Zuna
BACKGROUND: Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS: We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis...
January 14, 2016: New England Journal of Medicine
https://www.readbyqxmd.com/read/26271990/large-scale-profiling-of-micrornas-for-the-cancer-genome-atlas
#19
Andy Chu, Gordon Robertson, Denise Brooks, Andrew J Mungall, Inanc Birol, Robin Coope, Yussanne Ma, Steven Jones, Marco A Marra
The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute Genomics Cloud Pilots, such data resources will make intensive analysis of large-scale cancer genomics data widely accessible. To support such initiatives, and to enable comparison of TCGA microRNA data to data from other projects, we describe the process that we developed and used to generate the microRNA sequence data, from library construction through to submission of data to repositories...
January 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26095338/validation-and-calibration-of-next-generation-sequencing-to-identify-epstein-barr-virus-positive-gastric-cancer-in-the-cancer-genome-atlas
#20
M Constanza Camargo, Reanne Bowlby, Andy Chu, Chandra Sekhar Pedamallu, Vesteinn Thorsson, Sandra Elmore, Andrew J Mungall, Adam J Bass, Margaret L Gulley, Charles S Rabkin
The Epstein-Barr virus (EBV)-positive subtype of gastric adenocarcinoma is conventionally identified by in situ hybridization (ISH) for viral nucleic acids, but next-generation sequencing represents a potential alternative. We therefore determined normalized EBV read counts by whole-genome, whole-exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases. In pairwise comparisons, individual samples were either concordantly high or concordantly low by all genomic methods for which data were available...
April 2016: Gastric Cancer
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