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https://www.readbyqxmd.com/read/28346484/a-neighborhood-wide-association-study-nwas-example-of-prostate-cancer-aggressiveness
#1
Shannon M Lynch, Nandita Mitra, Michelle Ross, Craig Newcomb, Karl Dailey, Tara Jackson, Charnita M Zeigler-Johnson, Harold Riethman, Charles C Branas, Timothy R Rebbeck
PURPOSE: Cancer results from complex interactions of multiple variables at the biologic, individual, and social levels. Compared to other levels, social effects that occur geospatially in neighborhoods are not as well-studied, and empiric methods to assess these effects are limited. We propose a novel Neighborhood-Wide Association Study(NWAS), analogous to genome-wide association studies(GWAS), that utilizes high-dimensional computing approaches from biology to comprehensively and empirically identify neighborhood factors associated with disease...
2017: PloS One
https://www.readbyqxmd.com/read/28346479/rare-variants-in-fox-1-homolog-a-rbfox1-are-associated-with-lower-blood-pressure
#2
Karen Y He, Heming Wang, Brian E Cade, Priyanka Nandakumar, Ayush Giri, Erin B Ware, Jeffrey Haessler, Jingjing Liang, Jennifer A Smith, Nora Franceschini, Thu H Le, Charles Kooperberg, Todd L Edwards, Sharon L R Kardia, Xihong Lin, Aravinda Chakravarti, Susan Redline, Xiaofeng Zhu
Many large genome-wide association studies (GWAS) have identified common blood pressure (BP) variants. However, most of the identified BP variants do not overlap with the linkage evidence observed from family studies. We thus hypothesize that multiple rare variants contribute to the observed linkage evidence. We performed linkage analysis using 517 individuals in 130 European families from the Cleveland Family Study (CFS) who have been genotyped on the Illumina OmniExpress Exome array. The largest linkage peak was observed on chromosome 16p13 (MLOD = 2...
March 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28346466/common-and-rare-exonic-muc5b-variants-associated-with-type-2-diabetes-in-han-chinese
#3
Guanjie Chen, Zhenjian Zhang, Sally N Adebamowo, Guozheng Liu, Adebowale Adeyemo, Yanxun Zhou, Ayo P Doumatey, Chuntao Wang, Jie Zhou, Wenqiang Yan, Daniel Shriner, Fasil Tekola-Ayele, Amy R Bentley, Congqing Jiang, Charles N Rotimi
Genome-wide association studies have identified over one hundred common genetic risk variants associated with type 2 diabetes (T2D). However, most of the heritability of T2D has not been accounted for. In this study, we investigated the contribution of rare and common variants to T2D susceptibility by analyzing exome array data in 1,908 Han Chinese genotyped with Affymetrix Axiom® Exome Genotyping Arrays. Based on the joint common and rare variants analysis of 57,704 autosomal SNPs within 12,244 genes using Sequence Kernel Association Tests (SKAT), we identified significant associations between T2D and 25 variants (9 rare and 16 common) in MUC5B, p-value 1...
2017: PloS One
https://www.readbyqxmd.com/read/28346445/potential-energy-landscapes-identify-the-information-theoretic-nature-of-the-epigenome
#4
Garrett Jenkinson, Elisabet Pujadas, John Goutsias, Andrew P Feinberg
Epigenetics is the study of biochemical modifications carrying information independent of DNA sequence, which are heritable through cell division. In 1940, Waddington coined the term "epigenetic landscape" as a metaphor for pluripotency and differentiation, but methylation landscapes have not yet been rigorously computed. Using principles from statistical physics and information theory, we derive epigenetic energy landscapes from whole-genome bisulfite sequencing (WGBS) data that enable us to quantify methylation stochasticity genome-wide using Shannon's entropy, associating it with chromatin structure...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28346444/genetic-variants-associated-with-mosaic-y-chromosome-loss-highlight-cell-cycle-genes-and-overlap-with-cancer-susceptibility
#5
Daniel J Wright, Felix R Day, Nicola D Kerrison, Florian Zink, Alexia Cardona, Patrick Sulem, Deborah J Thompson, Svanhvit Sigurjonsdottir, Daniel F Gudbjartsson, Agnar Helgason, J Ross Chapman, Steve P Jackson, Claudia Langenberg, Nicholas J Wareham, Robert A Scott, Unnur Thorsteindottir, Ken K Ong, Kari Stefansson, John R B Perry
The Y chromosome is frequently lost in hematopoietic cells, which represents the most common somatic alteration in men. However, the mechanisms that regulate mosaic loss of chromosome Y (mLOY), and its clinical relevance, are unknown. We used genotype-array-intensity data and sequence reads from 85,542 men to identify 19 genomic regions (P < 5 × 10(-8)) that are associated with mLOY. Cumulatively, these loci also predicted X chromosome loss in women (n = 96,123; P = 4 × 10(-6)). Additional epigenome-wide methylation analyses using whole blood highlighted 36 differentially methylated sites associated with mLOY...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28346443/genome-wide-association-study-of-glioma-subtypes-identifies-specific-differences-in-genetic-susceptibility-to-glioblastoma-and-non-glioblastoma-tumors
#6
Beatrice S Melin, Jill S Barnholtz-Sloan, Margaret R Wrensch, Christoffer Johansen, Dora Il'yasova, Ben Kinnersley, Quinn T Ostrom, Karim Labreche, Yanwen Chen, Georgina Armstrong, Yanhong Liu, Jeanette E Eckel-Passow, Paul A Decker, Marianne Labussière, Ahmed Idbaih, Khe Hoang-Xuan, Anna-Luisa Di Stefano, Karima Mokhtari, Jean-Yves Delattre, Peter Broderick, Pilar Galan, Konstantinos Gousias, Johannes Schramm, Minouk J Schoemaker, Sarah J Fleming, Stefan Herms, Stefanie Heilmann, Markus M Nöthen, Heinz-Erich Wichmann, Stefan Schreiber, Anthony Swerdlow, Mark Lathrop, Matthias Simon, Marc Sanson, Ulrika Andersson, Preetha Rajaraman, Stephen Chanock, Martha Linet, Zhaoming Wang, Meredith Yeager, John K Wiencke, Helen Hansen, Lucie McCoy, Terri Rice, Matthew L Kosel, Hugues Sicotte, Christopher I Amos, Jonine L Bernstein, Faith Davis, Dan Lachance, Ching Lau, Ryan T Merrell, Joellen Shildkraut, Francis Ali-Osman, Siegal Sadetzki, Michael Scheurer, Sanjay Shete, Rose K Lai, Elizabeth B Claus, Sara H Olson, Robert B Jenkins, Richard S Houlston, Melissa L Bondy
Genome-wide association studies (GWAS) have transformed our understanding of glioma susceptibility, but individual studies have had limited power to identify risk loci. We performed a meta-analysis of existing GWAS and two new GWAS, which totaled 12,496 cases and 18,190 controls. We identified five new loci for glioblastoma (GBM) at 1p31.3 (rs12752552; P = 2.04 × 10(-9), odds ratio (OR) = 1.22), 11q14.1 (rs11233250; P = 9.95 × 10(-10), OR = 1.24), 16p13.3 (rs2562152; P = 1.93 × 10(-8), OR = 1.21), 16q12...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28346442/identification-of-12-new-susceptibility-loci-for-different-histotypes-of-epithelial-ovarian-cancer
#7
Catherine M Phelan, Karoline B Kuchenbaecker, Jonathan P Tyrer, Siddhartha P Kar, Kate Lawrenson, Stacey J Winham, Joe Dennis, Ailith Pirie, Marjorie J Riggan, Ganna Chornokur, Madalene A Earp, Paulo C Lyra, Janet M Lee, Simon Coetzee, Jonathan Beesley, Lesley McGuffog, Penny Soucy, Ed Dicks, Andrew Lee, Daniel Barrowdale, Julie Lecarpentier, Goska Leslie, Cora M Aalfs, Katja K H Aben, Marcia Adams, Julian Adlard, Irene L Andrulis, Hoda Anton-Culver, Natalia Antonenkova, Gerasimos Aravantinos, Norbert Arnold, Banu K Arun, Brita Arver, Jacopo Azzollini, Judith Balmaña, Susana N Banerjee, Laure Barjhoux, Rosa B Barkardottir, Yukie Bean, Matthias W Beckmann, Alicia Beeghly-Fadiel, Javier Benitez, Marina Bermisheva, Marcus Q Bernardini, Michael J Birrer, Line Bjorge, Amanda Black, Kenneth Blankstein, Marinus J Blok, Clara Bodelon, Natalia Bogdanova, Anders Bojesen, Bernardo Bonanni, Åke Borg, Angela R Bradbury, James D Brenton, Carole Brewer, Louise Brinton, Per Broberg, Angela Brooks-Wilson, Fiona Bruinsma, Joan Brunet, Bruno Buecher, Ralf Butzow, Saundra S Buys, Trinidad Caldes, Maria A Caligo, Ian Campbell, Rikki Cannioto, Michael E Carney, Terence Cescon, Salina B Chan, Jenny Chang-Claude, Stephen Chanock, Xiao Qing Chen, Yoke-Eng Chiew, Jocelyne Chiquette, Wendy K Chung, Kathleen B M Claes, Thomas Conner, Linda S Cook, Jackie Cook, Daniel W Cramer, Julie M Cunningham, Aimee A D'Aloisio, Mary B Daly, Francesca Damiola, Sakaeva Dina Damirovna, Agnieszka Dansonka-Mieszkowska, Fanny Dao, Rosemarie Davidson, Anna DeFazio, Capucine Delnatte, Kimberly F Doheny, Orland Diez, Yuan Chun Ding, Jennifer Anne Doherty, Susan M Domchek, Cecilia M Dorfling, Thilo Dörk, Laure Dossus, Mercedes Duran, Matthias Dürst, Bernd Dworniczak, Diana Eccles, Todd Edwards, Ros Eeles, Ursula Eilber, Bent Ejlertsen, Arif B Ekici, Steve Ellis, Mingajeva Elvira, Kevin H Eng, Christoph Engel, D Gareth Evans, Peter A Fasching, Sarah Ferguson, Sandra Fert Ferrer, James M Flanagan, Zachary C Fogarty, Renée T Fortner, Florentia Fostira, William D Foulkes, George Fountzilas, Brooke L Fridley, Tara M Friebel, Eitan Friedman, Debra Frost, Patricia A Ganz, Judy Garber, María J García, Vanesa Garcia-Barberan, Andrea Gehrig, Aleksandra Gentry-Maharaj, Anne-Marie Gerdes, Graham G Giles, Rosalind Glasspool, Gord Glendon, Andrew K Godwin, David E Goldgar, Teodora Goranova, Martin Gore, Mark H Greene, Jacek Gronwald, Stephen Gruber, Eric Hahnen, Christopher A Haiman, Niclas Håkansson, Ute Hamann, Thomas V O Hansen, Patricia A Harrington, Holly R Harris, Jan Hauke, Alexander Hein, Alex Henderson, Michelle A T Hildebrandt, Peter Hillemanns, Shirley Hodgson, Claus K Høgdall, Estrid Høgdall, Frans B L Hogervorst, Helene Holland, Maartje J Hooning, Karen Hosking, Ruea-Yea Huang, Peter J Hulick, Jillian Hung, David J Hunter, David G Huntsman, Tomasz Huzarski, Evgeny N Imyanitov, Claudine Isaacs, Edwin S Iversen, Louise Izatt, Angel Izquierdo, Anna Jakubowska, Paul James, Ramunas Janavicius, Mats Jernetz, Allan Jensen, Uffe Birk Jensen, Esther M John, Sharon Johnatty, Michael E Jones, Päivi Kannisto, Beth Y Karlan, Anthony Karnezis, Karin Kast, Catherine J Kennedy, Elza Khusnutdinova, Lambertus A Kiemeney, Johanna I Kiiski, Sung-Won Kim, Susanne K Kjaer, Martin Köbel, Reidun K Kopperud, Torben A Kruse, Jolanta Kupryjanczyk, Ava Kwong, Yael Laitman, Diether Lambrechts, Nerea Larrañaga, Melissa C Larson, Conxi Lazaro, Nhu D Le, Loic Le Marchand, Jong Won Lee, Shashikant B Lele, Arto Leminen, Dominique Leroux, Jenny Lester, Fabienne Lesueur, Douglas A Levine, Dong Liang, Clemens Liebrich, Jenna Lilyquist, Loren Lipworth, Jolanta Lissowska, Karen H Lu, Jan Lubinński, Craig Luccarini, Lene Lundvall, Phuong L Mai, Gustavo Mendoza-Fandiño, Siranoush Manoukian, Leon F A G Massuger, Taymaa May, Sylvie Mazoyer, Jessica N McAlpine, Valerie McGuire, John R McLaughlin, Iain McNeish, Hanne Meijers-Heijboer, Alfons Meindl, Usha Menon, Arjen R Mensenkamp, Melissa A Merritt, Roger L Milne, Gillian Mitchell, Francesmary Modugno, Joanna Moes-Sosnowska, Melissa Moffitt, Marco Montagna, Kirsten B Moysich, Anna Marie Mulligan, Jacob Musinsky, Katherine L Nathanson, Lotte Nedergaard, Roberta B Ness, Susan L Neuhausen, Heli Nevanlinna, Dieter Niederacher, Robert L Nussbaum, Kunle Odunsi, Edith Olah, Olufunmilayo I Olopade, Håkan Olsson, Curtis Olswold, David M O'Malley, Kai-Ren Ong, N Charlotte Onland-Moret, Nicholas Orr, Sandra Orsulic, Ana Osorio, Domenico Palli, Laura Papi, Tjoung-Won Park-Simon, James Paul, Celeste L Pearce, Inge Søkilde Pedersen, Petra H M Peeters, Bernard Peissel, Ana Peixoto, Tanja Pejovic, Liisa M Pelttari, Jennifer B Permuth, Paolo Peterlongo, Lidia Pezzani, Georg Pfeiler, Kelly-Anne Phillips, Marion Piedmonte, Malcolm C Pike, Anna M Piskorz, Samantha R Poblete, Timea Pocza, Elizabeth M Poole, Bruce Poppe, Mary E Porteous, Fabienne Prieur, Darya Prokofyeva, Elizabeth Pugh, Miquel Angel Pujana, Pascal Pujol, Paolo Radice, Johanna Rantala, Christine Rappaport-Fuerhauser, Gad Rennert, Kerstin Rhiem, Patricia Rice, Andrea Richardson, Mark Robson, Gustavo C Rodriguez, Cristina Rodríguez-Antona, Jane Romm, Matti A Rookus, Mary Anne Rossing, Joseph H Rothstein, Anja Rudolph, Ingo B Runnebaum, Helga B Salvesen, Dale P Sandler, Minouk J Schoemaker, Leigha Senter, V Wendy Setiawan, Gianluca Severi, Priyanka Sharma, Tameka Shelford, Nadeem Siddiqui, Lucy E Side, Weiva Sieh, Christian F Singer, Hagay Sobol, Honglin Song, Melissa C Southey, Amanda B Spurdle, Zsofia Stadler, Doris Steinemann, Dominique Stoppa-Lyonnet, Lara E Sucheston-Campbell, Grzegorz Sukiennicki, Rebecca Sutphen, Christian Sutter, Anthony J Swerdlow, Csilla I Szabo, Lukasz Szafron, Yen Y Tan, Jack A Taylor, Muy-Kheng Tea, Manuel R Teixeira, Soo-Hwang Teo, Kathryn L Terry, Pamela J Thompson, Liv Cecilie Vestrheim Thomsen, Darcy L Thull, Laima Tihomirova, Anna V Tinker, Marc Tischkowitz, Silvia Tognazzo, Amanda Ewart Toland, Alicia Tone, Britton Trabert, Ruth C Travis, Antonia Trichopoulou, Nadine Tung, Shelley S Tworoger, Anne M van Altena, David Van Den Berg, Annemarie H van der Hout, Rob B van der Luijt, Mattias Van Heetvelde, Els Van Nieuwenhuysen, Elizabeth J van Rensburg, Adriaan Vanderstichele, Raymonda Varon-Mateeva, Ana Vega, Digna Velez Edwards, Ignace Vergote, Robert A Vierkant, Joseph Vijai, Athanassios Vratimos, Lisa Walker, Christine Walsh, Dorothea Wand, Shan Wang-Gohrke, Barbara Wappenschmidt, Penelope M Webb, Clarice R Weinberg, Jeffrey N Weitzel, Nicolas Wentzensen, Alice S Whittemore, Juul T Wijnen, Lynne R Wilkens, Alicja Wolk, Michelle Woo, Xifeng Wu, Anna H Wu, Hannah Yang, Drakoulis Yannoukakos, Argyrios Ziogas, Kristin K Zorn, Steven A Narod, Douglas F Easton, Christopher I Amos, Joellen M Schildkraut, Susan J Ramus, Laura Ottini, Marc T Goodman, Sue K Park, Linda E Kelemen, Harvey A Risch, Mads Thomassen, Kenneth Offit, Jacques Simard, Rita Katharina Schmutzler, Dennis Hazelett, Alvaro N Monteiro, Fergus J Couch, Andrew Berchuck, Georgia Chenevix-Trench, Ellen L Goode, Thomas A Sellers, Simon A Gayther, Antonis C Antoniou, Paul D P Pharoah
To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28345861/identification-of-gene-transcription-start-sites-and-enhancers-responding-to-pulmonary-carbon-nanotube-exposure-in-vivo
#8
Jette Bornholdt, Anne Thoustrup Saber, Berit Lilje, Mette Boyd, Mette Jørgensen, Yun Chen, Morana Vitezic, Nicklas Raun Jacobsen, Sarah Søs Poulsen, Trine Berthing, Simon Bressendorff, Kristoffer Vitting-Seerup, Robin Andersson, Karin Sørig Hougaard, Carole L Yauk, Sabina Halappanavar, Håkan Wallin, Ulla Vogel, Albin Sandelin
Increased use of nanomaterials in industry, medicine and consumer products has raised concerns over their toxicity. To ensure safe use of nanomaterials, understanding their biological effects at the molecular level is crucial. In particular, the regulatory mechanisms responsible for the cascade of genes activated by nanomaterial exposure are not well characterized. To this end, we profiled the genome-wide usage of gene transcription start sites and linked active enhancer regions in lungs of C57BL/6 mice 24h after intratracheal instillation of a single dose of the multiwalled carbon nanotube Mitsui-7...
March 27, 2017: ACS Nano
https://www.readbyqxmd.com/read/28345651/epigenome-mapping-highlights-chromatin-mediated-gene-regulation-in-the-protozoan-parasite-trichomonas-vaginalis
#9
Min-Ji Song, Mikyoung Kim, Yeeun Choi, Myung-Hee Yi, Juri Kim, Soon-Jung Park, Tai-Soon Yong, Hyoung-Pyo Kim
Trichomonas vaginalis is an extracellular flagellated protozoan parasite that causes trichomoniasis, one of the most common non-viral sexually transmitted diseases. To survive and to maintain infection, T. vaginalis adapts to a hostile host environment by regulating gene expression. However, the mechanisms of transcriptional regulation are poorly understood for this parasite. Histone modification has a marked effect on chromatin structure and directs the recruitment of transcriptional machinery, thereby regulating essential cellular processes...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345454/genome-wide-profiling-of-micro-rna-expression-in-gefitinib-resistant-human-lung-adenocarcinoma-using-microarray-for-the-identification-of-mir-149-5p-modulation
#10
Yong Hu, Xiaobing Qin, Dali Yan, Haixia Cao, Leilei Zhou, Fan Fan, Jialan Zang, Jie Ni, Xiaoyue Xu, Huanhuan Sha, Siwen Liu, Shaorong Yu, Jianzhong Wu, Rong Ma, Jifeng Feng
To understand the mechanism involved in gefitinib resistance, we established gefitinib-resistant human HCC827/GR-8-1 cell line from the parental HCC827 cell line. We compared the micro-RNA expression profiles of the HCC827 cells HCC827/GR-8-1 using Agilent micro-RNA microarrays. The micro-RNAs, such as the miR-149-5p, were up- or downregulated and associated with acquired gefitinib resistance. Quantitative real-time polymerase chain reaction was then performed to verify the expression patterns of different micro-RNAs...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28345042/human-genetic-and-metabolite-variation-reveals-that-methylthioadenosine-is-a-prognostic-biomarker-and-an-inflammatory-regulator-in-sepsis
#11
Liuyang Wang, Emily R Ko, James J Gilchrist, Kelly J Pittman, Anna Rautanen, Matti Pirinen, J Will Thompson, Laura G Dubois, Raymond J Langley, Sarah L Jaslow, Raul E Salinas, D Clayburn Rouse, M Arthur Moseley, Salim Mwarumba, Patricia Njuguna, Neema Mturi, Thomas N Williams, J Anthony G Scott, Adrian V S Hill, Christopher W Woods, Geoffrey S Ginsburg, Ephraim L Tsalik, Dennis C Ko
Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mouse model demonstrate that the methionine salvage pathway is a regulator of sepsis that can accurately predict prognosis in patients. Pathway-based genome-wide association analysis of nontyphoidal Salmonella bacteremia showed a strong enrichment for single-nucleotide polymorphisms near the components of the methionine salvage pathway...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28345006/genome-wide-specificity-of-highly-efficient-talens-and-crispr-cas9-for-t-cell-receptor-modification
#12
Friederike Knipping, Mark J Osborn, Karl Petri, Jakub Tolar, Hanno Glimm, Christof von Kalle, Manfred Schmidt, Richard Gabriel
In T cells with transgenic high-avidity T cell receptors (TCRs), endogenous and transferred TCR chains compete for surface expression and may pair inappropriately, potentially causing autoimmunity. To knock out endogenous TCR expression, we assembled 12 transcription activator-like effector nucleases (TALENs) and five guide RNAs (gRNAs) from the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Using TALEN mRNA, TCR knockout was successful in up to 81% of T cells...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28344162/identification-of-genetic-markers-of-resistance-to-echinocandins-azoles-and-5-fluorocytosine-in-candida-glabrata-by-next-generation-sequencing-a-feasibility-study
#13
Chayanika Biswas, Sharon C-A Chen, Catriona Halliday, Karina Kennedy, E Geoffrey Playford, Deborah J Marriott, Monica A Slavin, Tania C Sorrell, Vitali Sintchenko
OBJECTIVES: Multi-antifungal drug resistance in Candida glabrata is increasing. We examined the feasibility of next generation sequencing (NGS) to investigate the presence of antifungal drug resistance markers in C. glabrata. METHODS: The antifungal susceptibility of 12 clinical isolates and one ATCC strain of C. glabrata was determined using the Sensititre YeastOne® YO10 assay. These included three isolate pairs where the second isolate of each pair had developed a rise in drug MICs...
March 23, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28344127/replicated-association-between-the-european-gwas-locus-rs10503253-at-csmd1-and-schizophrenia-in-asian-population
#14
Weiqing Liu, Fang Liu, Xiufeng Xu, Yan Bai
Schizophrenia is one of the most severe mental disorders with significant heritability. Recent genetic association studies including genome-wide association studies (GWAS) have identified multiple common variants conferring risk of schizophrenia. An intronic SNP within CSMD1, rs10503253, is one of the top risk SNPs for schizophrenia in Europeans discovered through large GWAS. However, whether rs10503253 is also a risk SNP for schizophrenia in other populations, such as Asians, is still unknown. To answer this question, we examined the association of rs10503253 with schizophrenia in a total of 7,514 schizophrenia patients, 9,058 healthy controls and 1,115 nuclear families originated from Asia using a meta-analytic approach...
March 23, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28343758/synergistic-expression-of-histone-deacetylase-9-and-matrix-metalloproteinase-12-in-m4-macrophages-in-advanced-carotid-plaques
#15
N K J Oksala, I Seppälä, R Rahikainen, K-M Mäkelä, E Raitoharju, T Illig, N Klopp, I Kholova, R Laaksonen, P J Karhunen, V P Hytönen, T Lehtimäki
OBJECTIVE/BACKGROUND: Expression patterns and association with cell specific gene expression signatures of the epigenetic regulator histone deacetylase 9 (HDAC9) and matrix metalloproteinase 12 (MMP12) in human plaque are not known. METHODS: This was a prospective cohort study. Genome wide expression analysis was performed in carotid, femoral, aortic plaques (n = 68) and left internal thoracic (LITA) controls (n = 28) and plaque histological severity assessed...
March 23, 2017: European Journal of Vascular and Endovascular Surgery
https://www.readbyqxmd.com/read/28343281/using-patterns-of-genetic-association-to-elucidate-shared-genetic-etiologies-across-psychiatric-disorders
#16
Seung Bin Cho, Fazil Aliev, Shaunna L Clark, Amy E Adkins, Howard J Edenberg, Kathleen K Bucholz, Bernice Porjesz, Danielle M Dick
Twin studies indicate that latent genetic factors overlap across comorbid psychiatric disorders. In this study, we used a novel approach to elucidate shared genetic factors across psychiatric outcomes by clustering single nucleotide polymorphisms based on their genome-wide association patterns. We applied latent profile analysis (LPA) to p-values resulting from genome-wide association studies across three phenotypes: symptom counts of alcohol dependence (AD), antisocial personality disorder (ASP), and major depression (MD), using the European-American case-control genome-wide association study subsample of the collaborative study on the genetics of alcoholism (N = 1399)...
March 25, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/28343277/pancreatic-alpha-cell-selective-deletion-of-tcf7l2-impairs-glucagon-secretion-and-counter-regulatory-responses-to-hypoglycaemia-in-mice
#17
Gabriela da Silva Xavier, Angeles Mondragon, Vishnou Mourougavelou, Céline Cruciani-Guglielmacci, Jessica Denom, Pedro Luis Herrera, Christophe Magnan, Guy A Rutter
AIMS/HYPOTHESIS: Transcription factor 7-like 2 (TCF7L2) is a high mobility group (HMG) box-containing transcription factor and downstream effector of the Wnt signalling pathway. SNPs in the TCF7L2 gene have previously been associated with an increased risk of type 2 diabetes in genome-wide association studies. In animal studies, loss of Tcf7l2 function is associated with defective islet beta cell function and survival. Here, we explore the role of TCF7L2 in the control of the counter-regulatory response to hypoglycaemia by generating mice with selective deletion of the Tcf7l2 gene in pancreatic alpha cells...
March 25, 2017: Diabetologia
https://www.readbyqxmd.com/read/28343239/improved-full-length-killer-cell-immunoglobulin-like-receptor-transcript-discovery-in-mauritian-cynomolgus-macaques
#18
Trent M Prall, Michael E Graham, Julie A Karl, Roger W Wiseman, Adam J Ericsen, Muthuswamy Raveendran, R Alan Harris, Donna M Muzny, Richard A Gibbs, Jeffrey Rogers, David H O'Connor
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS)...
March 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28342679/pharmacogenomic-aspects-of-bipolar-disorder-an-update
#19
M Budde, D Degner, J Brockmöller, T G Schulze
The hopes for readily implementable precision medicine are high. For many complex disorders, such as bipolar disorder, these hopes critically hinge on tangible successes in pharmacogenetics of treatment response or susceptibility to adverse events. In this article, we review the current state of pharmacogenomics of bipolar disorder including latest results from candidate genes and genome-wide association studies. The majority of studies focus on response to lithium treatment. Although a host of genes has been studied, hardly any replicated findings have emerged so far...
March 22, 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28341828/variants-in-the-host-genome-may-inhibit-tumour-growth-in-devil-facial-tumours-evidence-from-genome-wide-association
#20
Belinda Wright, Cali E Willet, Rodrigo Hamede, Menna Jones, Katherine Belov, Claire M Wade
Devil facial tumour disease (DFTD) has decimated wild populations of Tasmanian devils (Sarcophilus harrisii) due to its ability to avoid immune detection and pass from host to host by biting. A small number of devils have been observed to spontaneously recover from the disease which is otherwise fatal. We have sequenced the genomes of these rare cases and compared them to the genomes of devils who succumbed to the disease. Genome-wide association, based on this limited sampling, highlighted two key genomic regions potentially associated with ability to survive DFTD...
March 24, 2017: Scientific Reports
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