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https://www.readbyqxmd.com/read/29666071/b-type-natriuretic-peptide-assessment-in-patients-undergoing-revascularization-for-left-main-coronary-artery-disease-analysis-from-the-excel-trial
#1
Björn Redfors, Shmuel Chen, Aaron Crowley, Ori Ben-Yehuda, Bernard J Gersh, Nicholas J Lembo, W Morris Brown, Adrian P Banning, David P Taggart, Patrick W Serruys, Arie Pieter Kappetein, Joseph F Sabik, Gregg W Stone
Background -Elevated B-type natriuretic peptide (BNP) is reflective of impaired cardiac function and is associated with worse prognosis among patients with coronary artery disease (CAD). We sought to assess the association between baseline BNP, adverse outcomes, and the relative efficacy of percutaneous coronary intervention (PCI) versus coronary artery bypass grafting (CABG) in patients with left main (LM) CAD. Methods -The EXCEL trial randomized patients with LMCAD and low or intermediate SYNTAX scores to PCI with everolimus-eluting stents versus CABG...
April 17, 2018: Circulation
https://www.readbyqxmd.com/read/29665826/association-between-afterhours-admission-to-the-intensive-care-unit-strained-capacity-and-mortality-a-retrospective-cohort-study
#2
Adam M Hall, Henry T Stelfox, Xioaming Wang, Guanmin Chen, Danny J Zuege, Peter Dodek, Allan Garland, Damon C Scales, Luc Berthiaume, David A Zygun, Sean M Bagshaw
BACKGROUND: Admission to the intensive care unit (ICU) outside daytime hours has been shown to be variably associated with increased morbidity and mortality. We aimed to describe the characteristics and outcomes of patients admitted to the ICU afterhours (22:00-06:59 h) in a large Canadian health region. We further hypothesized that the association between afterhours admission and mortality would be modified by indicators of strained ICU capacity. METHODS: This is a population-based cohort study of 12,265 adults admitted to nine ICUs in Alberta from June 2012 to December 2014...
April 17, 2018: Critical Care: the Official Journal of the Critical Care Forum
https://www.readbyqxmd.com/read/29665752/histopathologic-findings-in-canine-pituitary-glands
#3
Margaret A Miller, David S Bruyette, J Catharine Scott-Moncrieff, Tina Jo Owen, José A Ramos-Vara, Hsin-Yi Weng, Andrea L Vanderpool, Annie V Chen, Linda G Martin, Deidre M DuSold, Sina Jahan
To optimize the histologic evaluation of hypophysectomy specimens, sections of 207 canine pituitary glands (196 postmortem, 11 hypophysectomy specimens) were reviewed. Adenohypophyseal proliferation was the most common (n = 79) lesion. Proliferative lesions were sparsely to densely granulated; the granules were usually basophilic to chromophobic and periodic acid-Schiff-positive. Adenohypophyseal proliferation was classified as hyperplasia (n = 40) if ≤2 mm diameter with intact reticulin network, as microadenoma (n = 22) for 1-5 mm homogeneous nodules with lost reticulin network, or as macroadenoma (n = 17) for larger tumors...
January 1, 2018: Veterinary Pathology
https://www.readbyqxmd.com/read/29661190/a-manually-annotated-actinidia-chinensis-var-chinensis-kiwifruit-genome-highlights-the-challenges-associated-with-draft-genomes-and-gene-prediction-in-plants
#4
Sarah M Pilkington, Ross Crowhurst, Elena Hilario, Simona Nardozza, Lena Fraser, Yongyan Peng, Kularajathevan Gunaseelan, Robert Simpson, Jibran Tahir, Simon C Deroles, Kerry Templeton, Zhiwei Luo, Marcus Davy, Canhong Cheng, Mark McNeilage, Davide Scaglione, Yifei Liu, Qiong Zhang, Paul Datson, Nihal De Silva, Susan E Gardiner, Heather Bassett, David Chagné, John McCallum, Helge Dzierzon, Cecilia Deng, Yen-Yi Wang, Lorna Barron, Kelvina Manako, Judith Bowen, Toshi M Foster, Zoe A Erridge, Heather Tiffin, Chethi N Waite, Kevin M Davies, Ella P Grierson, William A Laing, Rebecca Kirk, Xiuyin Chen, Marion Wood, Mirco Montefiori, David A Brummell, Kathy E Schwinn, Andrew Catanach, Christina Fullerton, Dawei Li, Sathiyamoorthy Meiyalaghan, Niels Nieuwenhuizen, Nicola Read, Roneel Prakash, Don Hunter, Huaibi Zhang, Marian McKenzie, Mareike Knäbel, Alastair Harris, Andrew C Allan, Andrew Gleave, Angela Chen, Bart J Janssen, Blue Plunkett, Charles Ampomah-Dwamena, Charlotte Voogd, Davin Leif, Declan Lafferty, Edwige J F Souleyre, Erika Varkonyi-Gasic, Francesco Gambi, Jenny Hanley, Jia-Long Yao, Joey Cheung, Karine M David, Ben Warren, Ken Marsh, Kimberley C Snowden, Kui Lin-Wang, Lara Brian, Marcela Martinez-Sanchez, Mindy Wang, Nadeesha Ileperuma, Nikolai Macnee, Robert Campin, Peter McAtee, Revel S M Drummond, Richard V Espley, Hilary S Ireland, Rongmei Wu, Ross G Atkinson, Sakuntala Karunairetnam, Sean Bulley, Shayhan Chunkath, Zac Hanley, Roy Storey, Amali H Thrimawithana, Susan Thomson, Charles David, Raffaele Testolin, Hongwen Huang, Roger P Hellens, Robert J Schaffer
BACKGROUND: Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. RESULTS: A second genome of an A...
April 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29657586/european-heart-rhythm-association-ehra-heart-rhythm-society-hrs-asia-pacific-heart-rhythm-society-aphrs-latin-american-heart-rhythm-society-lahrs-expert-consensus-on-arrhythmias-and-cognitive-function-what-is-the-best-practice
#5
Nikolaos Dagres, Tze-Fan Chao, Guilherme Fenelon, Luis Aguinaga, Daniel Benhayon, Emelia J Benjamin, T Jared Bunch, Lin Yee Chen, Shih-Ann Chen, Francisco Darrieux, Angelo de Paola, Laurent Fauchier, Andreas Goette, Jonathan Kalman, Lalit Kalra, Young-Hoon Kim, Deirdre A Lane, Gregory Y H Lip, Steven A Lubitz, Manlio F Márquez, Tatjana Potpara, Domingo Luis Pozzer, Jeremy N Ruskin, Irina Savelieva, Wee Siong Teo, Hung-Fat Tse, Atul Verma, Shu Zhang, Mina K Chung, William-Fernando Bautista-Vargas, Chern-En Chiang, Alejandro Cuesta, Gheorghe-Andrei Dan, David S Frankel, Yutao Guo, Robert Hatala, Young Soo Lee, Yuji Murakawa, Cara N Pellegrini, Claudio Pinho, David J Milan, Daniel P Morin, Elenir Nadalin, George Ntaios, Mukund A Prabhu, Marco Proietti, Lena Rivard, Mariana Valentino, Alena Shantsila
No abstract text is available yet for this article.
April 2018: Journal of Arrhythmia
https://www.readbyqxmd.com/read/29656931/synaptotagmin-4-regulates-pancreatic-%C3%AE-cell-maturation-by-modulating-the-ca-2-sensitivity-of-insulin-secretion-vesicles
#6
Chen Huang, Emily M Walker, Prasanna K Dadi, Ruiying Hu, Yanwen Xu, Wenjian Zhang, Tiziana Sanavia, Jisoo Mun, Jennifer Liu, Gopika G Nair, Hwee Yim Angeline Tan, Sui Wang, Mark A Magnuson, Christian J Stoeckert, Matthias Hebrok, Maureen Gannon, Weiping Han, Roland Stein, David A Jacobson, Guoqiang Gu
Islet β cells from newborn mammals exhibit high basal insulin secretion and poor glucose-stimulated insulin secretion (GSIS). Here we show that β cells of newborns secrete more insulin than adults in response to similar intracellular Ca2+ concentrations, suggesting differences in the Ca2+ sensitivity of insulin secretion. Synaptotagmin 4 (Syt4), a non-Ca2+ binding paralog of the β cell Ca2+ sensor Syt7, increased by ∼8-fold during β cell maturation. Syt4 ablation increased basal insulin secretion and compromised GSIS...
April 12, 2018: Developmental Cell
https://www.readbyqxmd.com/read/29656544/an-overview-on-the-identification-of-mait-cell-antigens
#7
Lars Kjer-Nielsen, Alexandra J Corbett, Zhenjun Chen, Ligong Liu, Jeffrey Y W Mak, Dale I Godfrey, Jamie Rossjohn, David P Fairlie, James McCluskey, Sidonia B G Eckle
Mucosal Associated Invariant T (MAIT) cells are restricted by the monomorphic MHC class I-like molecule, MHC-related protein-1 (MR1). Until 2012, the origin of the MAIT cell antigens (Ags) was unknown, although it was established that MAIT cells could be activated by a broad range of bacteria and yeasts, possibly suggesting a conserved Ag. Using a combination of protein chemistry, mass spectrometry, cellular biology, structural biology and chemistry, we discovered MAIT cell ligands derived from folic acid (vitamin B9) and from an intermediate in the microbial biosynthesis of riboflavin (vitamin B2)...
April 14, 2018: Immunology and Cell Biology
https://www.readbyqxmd.com/read/29652504/the-role-of-vibrational-dynamics-on-excited-state-electronic-coherence-in-a-binuclear-platinum-complex
#8
Joseph J Radler, David B Lingerfelt, Felix N Castellano, Lin X Chen, Xiaosong Li
Long-lived quantum coherence between excited electronic states can enable highly efficient energy and charge transport processes in chemical systems. Recent pump-probe experiments on binuclear platinum complexes identified persistent, periodic beating of transient absorption anisotropy signals, indicating long excited state coherence lifetimes. Our previous simulations of the electronic dynamics of these complexes indicate that coherence lifetimes are sensitive to the balance between competitive electronic couplings...
April 13, 2018: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29649062/national-mortality-rates-after-outpatient-cosmetic-surgery-and-low-rates-of-perioperative-deep-vein-thrombosis-screening-and-prophylaxis
#9
Alexandra Bucknor, Sabine Egeler, Austin Chen, Anmol Chattha, Parisa Kamali, Gary Brownstein, Lawrence Reed, David Watts, Samuel J Lin
BACKGROUND: Concerns have arisen over reports of deaths occurring after certain outpatient plastic surgery procedures. Here, we present a detailed analysis of the American Association for the Accreditation of Ambulatory Surgical Facilities (AAAASF) database and report on deaths occurring after outpatient cosmetic surgical procedures, causative factors, and venous thromboembolism (VTE) screening rates. METHODS: A retrospective analysis of the AAAASF database was performed for the years 2012-2017...
March 29, 2018: Plastic and Reconstructive Surgery
https://www.readbyqxmd.com/read/29648688/quantitative-signal-intensity-alteration-in-infrapatellar-fat-pad-predict-incident-radiographic-osteoarthritis-the-osteoarthritis-initiative
#10
Kang Wang, Changhai Ding, Michael J Hannon, Zhongshan Chen, C Kent Kwoh, David J Hunter
OBJECTIVES: To determine if infrapatellar fat pad (IPFP) signal intensity (SI) measures are predictive of incident radiographic osteoarthritis (iROA) over 4 years in the OA Initiative (OAI) study. METHODS: Case knees (n=355) defined by iROA were matched one-to-one by gender, age and radiographic status with control knees. T2-weighted MR images were assessed at P0 (the visit when iROA was found on radiograph), P-1 (1 year prior to P0) and baseline, and utilized to assess IPFP SI semi-automatically using MATLAB...
April 12, 2018: Arthritis Care & Research
https://www.readbyqxmd.com/read/29628937/a-meta-analysis-of-genome-wide-association-studies-of-growth-differentiation-factor-15-concentration-in-blood
#11
Jiyang Jiang, Anbupalam Thalamuthu, Jennifer E Ho, Anubha Mahajan, Weronica E Ek, David A Brown, Samuel N Breit, Thomas J Wang, Ulf Gyllensten, Ming-Huei Chen, Stefan Enroth, James L Januzzi, Lars Lind, Nicola J Armstrong, John B Kwok, Peter R Schofield, Wei Wen, Julian N Trollor, Åsa Johansson, Andrew P Morris, Ramachandran S Vasan, Perminder S Sachdev, Karen A Mather
Blood levels of growth differentiation factor-15 (GDF-15), also known as macrophage inhibitory cytokine-1 (MIC-1), have been associated with various pathological processes and diseases, including cardiovascular disease and cancer. Prior studies suggest genetic factors play a role in regulating blood MIC-1/GDF-15 concentration. In the current study, we conducted the largest genome-wide association study (GWAS) to date using a sample of ∼5,400 community-based Caucasian participants, to determine the genetic variants associated with MIC-1/GDF-15 blood concentration...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29628290/the-immune-landscape-of-cancer
#12
Vésteinn Thorsson, David L Gibbs, Scott D Brown, Denise Wolf, Dante S Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, Galen F Gao, Christopher L Plaisier, James A Eddy, Elad Ziv, Aedin C Culhane, Evan O Paull, I K Ashok Sivakumar, Andrew J Gentles, Raunaq Malhotra, Farshad Farshidfar, Antonio Colaprico, Joel S Parker, Lisle E Mose, Nam Sy Vo, Jianfang Liu, Yuexin Liu, Janet Rader, Varsha Dhankani, Sheila M Reynolds, Reanne Bowlby, Andrea Califano, Andrew D Cherniack, Dimitris Anastassiou, Davide Bedognetti, Arvind Rao, Ken Chen, Alexander Krasnitz, Hai Hu, Tathiane M Malta, Houtan Noushmehr, Chandra Sekhar Pedamallu, Susan Bullman, Akinyemi I Ojesina, Andrew Lamb, Wanding Zhou, Hui Shen, Toni K Choueiri, John N Weinstein, Justin Guinney, Joel Saltz, Robert A Holt, Charles E Rabkin, Alexander J Lazar, Jonathan S Serody, Elizabeth G Demicco, Mary L Disis, Benjamin G Vincent, Llya Shmulevich
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant-characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis...
April 4, 2018: Immunity
https://www.readbyqxmd.com/read/29627023/motor-and-non-motor-features-of-parkinson-s-disease-in-lrrk2-g2019s-carriers-versus-matched-controls
#13
Steven A Gunzler, David E Riley, Shu G Chen, Curtis M Tatsuoka, William M Johnson, John J Mieyal, Ellen M Walter, Christina M Whitney, I Jung Feng, Harry Owusu-Dapaah, Shivam O Mittal, Amy L Wilson-Delfosse
INTRODUCTION: LRRK2 G2019S mutation carriers with Parkinson's disease (PD) have been generally indistinguishable from those with idiopathic PD, with the exception of variable differences in some motor and non-motor domains, including cognition, gait, and balance. LRRK2 G2019S is amongst the most common genetic etiologies for PD, particularly in Ashkenazi Jewish (AJ) populations. METHODS: This cross-sectional data collection study sought to clarify the phenotype of LRRK2 G2019S mutation carriers with PD...
May 15, 2018: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/29625308/the-effect-of-underlying-liver-disease-on-perioperative-outcomes-following-craniotomy-for-tumor-an-acs-nsqip-analysis
#14
Nicholas J Goel, Kalil G Abdullah, Omar A Choudhri, David K Kung, Timothy H Lucas, Han-Chiao Isaac Chen
BACKGROUND: The association between underlying liver disease and poor surgical outcomes has been well-documented across a wide variety of surgical disciplines. However, very little is known about the importance of liver disease in neurosurgery. Here, we assess the independent effect of liver disease on perioperative outcomes in patients undergoing craniotomy for tumor. METHODS: The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database was queried for patients undergoing craniotomy for tumor from 2006 to 2015...
April 3, 2018: World Neurosurgery
https://www.readbyqxmd.com/read/29625056/influenza-infection-in-humans-induces-broadly-cross-reactive-and-protective-neuraminidase-reactive-antibodies
#15
Yao-Qing Chen, Teddy John Wohlbold, Nai-Ying Zheng, Min Huang, Yunping Huang, Karlynn E Neu, Jiwon Lee, Hongquan Wan, Karla Thatcher Rojas, Ericka Kirkpatrick, Carole Henry, Anna-Karin E Palm, Christopher T Stamper, Linda Yu-Ling Lan, David J Topham, John Treanor, Jens Wrammert, Rafi Ahmed, Maryna C Eichelberger, George Georgiou, Florian Krammer, Patrick C Wilson
Antibodies to the hemagglutinin (HA) and neuraminidase (NA) glycoproteins are the major mediators of protection against influenza virus infection. Here, we report that current influenza vaccines poorly display key NA epitopes and rarely induce NA-reactive B cells. Conversely, influenza virus infection induces NA-reactive B cells at a frequency that approaches (H1N1) or exceeds (H3N2) that of HA-reactive B cells. NA-reactive antibodies display broad binding activity spanning the entire history of influenza A virus circulation in humans, including the original pandemic strains of both H1N1 and H3N2 subtypes...
April 5, 2018: Cell
https://www.readbyqxmd.com/read/29625053/comprehensive-characterization-of-cancer-driver-genes-and-mutations
#16
Matthew H Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C Wendl, Jaegil Kim, Brendan Reardon, Patrick Kwok-Shing Ng, Kang Jin Jeong, Song Cao, Zixing Wang, Jianjiong Gao, Qingsong Gao, Fang Wang, Eric Minwei Liu, Loris Mularoni, Carlota Rubio-Perez, Niranjan Nagarajan, Isidro Cortés-Ciriano, Daniel Cui Zhou, Wen-Wei Liang, Julian M Hess, Venkata D Yellapantula, David Tamborero, Abel Gonzalez-Perez, Chayaporn Suphavilai, Jia Yu Ko, Ekta Khurana, Peter J Park, Eliezer M Van Allen, Han Liang, Michael S Lawrence, Adam Godzik, Nuria Lopez-Bigas, Josh Stuart, David Wheeler, Gad Getz, Ken Chen, Alexander J Lazar, Gordon B Mills, Rachel Karchin, Li Ding
Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types...
April 5, 2018: Cell
https://www.readbyqxmd.com/read/29625052/pathogenic-germline-variants-in-10-389-adult-cancers
#17
Kuan-Lin Huang, R Jay Mashl, Yige Wu, Deborah I Ritter, Jiayin Wang, Clara Oh, Marta Paczkowska, Sheila Reynolds, Matthew A Wyczalkowski, Ninad Oak, Adam D Scott, Michal Krassowski, Andrew D Cherniack, Kathleen E Houlahan, Reyka Jayasinghe, Liang-Bo Wang, Daniel Cui Zhou, Di Liu, Song Cao, Young Won Kim, Amanda Koire, Joshua F McMichael, Vishwanathan Hucthagowder, Tae-Beom Kim, Abigail Hahn, Chen Wang, Michael D McLellan, Fahd Al-Mulla, Kimberly J Johnson, Olivier Lichtarge, Paul C Boutros, Benjamin Raphael, Alexander J Lazar, Wei Zhang, Michael C Wendl, Ramaswamy Govindan, Sanjay Jain, David Wheeler, Shashikant Kulkarni, John F Dipersio, Jüri Reimand, Funda Meric-Bernstam, Ken Chen, Ilya Shmulevich, Sharon E Plon, Feng Chen, Li Ding
We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including novel associations of SDHA in melanoma and PALB2 in stomach adenocarcinoma. The 659 predisposition variants and 18 additional large deletions in tumor suppressors, including ATM, BRCA1, and NF1, showed low gene expression and frequent (43%) loss of heterozygosity or biallelic two-hit events...
April 5, 2018: Cell
https://www.readbyqxmd.com/read/29625050/oncogenic-signaling-pathways-in-the-cancer-genome-atlas
#18
Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K Chatila, Augustin Luna, Konnor C La, Sofia Dimitriadoy, David L Liu, Havish S Kantheti, Sadegh Saghafinia, Debyani Chakravarty, Foysal Daian, Qingsong Gao, Matthew H Bailey, Wen-Wei Liang, Steven M Foltz, Ilya Shmulevich, Li Ding, Zachary Heins, Angelica Ochoa, Benjamin Gross, Jianjiong Gao, Hongxin Zhang, Ritika Kundra, Cyriac Kandoth, Istemi Bahceci, Leonard Dervishi, Ugur Dogrusoz, Wanding Zhou, Hui Shen, Peter W Laird, Gregory P Way, Casey S Greene, Han Liang, Yonghong Xiao, Chen Wang, Antonio Iavarone, Alice H Berger, Trever G Bivona, Alexander J Lazar, Gary D Hammer, Thomas Giordano, Lawrence N Kwong, Grant McArthur, Chenfei Huang, Aaron D Tward, Mitchell J Frederick, Frank McCormick, Matthew Meyerson, Eliezer M Van Allen, Andrew D Cherniack, Giovanni Ciriello, Chris Sander, Nikolaus Schultz
Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFβ signaling, p53 and β-catenin/Wnt...
April 5, 2018: Cell
https://www.readbyqxmd.com/read/29625049/perspective-on-oncogenic-processes-at-the-end-of-the-beginning-of-cancer-genomics
#19
Li Ding, Matthew H Bailey, Eduard Porta-Pardo, Vesteinn Thorsson, Antonio Colaprico, Denis Bertrand, David L Gibbs, Amila Weerasinghe, Kuan-Lin Huang, Collin Tokheim, Isidro Cortés-Ciriano, Reyka Jayasinghe, Feng Chen, Lihua Yu, Sam Sun, Catharina Olsen, Jaegil Kim, Alison M Taylor, Andrew D Cherniack, Rehan Akbani, Chayaporn Suphavilai, Niranjan Nagarajan, Joshua M Stuart, Gordon B Mills, Matthew A Wyczalkowski, Benjamin G Vincent, Carolyn M Hutter, Jean Claude Zenklusen, Katherine A Hoadley, Michael C Wendl, Llya Shmulevich, Alexander J Lazar, David A Wheeler, Gad Getz
The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies...
April 5, 2018: Cell
https://www.readbyqxmd.com/read/29617666/systematic-analysis-of-splice-site-creating-mutations-in-cancer
#20
Reyka G Jayasinghe, Song Cao, Qingsong Gao, Michael C Wendl, Nam Sy Vo, Sheila M Reynolds, Yanyan Zhao, Héctor Climente-González, Shengjie Chai, Fang Wang, Rajees Varghese, Mo Huang, Wen-Wei Liang, Matthew A Wyczalkowski, Sohini Sengupta, Zhi Li, Samuel H Payne, David Fenyö, Jeffrey H Miner, Matthew J Walter, Benjamin Vincent, Eduardo Eyras, Ken Chen, Ilya Shmulevich, Feng Chen, Li Ding
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function...
April 3, 2018: Cell Reports
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