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Watson for genomics

Edgar A Rivera-Muñoz, Laura V Milko, Steven M Harrison, Danielle R Azzariti, C Lisa Kurtz, Kristy Lee, Jessica L Mester, Meredith A Weaver, Erin Currey, William Craigen, Charis Eng, Birgit Funke, Madhuri Hegde, Ray E Hershberger, Rong Mao, Robert D Steiner, Lisa M Vincent, Christa L Martin, Sharon E Plon, Erin Ramos, Heidi L Rehm, Michael Watson, Jonathan S Berg
Genome-scale sequencing creates vast amounts of genomic data, increasing the challenge of clinical sequence variant interpretation. The demand for high-quality interpretation requires multiple specialties to join forces to accelerate the interpretation of sequence variant pathogenicity. With over 600 international members including clinicians, researchers, and laboratory diagnosticians, the Clinical Genome Resource (ClinGen), funded by the National Institutes of Health, is forming expert groups to systematically evaluate variants in clinically relevant genes...
November 2018: Human Mutation
Laura M Thornton, Melissa A Munn-Chernoff, Jessica H Baker, Anders Juréus, Richard Parker, Anjali K Henders, Janne T Larsen, Liselotte Petersen, Hunna J Watson, Zeynep Yilmaz, Katherine M Kirk, Scott Gordon, Virpi M Leppä, Felicity C Martin, David C Whiteman, Catherine M Olsen, Thomas M Werge, Nancy L Pedersen, Walter Kaye, Andrew W Bergen, Katherine A Halmi, Michael Strober, Allan S Kaplan, D Blake Woodside, James Mitchell, Craig L Johnson, Harry Brandt, Steven Crawford, L John Horwood, Joseph M Boden, John F Pearson, Laramie E Duncan, Jakob Grove, Manuel Mattheisen, Jennifer Jordan, Martin A Kennedy, Andreas Birgegård, Paul Lichtenstein, Claes Norring, Tracey D Wade, Grant W Montgomery, Nicholas G Martin, Mikael Landén, Preben Bo Mortensen, Patrick F Sullivan, Cynthia M Bulik
BACKGROUND: Genetic factors contribute to anorexia nervosa (AN); and the first genome-wide significant locus has been identified. We describe methods and procedures for the Anorexia Nervosa Genetics Initiative (ANGI), an international collaboration designed to rapidly recruit 13,000 individuals with AN and ancestrally matched controls. We present sample characteristics and the utility of an online eating disorder diagnostic questionnaire suitable for large-scale genetic and population research...
October 1, 2018: Contemporary Clinical Trials
Paras Garg, Ricky S Joshi, Corey Watson, Andrew J Sharp
While population studies have resulted in detailed maps of genetic variation in humans, to date there are few robust maps of epigenetic variation. We identified sites containing clusters of CpGs with high inter-individual epigenetic variation, termed Variably Methylated Regions (VMRs) in five purified cell types. We observed that VMRs occur preferentially at enhancers and 3' UTRs. While the majority of VMRs have high heritability, a subset of VMRs within the genome show highly correlated variation in trans, forming co-regulated networks that have low heritability, differ between cell types and are enriched for specific transcription factor binding sites and biological pathways of functional relevance to each tissue...
October 2018: PLoS Genetics
Hui Yu, Zhengming Chen, Karla Ballman, Mark A Watson, Ramaswamy Govindan, Irena Lanc, David G Beer, Raphael Bueno, Lucian Chirieac, M Herman Chui, Guoan Chen, Wilbur A Franklin, David R Gandara, Carlo Genova, Kristine Brovsky, David Harpole, Marybeth Joshi, Daniel T Merrick, William Richards, Christopher J Rivard, Ming-Sound Tsao, Adrie van Bokhoven, Frances A Shepherd, Fred R Hirsch
PURPOSE: Anti-PD1/PD-L1 immunotherapy has demonstrated success in the treatment of advanced non-small cell lung cancer (NSCLC). Recently, PD1/PD-L1 blockade also has demonstrated interesting results in small trials of neo-adjuvant treatment in Stage IB-IIIA NSCLC. In addition, several clinical trials using anti-PD1/PD-L1 as an adjuvant or neo-adjuvant treatment in resectable stage NSCLC patients are ongoing. However, few analyses of anti-PD1/PD-L1 immunotherapy related biomarkers in early stage squamous cell lung carcinoma (SqCLC) have been reported...
September 22, 2018: Journal of Thoracic Oncology
Eduardo Corel, Jananan S Pathmanathan, Andrew K Watson, Slim Karkar, Philippe Lopez, Eric Bapteste
The inclusion of introgressive processes in evolutionary studies induces a less constrained view of evolution. Network-based methods (like large-scale similarity networks) allow to include in comparative genomics all extra-chromosomic carriers (like viruses, the most abundant biological entities on the planet) with their cellular hosts. The integration of several levels of biological organization (genes, genomes, communities, environments) enables more comprehensive analyses of gene sharing and improved sequence-based classifications...
September 22, 2018: Genome Biology and Evolution
Laura V Milko, Birgit H Funke, Ray E Hershberger, Danielle R Azzariti, Kristy Lee, Erin R Riggs, Edgar A Rivera-Munoz, Meredith A Weaver, Annie Niehaus, Erin L Currey, William J Craigen, Rong Mao, Kenneth Offit, Robert D Steiner, Christa L Martin, Heidi L Rehm, Michael S Watson, Erin M Ramos, Sharon E Plon, Jonathan S Berg
The Clinical Genome Resource (ClinGen) is supported by the National Institutes of Health (NIH) to develop expertly curated and freely accessible resources defining the clinical relevance of genes and variants for use in precision medicine and research. To facilitate expert input, ClinGen has formed Clinical Domain Working Groups (CDWGs) to leverage the collective knowledge of clinicians, laboratory diagnosticians, and researchers. In the initial phase of ClinGen, CDWGs were launched in the cardiovascular, hereditary cancer, and inborn errors of metabolism clinical fields...
September 5, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Steven M Sanders, Zhiwei Ma, Julia M Hughes, Brooke M Riscoe, Gregory A Gibson, Alan M Watson, Hakima Flici, Uri Frank, Christine E Schnitzler, Andreas D Baxevanis, Matthew L Nicotra
BACKGROUND: Hydractinia symbiolongicarpus, a colonial cnidarian, is a tractable model system for many cnidarian-specific and general biological questions. Until recently, tests of gene function in Hydractinia have relied on laborious forward genetic approaches, randomly integrated transgenes, or transient knockdown of mRNAs. RESULTS: Here, we report the use of CRISPR/Cas9 genome editing to generate targeted genomic insertions in H. symbiolonigcarpus. We used CRISPR/Cas9 to promote homologous recombination of two fluorescent reporters, eGFP and tdTomato, into the Eukaryotic elongation factor 1 alpha (Eef1a) locus...
September 3, 2018: BMC Genomics
Emma V A Sylvester, Robert G Beiko, Paul Bentzen, Ian Paterson, John B Horne, Beth Watson, Sarah Lehnert, Steven Duffy, Marie Clément, Martha J Robertson, Ian R Bradbury
Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations...
August 27, 2018: Molecular Ecology
Kyren A Lazarus, Fazal Hadi, Elisabetta Zambon, Karsten Bach, Maria-Francesca Santolla, Julie K Watson, Lucia L Correia, Madhumita Das, Rosemary Ugur, Sara Pensa, Lukas Becker, Lia S Campos, Graham Ladds, Pentao Liu, Gerard I Evan, Frank M McCaughan, John Le Quesne, Joo-Hyeon Lee, Dinis Calado, Walid T Khaled
Patients diagnosed with lung squamous cell carcinoma (LUSC) have limited targeted therapies. We report here the identification and characterisation of BCL11A, as a LUSC oncogene. Analysis of cancer genomics datasets revealed BCL11A to be upregulated in LUSC but not in lung adenocarcinoma (LUAD). Experimentally we demonstrate that non-physiological levels of BCL11A in vitro and in vivo promote squamous-like phenotypes, while its knockdown abolishes xenograft tumour formation. At the molecular level we found that BCL11A is transcriptionally regulated by SOX2 and is required for its oncogenic functions...
August 20, 2018: Nature Communications
Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, Raj Pasam, Matthew Hayden, Kerrie Forrest, Zeev Frenkel, Abraham Korol, B Emma Huang, Colin Cavanagh, Jen Taylor, Michael Abrouk, Andrew Sharpe, David Konkin, Pierre Sourdille, Benoît Darrier, Frédéric Choulet, Aurélien Bernard, Simone Rochfort, Adam Dimech, Nathan Watson-Haigh, Ute Baumann, Paul Eckermann, Delphine Fleury, Angela Juhasz, Sébastien Boisvert, Marc-Alexandre Nolin, Jaroslav Doležel, Hana Šimková, Helena Toegelová, Jan Šafář, Ming-Cheng Luo, Francisco Câmara, Matthias Pfeifer, Don Isdale, Johan Nyström-Persson, Iwgsc, Dal-Hoe Koo, Matthew Tinning, Dangqun Cui, Zhengang Ru, Rudi Appels
BACKGROUND: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. RESULTS: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1...
August 17, 2018: Genome Biology
Richard J George, Stephen Plog, Adam S Watson, Kari L Schmidt, Brendan J Culleton, Thomas K Harper, Patricia A Gilman, Steven A LeBlanc, George Amato, Peter Whiteley, Logan Kistler, Douglas J Kennett
Hundreds of scarlet macaw ( Ara macao cyanoptera ) skeletons have been recovered from archaeological contexts in the southwestern United States and northwestern Mexico (SW/NW). The location of these skeletons, >1,000 km outside their Neotropical endemic range, has suggested a far-reaching pre-Hispanic acquisition network. Clear evidence for scarlet macaw breeding within this network is only known from the settlement of Paquimé in NW dating between 1250 and 1450 CE. Although some scholars have speculated on the probable existence of earlier breeding centers in the SW/NW region, there has been no supporting evidence...
August 28, 2018: Proceedings of the National Academy of Sciences of the United States of America
James J Lee, Robbee Wedow, Aysu Okbay, Edward Kong, Omeed Maghzian, Meghan Zacher, Tuan Anh Nguyen-Viet, Peter Bowers, Julia Sidorenko, Richard Karlsson Linnér, Mark Alan Fontana, Tushar Kundu, Chanwook Lee, Hui Li, Ruoxi Li, Rebecca Royer, Pascal N Timshel, Raymond K Walters, Emily A Willoughby, Loïc Yengo, Maris Alver, Yanchun Bao, David W Clark, Felix R Day, Nicholas A Furlotte, Peter K Joshi, Kathryn E Kemper, Aaron Kleinman, Claudia Langenberg, Reedik Mägi, Joey W Trampush, Shefali Setia Verma, Yang Wu, Max Lam, Jing Hua Zhao, Zhili Zheng, Jason D Boardman, Harry Campbell, Jeremy Freese, Kathleen Mullan Harris, Caroline Hayward, Pamela Herd, Meena Kumari, Todd Lencz, Jian'an Luan, Anil K Malhotra, Andres Metspalu, Lili Milani, Ken K Ong, John R B Perry, David J Porteous, Marylyn D Ritchie, Melissa C Smart, Blair H Smith, Joyce Y Tung, Nicholas J Wareham, James F Wilson, Jonathan P Beauchamp, Dalton C Conley, Tõnu Esko, Steven F Lehrer, Patrik K E Magnusson, Sven Oskarsson, Tune H Pers, Matthew R Robinson, Kevin Thom, Chelsea Watson, Christopher F Chabris, Michelle N Meyer, David I Laibson, Jian Yang, Magnus Johannesson, Philipp D Koellinger, Patrick Turley, Peter M Visscher, Daniel J Benjamin, David Cesarini
Here we conducted a large-scale genetic association analysis of educational attainment in a sample of approximately 1.1 million individuals and identify 1,271 independent genome-wide-significant SNPs. For the SNPs taken together, we found evidence of heterogeneous effects across environments. The SNPs implicate genes involved in brain-development processes and neuron-to-neuron communication. In a separate analysis of the X chromosome, we identify 10 independent genome-wide-significant SNPs and estimate a SNP heritability of around 0...
August 2018: Nature Genetics
Neneh Sallah, Anne L Palser, Simon J Watson, Nazzarena Labo, Gershim Asiki, Vickie Marshall, Robert Newton, Denise Whitby, Paul Kellam, Inês Barroso
Background: Kaposi's Sarcoma-associated herpesvirus (KSHV) establishes lifelong infection in the human host and has been associated with a variety of malignancies. KSHV displays striking geographic variation in prevalence, which is highest in sub-Saharan Africa. The current KSHV genomes sequences available are all tumour cell line-derived or primary tumour associated viruses, which have provided valuable insights into KSHV genetic diversity. Methods: Here, we sequenced 45 KSHV genomes from a Ugandan population cohort in which KSHV is endemic; these are the only genome sequences obtained from non-diseased individuals and of KSHV DNA isolated from saliva...
July 14, 2018: Journal of Infectious Diseases
Connor B Driscoll, Kevin A Meyer, Sigitas Šulčius, Nathan M Brown, Gregory J Dick, Huansheng Cao, Giedrius Gasiūnas, Albertas Timinskas, Yanbin Yin, Zachary C Landry, Timothy G Otten, Timothy W Davis, Susan B Watson, Theo W Dreher
In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology...
July 2018: Harmful Algae
Felipe S Barreto, Eric T Watson, Thiago G Lima, Christopher S Willett, Suzanne Edmands, Weizhong Li, Ronald S Burton
The copepod Tigriopus californicus shows extensive population divergence and is becoming a model for understanding allopatric differentiation and the early stages of speciation. Here, we report a high-quality reference genome for one population (~190 megabases across 12 scaffolds, and ~15,500 protein-coding genes). Comparison with other arthropods reveals 2,526 genes presumed to be specific to T. californicus, with an apparent proliferation of genes involved in ion transport and receptor activity. Beyond the reference population, we report re-sequenced genomes of seven additional populations, spanning the continuum of reproductive isolation...
August 2018: Nature Ecology & Evolution
Ryan Clarke, Robert Heler, Matthew S MacDougall, Nan Cher Yeo, Alejandro Chavez, Maureen Regan, Leslyn Hanakahi, George M Church, Luciano A Marraffini, Bradley J Merrill
The ability to target the Cas9 nuclease to DNA sequences via Watson-Crick base pairing with a single guide RNA (sgRNA) has provided a dynamic tool for genome editing and an essential component of adaptive immune systems in bacteria. After generating a double-stranded break (DSB), Cas9 remains stably bound to DNA. Here, we show persistent Cas9 binding blocks access to the DSB by repair enzymes, reducing genome editing efficiency. Cas9 can be dislodged by translocating RNA polymerases, but only if the polymerase approaches from one direction toward the Cas9-DSB complex...
July 5, 2018: Molecular Cell
Yun Yeong Kim, Se Jeong Oh, Yong Soon Chun, Woon Kee Lee, Heung Kyu Park
BACKGROUND: Personalized treatment for cancer patients is a hot topic of debate, particularly the decision to initiate chemotherapy in patients with Estrogen receptor (ER)-positive, HER2-negative tumors in the early stages of breast cancer (BC). Owing to significant advancements in information technology (IT) and genomics, clinicians are increasingly attaining therapeutic goals rapidly and safely by effectively differentiating patient subsets that require chemotherapy. IBM Watson for Oncology (WFO) is a cognitive computing system employed by clinicians to provide evidence-based treatment options for cancer...
2018: PloS One
Percy Tumbale, Matthew J Schellenberg, Geoffrey A Mueller, Emma Fairweather, Mandy Watson, Jessica N Little, Juno Krahn, Ian Waddell, Robert E London, R Scott Williams
The failure of DNA ligases to complete their catalytic reactions generates cytotoxic adenylated DNA strand breaks. The APTX RNA-DNA deadenylase protects genome integrity and corrects abortive DNA ligation arising during ribonucleotide excision repair and base excision DNA repair, and APTX human mutations cause the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1). How APTX senses cognate DNA nicks and is inactivated in AOA1 remains incompletely defined. Here, we report X-ray structures of APTX engaging nicked RNA-DNA substrates that provide direct evidence for a wedge-pivot-cut strategy for 5'-AMP resolution shared with the alternate 5'-AMP processing enzymes POLβ and FEN1...
July 13, 2018: EMBO Journal
Ian R Bradbury, Brendan F Wringe, Beth Watson, Ian Paterson, John Horne, Robert Beiko, Sarah J Lehnert, Marie Clément, Eric C Anderson, Nicholas W Jeffery, Steven Duffy, Emma Sylvester, Martha Robertson, Paul Bentzen
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3...
July 2018: Evolutionary Applications
S M Ashiqul Islam, Christopher Michel Kearney, Erich J Baker
Cystine-stabilized peptides have great utility as they naturally block ion channels, inhibit acetylcholine receptors, or inactivate microbes. However, only a tiny fraction of these peptides has been characterized. Exploration for novel peptides most efficiently starts with the identification of candidates from genome sequence data. Unfortunately, though cystine-stabilized peptides have shared structures, they have low DNA sequence similarity, restricting the utility of BLAST and even more powerful sequence alignment-based annotation algorithms, such as PSI-BLAST and HMMER...
June 13, 2018: Scientific Reports
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