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Andrew J Mungall

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https://www.readbyqxmd.com/read/29127278/the-north-american-bullfrog-draft-genome-provides-insight-into-hormonal-regulation-of-long-noncoding-rna
#1
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
#2
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
#3
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
#4
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/28854171/fate-mapping-of-human-glioblastoma-reveals-an-invariant-stem-cell-hierarchy
#5
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/28825729/a-children-s-oncology-group-and-target-initiative-exploring-the-genetic-landscape-of-wilms-tumor
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28726821/the-whole-genome-landscape-of-medulloblastoma-subtypes
#10
Paul A Northcott, Ivo Buchhalter, A Sorana Morrissy, Volker Hovestadt, Joachim Weischenfeldt, Tobias Ehrenberger, Susanne Gröbner, Maia Segura-Wang, Thomas Zichner, Vasilisa A Rudneva, Hans-Jörg Warnatz, Nikos Sidiropoulos, Aaron H Phillips, Steven Schumacher, Kortine Kleinheinz, Sebastian M Waszak, Serap Erkek, David T W Jones, Barbara C Worst, Marcel Kool, Marc Zapatka, Natalie Jäger, Lukas Chavez, Barbara Hutter, Matthias Bieg, Nagarajan Paramasivam, Michael Heinold, Zuguang Gu, Naveed Ishaque, Christina Jäger-Schmidt, Charles D Imbusch, Alke Jugold, Daniel Hübschmann, Thomas Risch, Vyacheslav Amstislavskiy, Francisco German Rodriguez Gonzalez, Ursula D Weber, Stephan Wolf, Giles W Robinson, Xin Zhou, Gang Wu, David Finkelstein, Yanling Liu, Florence M G Cavalli, Betty Luu, Vijay Ramaswamy, Xiaochong Wu, Jan Koster, Marina Ryzhova, Yoon-Jae Cho, Scott L Pomeroy, Christel Herold-Mende, Martin Schuhmann, Martin Ebinger, Linda M Liau, Jaume Mora, Roger E McLendon, Nada Jabado, Toshihiro Kumabe, Eric Chuah, Yussanne Ma, Richard A Moore, Andrew J Mungall, Karen L Mungall, Nina Thiessen, Kane Tse, Tina Wong, Steven J M Jones, Olaf Witt, Till Milde, Andreas Von Deimling, David Capper, Andrey Korshunov, Marie-Laure Yaspo, Richard Kriwacki, Amar Gajjar, Jinghui Zhang, Rameen Beroukhim, Ernest Fraenkel, Jan O Korbel, Benedikt Brors, Matthias Schlesner, Roland Eils, Marco A Marra, Stefan M Pfister, Michael D Taylor, Peter Lichter
Current therapies for medulloblastoma, a highly malignant childhood brain tumour, impose debilitating effects on the developing child, and highlight the need for molecularly targeted treatments with reduced toxicity. Previous studies have been unable to identify the full spectrum of driver genes and molecular processes that operate in medulloblastoma subgroups. Here we analyse the somatic landscape across 491 sequenced medulloblastoma samples and the molecular heterogeneity among 1,256 epigenetically analysed cases, and identify subgroup-specific driver alterations that include previously undiscovered actionable targets...
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28679365/increasing-quality-throughput-and-speed-of-sample-preparation-for-strand-specific-messenger-rna-sequencing
#11
Simon Haile, Richard D Corbett, Tina MacLeod, Steve Bilobram, Duane Smailus, Philip Tsao, Heather Kirk, Helen McDonald, Pawan Pandoh, Miruna Bala, Martin Hirst, Diane Miller, Richard A Moore, Andrew J Mungall, Jacquie Schein, Robin J Coope, Yussanne Ma, Yongjun Zhao, Rob A Holt, Steven J Jones, Marco A Marra
BACKGROUND: RNA-Sequencing (RNA-seq) is now commonly used to reveal quantitative spatiotemporal snapshots of the transcriptome, the structures of transcripts (splice variants and fusions) and landscapes of expressed mutations. However, standard approaches for library construction typically require relatively high amounts of input RNA, are labor intensive, and are time consuming. METHODS: Here, we report the outcome of a systematic effort to optimize and streamline steps in strand-specific RNA-seq library construction...
July 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28570594/automated-high-throughput-nucleic-acid-purification-from-formalin-fixed-paraffin-embedded-tissue-samples-for-next-generation-sequence-analysis
#12
Simon Haile, Pawan Pandoh, Helen McDonald, Richard D Corbett, Philip Tsao, Heather Kirk, Tina MacLeod, Martin Jones, Steve Bilobram, Denise Brooks, Duane Smailus, Christian Steidl, David W Scott, Miruna Bala, Martin Hirst, Diane Miller, Richard A Moore, Andrew J Mungall, Robin J Coope, Yussanne Ma, Yongjun Zhao, Rob A Holt, Steven J Jones, Marco A Marra
Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification...
2017: PloS One
https://www.readbyqxmd.com/read/28515149/pyruvate-kinase-inhibits-proliferation-during-postnatal-cerebellar-neurogenesis-and-suppresses-medulloblastoma-formation
#13
Katherine Tech, Andrey P Tikunov, Hamza Farooq, A Sorana Morrissy, Jessica Meidinger, Taylor Fish, Sarah C Green, Hedi Liu, Yisu Li, Andrew J Mungall, Richard A Moore, Yussanne Ma, Steven J M Jones, Marco A Marra, Matthew G Vander Heiden, Michael D Taylor, Jeffrey M Macdonald, Timothy R Gershon
Aerobic glycolysis supports proliferation through unresolved mechanisms. We have previously shown that aerobic glycolysis is required for the regulated proliferation of cerebellar granule neuron progenitors (CGNP) and for the growth of CGNP-derived medulloblastoma. Blocking the initiation of glycolysis via deletion of hexokinase-2 (Hk2) disrupts CGNP proliferation and restricts medulloblastoma growth. Here, we assessed whether disrupting pyruvate kinase-M (Pkm), an enzyme that acts in the terminal steps of glycolysis, would alter CGNP metabolism, proliferation, and tumorigenesis...
June 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28514723/genomic-profiling-of-pelvic-genital-type-leiomyosarcoma-in-a-woman-with-a-germline-chek2-c-1100delc-mutation-and-a-concomitant-diagnosis-of-metastatic-invasive-ductal-breast-carcinoma
#14
My Linh Thibodeau, Caralyn Reisle, Eric Zhao, Lee Ann Martin, Yazeed Alwelaie, Karen L Mungall, Carolyn Ch'ng, Ruth Thomas, Tony Ng, Stephen Yip, Howard J Lim, Sophie Sun, Sean S Young, Aly Karsan, Yongjun Zhao, Andrew J Mungall, Richard A Moore, Daniel J Renouf, Karen Gelmon, Yussanne P Ma, Malcolm Hayes, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
We describe a woman with the known pathogenic germline variant CHEK2:c.1100delC and synchronous diagnoses of both pelvic genital type leiomyosarcoma (LMS) and metastatic invasive ductal breast carcinoma. CHEK2 (checkpoint kinase 2) is a tumor-suppressor gene encoding a serine/threonine-protein kinase (CHEK2) involved in double-strand DNA break repair and cell cycle arrest. The CHEK2:c.1100delC variant is a moderate penetrance allele resulting in an approximately twofold increase in breast cancer risk. Whole-genome and whole-transcriptome sequencing were performed on the leiomyosarcoma and matched blood-derived DNA...
September 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28436987/genomic-consequences-of-aberrant-dna-repair-mechanisms-stratify-ovarian-cancer-histotypes
#15
MULTICENTER STUDY
Yi Kan Wang, Ali Bashashati, Michael S Anglesio, Dawn R Cochrane, Diljot S Grewal, Gavin Ha, Andrew McPherson, Hugo M Horlings, Janine Senz, Leah M Prentice, Anthony N Karnezis, Daniel Lai, Mohamed R Aniba, Allen W Zhang, Karey Shumansky, Celia Siu, Adrian Wan, Melissa K McConechy, Hector Li-Chang, Alicia Tone, Diane Provencher, Manon de Ladurantaye, Hubert Fleury, Aikou Okamoto, Satoshi Yanagida, Nozomu Yanaihara, Misato Saito, Andrew J Mungall, Richard Moore, Marco A Marra, C Blake Gilks, Anne-Marie Mes-Masson, Jessica N McAlpine, Samuel Aparicio, David G Huntsman, Sohrab P Shah
We studied the whole-genome point mutation and structural variation patterns of 133 tumors (59 high-grade serous (HGSC), 35 clear cell (CCOC), 29 endometrioid (ENOC), and 10 adult granulosa cell (GCT)) as a substrate for class discovery in ovarian cancer. Ab initio clustering of integrated point mutation and structural variation signatures identified seven subgroups both between and within histotypes. Prevalence of foldback inversions identified a prognostically significant HGSC group associated with inferior survival...
June 2017: Nature Genetics
https://www.readbyqxmd.com/read/28403581/correction-mir-509-3p-is-clinically-significant-and-strongly-attenuates-cellular-migration-and-multi-cellular-spheroids-in-ovarian-cancer
#16
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
No abstract text is available yet for this article.
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28394352/spatial-heterogeneity-in-medulloblastoma
#17
A Sorana Morrissy, Florence M G Cavalli, Marc Remke, Vijay Ramaswamy, David J H Shih, Borja L Holgado, Hamza Farooq, Laura K Donovan, Livia Garzia, Sameer Agnihotri, Erin N Kiehna, Eloi Mercier, Chelsea Mayoh, Simon Papillon-Cavanagh, Hamid Nikbakht, Tenzin Gayden, Jonathon Torchia, Daniel Picard, Diana M Merino, Maria Vladoiu, Betty Luu, Xiaochong Wu, Craig Daniels, Stuart Horswell, Yuan Yao Thompson, Volker Hovestadt, Paul A Northcott, David T W Jones, John Peacock, Xin Wang, Stephen C Mack, Jüri Reimand, Steffen Albrecht, Adam M Fontebasso, Nina Thiessen, Yisu Li, Jacqueline E Schein, Darlene Lee, Rebecca Carlsen, Michael Mayo, Kane Tse, Angela Tam, Noreen Dhalla, Adrian Ally, Eric Chuah, Young Cheng, Patrick Plettner, Haiyan I Li, Richard D Corbett, Tina Wong, William Long, James Loukides, Pawel Buczkowicz, Cynthia E Hawkins, Uri Tabori, Brian R Rood, John S Myseros, Roger J Packer, Andrey Korshunov, Peter Lichter, Marcel Kool, Stefan M Pfister, Ulrich Schüller, Peter Dirks, Annie Huang, Eric Bouffet, James T Rutka, Gary D Bader, Charles Swanton, Yusanne Ma, Richard A Moore, Andrew J Mungall, Jacek Majewski, Steven J M Jones, Sunit Das, David Malkin, Nada Jabado, Marco A Marra, Michael D Taylor
Spatial heterogeneity of transcriptional and genetic markers between physically isolated biopsies of a single tumor poses major barriers to the identification of biomarkers and the development of targeted therapies that will be effective against the entire tumor. We analyzed the spatial heterogeneity of multiregional biopsies from 35 patients, using a combination of transcriptomic and genomic profiles. Medulloblastomas (MBs), but not high-grade gliomas (HGGs), demonstrated spatially homogeneous transcriptomes, which allowed for accurate subgrouping of tumors from a single biopsy...
May 2017: Nature Genetics
https://www.readbyqxmd.com/read/27899602/the-human-phenotype-ontology-in-2017
#18
REVIEW
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...
January 4, 2017: 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
#19
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
#20
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
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