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https://www.readbyqxmd.com/read/29234806/diagnostic-assessment-of-deep-learning-algorithms-for-detection-of-lymph-node-metastases-in-women-with-breast-cancer
#1
Babak Ehteshami Bejnordi, Mitko Veta, Paul Johannes van Diest, Bram van Ginneken, Nico Karssemeijer, Geert Litjens, Jeroen A W M van der Laak, Meyke Hermsen, Quirine F Manson, Maschenka Balkenhol, Oscar Geessink, Nikolaos Stathonikos, Marcory Crf van Dijk, Peter Bult, Francisco Beca, Andrew H Beck, Dayong Wang, Aditya Khosla, Rishab Gargeya, Humayun Irshad, Aoxiao Zhong, Qi Dou, Quanzheng Li, Hao Chen, Huang-Jing Lin, Pheng-Ann Heng, Christian Haß, Elia Bruni, Quincy Wong, Ugur Halici, Mustafa Ümit Öner, Rengul Cetin-Atalay, Matt Berseth, Vitali Khvatkov, Alexei Vylegzhanin, Oren Kraus, Muhammad Shaban, Nasir Rajpoot, Ruqayya Awan, Korsuk Sirinukunwattana, Talha Qaiser, Yee-Wah Tsang, David Tellez, Jonas Annuscheit, Peter Hufnagl, Mira Valkonen, Kimmo Kartasalo, Leena Latonen, Pekka Ruusuvuori, Kaisa Liimatainen, Shadi Albarqouni, Bharti Mungal, Ami George, Stefanie Demirci, Nassir Navab, Seiryo Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda, Hady Ahmady Phoulady, Vassili Kovalev, Alexander Kalinovsky, Vitali Liauchuk, Gloria Bueno, M Milagro Fernandez-Carrobles, Ismael Serrano, Oscar Deniz, Daniel Racoceanu, Rui Venâncio
Importance: Application of deep learning algorithms to whole-slide pathology images can potentially improve diagnostic accuracy and efficiency. Objective: Assess the performance of automated deep learning algorithms at detecting metastases in hematoxylin and eosin-stained tissue sections of lymph nodes of women with breast cancer and compare it with pathologists' diagnoses in a diagnostic setting. Design, Setting, and Participants: Researcher challenge competition (CAMELYON16) to develop automated solutions for detecting lymph node metastases (November 2015-November 2016)...
December 12, 2017: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/29232881/the-genome-of-the-beluga-whale-delphinapterus-leucas
#2
Steven J M Jones, Gregory A Taylor, Simon Chan, René L Warren, S Austin Hammond, Steven Bilobram, Gideon Mordecai, Curtis A Suttle, Kristina M Miller, Angela Schulze, Amy M Chan, Samantha J Jones, Kane Tse, Irene Li, Dorothy Cheung, Karen L Mungall, Caleb Choo, Adrian Ally, Noreen Dhalla, Angela K Y Tam, Armelle Troussard, Heather Kirk, Pawan Pandoh, Daniel Paulino, Robin J N Coope, Andrew J Mungall, Richard Moore, Yongjun Zhao, Inanc Birol, Yussanne Ma, Marco Marra, Martin Haulena
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue...
December 11, 2017: Genes
https://www.readbyqxmd.com/read/29232880/the-genome-of-the-northern-sea-otter-enhydra-lutris-kenyoni
#3
Samantha J Jones, Martin Haulena, Gregory A Taylor, Simon Chan, Steven Bilobram, René L Warren, S Austin Hammond, Karen L Mungall, Caleb Choo, Heather Kirk, Pawan Pandoh, Adrian Ally, Noreen Dhalla, Angela K Y Tam, Armelle Troussard, Daniel Paulino, Robin J N Coope, Andrew J Mungall, Richard Moore, Yongjun Zhao, Inanc Birol, Yussanne Ma, Marco Marra, Steven J M Jones
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements...
December 11, 2017: Genes
https://www.readbyqxmd.com/read/29227476/the-molecular-landscape-of-pediatric-acute-myeloid-leukemia-reveals-recurrent-structural-alterations-and-age-specific-mutational-interactions
#4
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, Todd A Alonzo, Yussanne Ma, Richard Moore, Andrew J Mungall, Marco A Marra, Jinghui Zhang, Xiaotu Ma, Yu Liu, Yanling Liu, Jaime M Guidry Auvil, Tanja M Davidsen, Patee Gesuwan, Leandro C Hermida, Bodour Salhia, Stephen Capone, Giridharan Ramsingh, Christian Michel Zwaan, Sanne Noort, Stephen R Piccolo, E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG-National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults...
December 11, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29186578/the-planteome-database-an-integrated-resource-for-reference-ontologies-plant-genomics-and-phenomics
#5
Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L Elser, Chris Mungall, Brandon T Sinn, Dario Cavaliere, Seth Carbon, Nathan A Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios Gkoutos, John H Doonan, Dennis W Stevenson, Elizabeth Arnaud, Pankaj Jaiswal
The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others...
November 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29137143/evaluation-of-a-mass-media-campaign-to-increase-the-awareness-of-the-need-to-reduce-discretionary-salt-use-in-the-south-african-population
#6
Edelweiss Wentzel-Viljoen, Krisela Steyn, Carl Lombard, Anniza De Villiers, Karen Charlton, Sabine Frielinghaus, Christelle Crickmore, Vash Mungal-Singh
The South African strategic plan to reduce cardiovascular disease (CVD) includes reducing population salt intake to less than 5 g/day. A mass media campaign was undertaken to increase public awareness of the association between high salt intake, blood pressure and CVD, and focused on the reduction of discretionary salt intake. Community based surveys, before and after the campaign, were conducted in a cohort of black women aged 18-55 years. Questions on knowledge, attitudes and beliefs regarding salt use were asked...
November 12, 2017: Nutrients
https://www.readbyqxmd.com/read/29127742/literature-review-of-the-epidemiology-of-influenza-b-disease-in-15-countries-in-the-asia-pacific-region
#7
Lance Jennings, Qiu Sue Huang, Ian Barr, Ping-Ing Lee, Woo Joo Kim, Philippe Buchy, Melvin Sanicas, Bruce A Mungall, Jing Chen
AIM: Influenza control strategies focus on the use of trivalent influenza vaccines containing two influenza A virus subtypes and one of the two circulating influenza type B lineages (Yamagata or Victoria). Mismatches between the vaccine B lineage and the circulating lineage have been regularly documented in many countries, including those in the Asia-Pacific region. We conducted a literature review with the aim of understanding the relative circulation of influenza B viruses in Asia-Pacific countries...
November 11, 2017: Influenza and Other Respiratory Viruses
https://www.readbyqxmd.com/read/29127278/the-north-american-bullfrog-draft-genome-provides-insight-into-hormonal-regulation-of-long-noncoding-rna
#8
S Austin Hammond, René L Warren, Benjamin P Vandervalk, Erdi Kucuk, Hamza Khan, Ewan A Gibb, Pawan Pandoh, Heather Kirk, Yongjun Zhao, Martin Jones, Andrew J Mungall, Robin Coope, Stephen Pleasance, Richard A Moore, Robert A Holt, Jessica M Round, Sara Ohora, Branden V Walle, Nik Veldhoen, Caren C Helbing, Inanc Birol
Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there are currently no genomic resources for the former, important group of amphibians. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines...
November 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/29092957/molecular-characterisation-of-metastatic-pancreatic-neuroendocrine-tumours-pnets-using-whole-genome-and-transcriptome-sequencing
#9
Hui-Li Wong, Kevin C Yang, Yaoqing Shen, Eric Y Zhao, Jonathan M Loree, Hagen F Kennecke, Steve E Kalloger, Joanna M Karasinska, Howard J Lim, Andrew J Mungall, Xiaolan Feng, Janine M Davies, Kasmintan Schrader, Chen Zhou, Aly Karsan, Steven Jm Jones, Janessa Laskin, Marco A Marra, David F Schaeffer, Sharon M Gorski, Daniel J Renouf
Pancreatic neuroendocrine tumours (PNETs) are a genomically and clinically heterogeneous group of pancreatic neoplasms often diagnosed with distant metastases. Recurrent somatic mutations, chromosomal aberrations and gene expression signatures in PNETs have been described, but the clinical significance of these molecular changes is still poorly understood, and the clinical outcomes of PNET patients remain highly variable. To help identify the molecular factors that contribute to PNET progression and metastasis, and as part of an ongoing clinical trial at the BC Cancer Agency (clinicaltrials...
November 1, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29068783/microrna-expression-based-model-indicates-event-free-survival-in-pediatric-acute-myeloid-leukemia
#10
Emilia L Lim, Diane L Trinh, Rhonda E Ries, Jim Wang, Robert B Gerbing, Yussanne Ma, James Topham, Maya Hughes, Erin Pleasance, Andrew J Mungall, Richard Moore, Yongjun Zhao, Richard Aplenc, Lillian Sung, E Anders Kolb, Alan Gamis, Malcolm Smith, Daniela S Gerhard, Todd A Alonzo, Soheil Meshinchi, Marco A Marra
Purpose Children with acute myeloid leukemia (AML) whose disease is refractory to standard induction chemotherapy therapy or who experience relapse after initial response have dismal outcomes. We sought to comprehensively profile pediatric AML microRNA (miRNA) samples to identify dysregulated genes and assess the utility of miRNAs for improved outcome prediction. Patients and Methods To identify miRNA biomarkers that are associated with treatment failure, we performed a comprehensive sequence-based characterization of the pediatric AML miRNA landscape...
October 25, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28988769/comprehensive-molecular-characterization-of-muscle-invasive-bladder-cancer
#11
A Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, Joaquim Bellmunt, Guangwu Guo, Andrew D Cherniack, Toshinori Hinoue, Peter W Laird, Katherine A Hoadley, Rehan Akbani, Mauro A A Castro, Ewan A Gibb, Rupa S Kanchi, Dmitry A Gordenin, Sachet A Shukla, Francisco Sanchez-Vega, Donna E Hansel, Bogdan A Czerniak, Victor E Reuter, Xiaoping Su, Benilton de Sa Carvalho, Vinicius S Chagas, Karen L Mungall, Sara Sadeghi, Chandra Sekhar Pedamallu, Yiling Lu, Leszek J Klimczak, Jiexin Zhang, Caleb Choo, Akinyemi I Ojesina, Susan Bullman, Kristen M Leraas, Tara M Lichtenberg, Catherine J Wu, Nicholaus Schultz, Gad Getz, Matthew Meyerson, Gordon B Mills, David J McConkey, John N Weinstein, David J Kwiatkowski, Seth P Lerner
We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology...
October 19, 2017: Cell
https://www.readbyqxmd.com/read/28950338/successful-targeting-of-the-nrg1-pathway-indicates-novel-treatment-strategy-for-metastatic-cancer
#12
M R Jones, H Lim, Y Shen, E Pleasance, C Ch'ng, C Reisle, S Leelakumari, C Zhao, S Yip, J Ho, E Zhong, T Ng, D Ionescu, D F Schaeffer, A J Mungall, K L Mungall, Y Zhao, R A Moore, Y Ma, S Chia, C Ho, D J Renouf, K Gelmon, S J M Jones, M A Marra, J Laskin
Background: NRG1 fusion-positive lung cancers have emerged as potentially actionable events in lung cancer but clinical support is currently limited and no evidence of efficacy of this approach in cancers beyond lung has been shown. Patients and Methods: Here we describe two patients with advanced cancers refractory to standard therapies. Patient 1 had lung adenocarcinoma and patient 2 cholangiocarcinoma. Whole-genome and transcriptome sequencing were carried out for these cases with select findings validated by fluorescence in situ hybridization...
September 18, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28877932/detection-and-genomic-characterization-of-a-mammary-like-adenocarcinoma
#13
Jasleen K Grewal, Peter Eirew, Martin Jones, Kenrry Chiu, Basile Tessier-Cloutier, Anthony N Karnezis, Aly Karsan, Andy Mungall, Chen Zhou, Stephen Yip, Anna V Tinker, Janessa Laskin, Marco Marra, Steven J M Jones
Whole-genome and transcriptome sequencing were performed to identify potential therapeutic strategies in the absence of viable treatment options for a patient initially diagnosed with vulvar adenocarcinoma. Genomic events were prioritized by comparison against variant distributions in the TCGA pan-cancer dataset, and complemented with detailed transcriptome sequencing and copy number analysis. These findings were considered against published scientific literature in order to evaluate the functional effects of potentially relevant genomic events...
September 6, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28854430/genomic-and-cytogenetic-characterization-of-a-balanced-translocation-disrupting-nup98
#14
My Linh Thibodeau, Michelle Steinraths, Lindsay Brown, Zheyuan Zong, Naomi Shomer, Stefan Taubert, Karen L Mungall, Yussanne P Ma, Rosemary Mueller, Inanc Birol, Anna Lehman
A 41-year-old Asian woman with bilateral renal angiomyolipomas (AML) was incidentally identified to have a balanced translocation, 46,XX,t(11;12)(p15.4;q15). She had no other features or family history to suggest a diagnosis of tuberous sclerosis. Her healthy daughter had the same translocation and no renal AML at the age of 3 years. Whole-genome sequencing was performed on genomic maternal DNA isolated from blood. A targeted de novo assembly was then conducted with ABySS for chromosomes 11 and 12. Sanger sequencing was used to validate the translocation breakpoints...
2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28854171/fate-mapping-of-human-glioblastoma-reveals-an-invariant-stem-cell-hierarchy
#15
Xiaoyang Lan, David J Jörg, Florence M G Cavalli, Laura M Richards, Long V Nguyen, Robert J Vanner, Paul Guilhamon, Lilian Lee, Michelle M Kushida, Davide Pellacani, Nicole I Park, Fiona J Coutinho, Heather Whetstone, Hayden J Selvadurai, Clare Che, Betty Luu, Annaick Carles, Michelle Moksa, Naghmeh Rastegar, Renee Head, Sonam Dolma, Panagiotis Prinos, Michael D Cusimano, Sunit Das, Mark Bernstein, Cheryl H Arrowsmith, Andrew J Mungall, Richard A Moore, Yussanne Ma, Marco Gallo, Mathieu Lupien, Trevor J Pugh, Michael D Taylor, Martin Hirst, Connie J Eaves, Benjamin D Simons, Peter B Dirks
Human glioblastomas harbour a subpopulation of glioblastoma stem cells that drive tumorigenesis. However, the origin of intratumoural functional heterogeneity between glioblastoma cells remains poorly understood. Here we study the clonal evolution of barcoded glioblastoma cells in an unbiased way following serial xenotransplantation to define their individual fate behaviours. Independent of an evolving mutational signature, we show that the growth of glioblastoma clones in vivo is consistent with a remarkably neutral process involving a conserved proliferative hierarchy rooted in glioblastoma stem cells...
September 14, 2017: Nature
https://www.readbyqxmd.com/read/28829439/an-integrated-expression-atlas-of-mirnas-and-their-promoters-in-human-and-mouse
#16
Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Åström, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, Ailsa J Carlisle, Carsten O Daub, Michael Detmar, Ruslan Deviatiiarov, Alexandre Fort, Claudia Gebhard, Daniel Goldowitz, Sven Guhl, Thomas J Ha, Jayson Harshbarger, Akira Hasegawa, Kosuke Hashimoto, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, Chung Chau Hon, Edward Huang, Yuri Ishizu, Chieko Kai, Takeya Kasukawa, Peter Klinken, Timo Lassmann, Charles-Henri Lecellier, Weonju Lee, Marina Lizio, Vsevolod Makeev, Anthony Mathelier, Yulia A Medvedeva, Niklas Mejhert, Christopher J Mungall, Shohei Noma, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Helena Persson, Patrizia Rizzu, Filip Roudnicky, Pål Sætrom, Hiroki Sato, Jessica Severin, Jay W Shin, Rolf K Swoboda, Hiroshi Tarui, Hiroo Toyoda, Kristoffer Vitting-Seerup, Louise Winteringham, Yoko Yamaguchi, Kayoko Yasuzawa, Misako Yoneda, Noriko Yumoto, Susan Zabierowski, Peter G Zhang, Christine A Wells, Kim M Summers, Hideya Kawaji, Albin Sandelin, Michael Rehli, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Michiel J L de Hoon
MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species...
September 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28825729/a-children-s-oncology-group-and-target-initiative-exploring-the-genetic-landscape-of-wilms-tumor
#17
Samantha Gadd, Vicki Huff, Amy L Walz, Ariadne H A G Ooms, Amy E Armstrong, Daniela S Gerhard, Malcolm A Smith, Jaime M Guidry Auvil, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan, Cu Nguyen, Ying Hu, Leandro C Hermida, Tanja Davidsen, Patee Gesuwan, Yussanne Ma, Zusheng Zong, Andrew J Mungall, Richard A Moore, Marco A Marra, Jeffrey S Dome, Charles G Mullighan, Jing Ma, David A Wheeler, Oliver A Hampton, Nicole Ross, Julie M Gastier-Foster, Stefan T Arold, Elizabeth J Perlman
We performed genome-wide sequencing and analyzed mRNA and miRNA expression, DNA copy number, and DNA methylation in 117 Wilms tumors, followed by targeted sequencing of 651 Wilms tumors. In addition to genes previously implicated in Wilms tumors (WT1, CTNNB1, AMER1, DROSHA, DGCR8, XPO5, DICER1, SIX1, SIX2, MLLT1, MYCN, and TP53), we identified mutations in genes not previously recognized as recurrently involved in Wilms tumors, the most frequent being BCOR, BCORL1, NONO, MAX, COL6A3, ASXL1, MAP3K4, and ARID1A...
October 2017: Nature Genetics
https://www.readbyqxmd.com/read/28811957/mapping-the-human-t-cell-repertoire-to-recurrent-driver-mutations-in-myd88-and-ezh2-in-lymphoma
#18
Julie S Nielsen, Andrew R Chang, Darin A Wick, Colin G Sedgwick, Zusheng Zong, Andrew J Mungall, Spencer D Martin, Natalie N Kinloch, Susann Ott-Langer, Zabrina L Brumme, Steven P Treon, Joseph M Connors, Randy D Gascoyne, John R Webb, Brian R Berry, Ryan D Morin, Nicol Macpherson, Brad H Nelson
Oncogenic "driver" mutations are theoretically attractive targets for the immunotherapy of lymphoid cancers, yet the proportion that can be recognized by T cells remains poorly defined. To address this issue without any confounding effects of the patient's immune system, we assessed T cells from 19 healthy donors for recognition of three common driver mutations in lymphoma: MYD88(L265P), EZH2(Y641F) , and EZH2(Y641N) . Donors collectively expressed the 10 most prevalent HLA class I alleles, including HLA-A*02:01...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28810145/integrative-analysis-identifies-four-molecular-and-clinical-subsets-in-uveal-melanoma
#19
A Gordon Robertson, Juliann Shih, Christina Yau, Ewan A Gibb, Junna Oba, Karen L Mungall, Julian M Hess, Vladislav Uzunangelov, Vonn Walter, Ludmila Danilova, Tara M Lichtenberg, Melanie Kucherlapati, Patrick K Kimes, Ming Tang, Alexander Penson, Ozgun Babur, Rehan Akbani, Christopher A Bristow, Katherine A Hoadley, Lisa Iype, Matthew T Chang, Andrew D Cherniack, Christopher Benz, Gordon B Mills, Roel G W Verhaak, Klaus G Griewank, Ina Felau, Jean C Zenklusen, Jeffrey E Gershenwald, Lynn Schoenfield, Alexander J Lazar, Mohamed H Abdel-Rahman, Sergio Roman-Roman, Marc-Henri Stern, Colleen M Cebulla, Michelle D Williams, Martine J Jager, Sarah E Coupland, Bita Esmaeli, Cyriac Kandoth, Scott E Woodman
Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis monosomy 3 (M3) and two with better-prognosis disomy 3 (D3). We show that BAP1 loss follows M3 occurrence and correlates with a global DNA methylation state that is distinct from D3-UM. Poor-prognosis M3-UM divide into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. We report change-of-function SRSF2 mutations...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28808080/characterization-of-the-human-thyroid-epigenome
#20
Celia Siu, Sam Wiseman, Sitanshu Gakkhar, Alireza Heravi-Moussavi, Misha Bilenky, Annaick Carles, Thomas Sierocinski, Angela Tam, Eric Zhao, Katayoon Kasaian, Richard A Moore, Andrew J Mungall, Blair Walker, Thomas Thomson, Marco A Marra, Martin Hirst, Steven J M Jones
The thyroid gland, necessary for normal human growth and development, functions as an essential regulator of metabolism by the production and secretion of appropriate levels of thyroid hormone. However, assessment of abnormal thyroid function may be challenging suggesting a more fundamental understanding of normal function is needed. One way to characterize normal gland function is to study the epigenome and resulting transcriptome within its constituent cells. This study generates the first published reference epigenomes for human thyroid from four individuals using ChIP-seq and RNA-seq...
November 2017: Journal of Endocrinology
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