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https://www.readbyqxmd.com/read/28446001/a-post-genome-wide-association-study-validating-the-association-of-the-glycophorin-c-gene-with-serum-hemoglobin-level-in-pig
#1
Yang Liu, Zhengzheng Hu, Chen Yang, Shiwei Wang, Wenwen Wang, Qin Zhang
OBJECTIVE: This study aimed to validate the statistical evidence from the genome-wide association study (GWAS) as true-positive and to better understand the effects of the glycophorin C (GYPC) gene on serum hemoglobin traits. METHODS: Our initial GWAS revealed the presence of two single nucleotide polymorphisms (SNPs) (ASGA0069038 and ALGA0084612) for the hemoglobin concentration trait (HGB) in the 2.48 Mb region of SSC15. From this target region, GYPC was selected as a promising gene that associated with serum HGB traits in pigs...
May 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28445865/associations-between-lmo1-gene-polymorphisms-and-wilms-tumor-susceptibility
#2
Guo-Chang Liu, Zhen-Jian Zhuo, Shi-Bo Zhu, Jinhong Zhu, Wei Jia, Zhang Zhao, Jin-Hua Hu, Jing He, Feng-Hua Wang, Wen Fu
Wilms' tumor is the most common childhood renal malignancy. A genome-wide association study identified LIM domain only 1 (LMO1) as having oncogenic potential. We examined the associations between LMO1 gene polymorphisms and susceptibility to Wilms' tumor. In this hospital-based, case-control study, we recruited 145 children with Wilms' tumor and 531 cancer-free children. Four polymorphisms (rs110419 A>G, rs4758051 G>A, rs10840002 A>G and rs204938 A>G) were genotyped using Taqman methodology. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to measure the associations between selected polymorphisms and Wilms' tumor susceptibility...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445522/revealing-phenotype-associated-functional-differences-by-genome-wide-scan-of-ancient-haplotype-blocks
#3
Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, Susumu Goto
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data...
2017: PloS One
https://www.readbyqxmd.com/read/28445509/functional-genetic-variants-within-the-sirt2-gene-promoter-in-acute-myocardial-infarction
#4
Wentao Yang, Feng Gao, Pei Zhang, Shuchao Pang, Yinghua Cui, Lixin Liu, Guanghe Wei, Bo Yan
Coronary artery disease (CAD), including acute myocardial infarction (AMI) is the complication of atherosclerosis. Recently, genome-wide association studies have identified a large number of CAD-related genetic variants. However, only 10% of CAD cases could be explained. Low frequent and rare genetic variants have been recently proposed to be main causes for CAD. SIRT2 is a member of sirtuin family, NAD(+)-dependent class III deacetylases. SIRT2 is involved in genomic stability, metabolism, inflammation, oxidative stress and autophagy, as well as in platelet function...
2017: PloS One
https://www.readbyqxmd.com/read/28444735/from-genetic-single-candidate-gene-studies-to-complex-genomics-of-gvhd
#5
REVIEW
Katarzyna Bogunia-Kubik, Piotr Łacina
Graft-versus-host disease (GvHD) is a serious complication affecting the recipients of allogeneic haematopoietic stem cells. In this present review we attempt to summarize the current knowledge on the effect of the donor and recipient genotypes on GvHD, starting from human leucocyte antigen (HLA) matching for an optimal donor selection, typing of non-classical HLA and minor histocompatibility antigens through the polymorphic variations in genes coding for non-HLA proteins contributing to the development of GvHD and response to treatment...
April 26, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28444616/genome-wide-identification-of-grain-filling-genes-regulated-by-the-ossmf1-transcription-factor-in-rice
#6
Joung Sug Kim, Songhwa Chae, Kyong Mi Jun, Yoon-Mok Pahk, Tae-Ho Lee, Pil Joong Chung, Yeon-Ki Kim, Baek Hie Nahm
BACKGROUND: Spatial- and temporal-specific expression patterns are primarily regulated at the transcriptional level by gene promoters. Therefore, it is important to identify the binding motifs of transcription factors to better understand the networks associated with embryogenesis. RESULTS: Here, we used a protein-binding microarray (PBM) to identify the binding motifs of OsSMF1, which is a basic leucine zipper transcription factor involved in the regulation of rice seed maturation...
December 2017: Rice
https://www.readbyqxmd.com/read/28444502/preliminary-study-on-the-role-of-tmem39a-gene-in-multiple-sclerosis
#7
Marta Wagner, Maciej Sobczyński, Małgorzata Bilińska, Anna Pokryszko-Dragan, Małgorzata Cyrul, Piotr Kuśnierczyk, Monika Jasek
Genome-wide association studies (GWAS) have identified hundreds of new potential genetic risk loci associated with numerous complex diseases such as multiple sclerosis (MS). Genes which have been discovered by GWAS are now the focus of numerous ongoing studies. The goal of this study was to confirm and understand the potential role of one of such genes-transmembrane protein 39A gene (TMEM39A)-in multiple sclerosis.We showed the difference in TMEM39A messenger RNA (mRNA) expression between MS patients and controls (T (2)2;74 = 5...
April 25, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28444381/evidence-for-very-recent-positive-selection-in-mongolians
#8
Kazuhiro Nakayama, Jun Ohashi, Kazuhisa Watanabe, Lkagvasuren Munkhtulga, Sadahiko Iwamoto
Mongols, the founders of the largest continental empire in history, successfully adapted to the harsh environments of Inner Asia through nomadic pastoralism. Considerable interest exists in ascertaining whether genetic adaptation also contributed to the Mongols' success, and dissecting the genome diversity of present-day populations in Mongolia can help address this question. To this end, we determined the genotypes of nearly 2.4 million single nucleotide polymorphisms (SNPs) of 96 unrelated Mongolian individuals in Ulaanbaatar city, and performed genome-wide scans for population-specific positive selection...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28444219/dna-methylation-of-a-novel-pak4-locus-influences-ototoxicity-susceptibility-following-cisplatin-and-radiation-therapy-for-pediatric-embryonal-tumors
#9
Austin L Brown, Kayla L Foster, Philip J Lupo, Erin C Peckham-Gregory, Jeffrey C Murray, M Fatih Okcu, Ching C Lau, Surya P Rednam, Murali Chintagumpala, Michael E Scheurer
Background: Ototoxicity is a common adverse side effect of platinum chemotherapy and cranial radiation therapy; however, individual susceptibility is highly variable. Therefore, the objective of this study was to conduct an epigenome-wide association study to identify differentially methylated CpG sites associated with ototoxicity susceptibility among cisplatin-treated pediatric patients with embryonal tumors. Methods: Samples were collected for a discovery (n=62) and a replication cohort (n=18) of medulloblastoma and primitive neuroectodermal tumor patients...
April 24, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28444195/dna-methylome-analysis-reveals-distinct-epigenetic-patterns-of-ascending-aortic-dissection-and-bicuspid-aortic-valve
#10
Sun Pan, Hao Lai, Yiru Shen, Charles Breeze, Stephan Beck, Tao Hong, Chunsheng Wang, Andrew E Teschendorff
Epigenetics may mediate the effects of environmental risk factors on disease, including heart disease. Thus, measuring the DNA methylome offers the opportunity to identify novel disease biomarkers and novel insights into disease mechanisms. The DNA methylation landscape of ascending aortic dissection (AD) and bicuspid aortic valve (BAV) with aortic aneurysmal dilatation remain uncharacterized. The present study aimed to explore the genome-wide DNA methylation landscape underpinning these two diseases. Methods and results: We used Illumina 450k DNA methylation beadarrays to analyze 21 ascending aorta samples, including 10 cases with AD, 5 with BAV and 6 healthy controls...
April 19, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28443631/a-peripheral-epigenetic-signature-of-immune-system-genes-is-linked-to-neocortical-thickness-and-memory
#11
Virginie Freytag, Tania Carrillo-Roa, Annette Milnik, Philipp G Sämann, Vanja Vukojevic, David Coynel, Philippe Demougin, Tobias Egli, Leo Gschwind, Frank Jessen, Eva Loos, Wolfgang Maier, Steffi G Riedel-Heller, Martin Scherer, Christian Vogler, Michael Wagner, Elisabeth B Binder, Dominique J-F de Quervain, Andreas Papassotiropoulos
Increasing age is tightly linked to decreased thickness of the human neocortex. The biological mechanisms that mediate this effect are hitherto unknown. The DNA methylome, as part of the epigenome, contributes significantly to age-related phenotypic changes. Here, we identify an epigenetic signature that is associated with cortical thickness (P=3.86 × 10(-8)) and memory performance in 533 healthy young adults. The epigenetic effect on cortical thickness was replicated in a sample comprising 596 participants with major depressive disorder and healthy controls...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28443625/genome-wide-meta-analysis-of-241-258-adults-accounting-for-smoking-behaviour-identifies-novel-loci-for-obesity-traits
#12
Anne E Justice, Thomas W Winkler, Mary F Feitosa, Misa Graff, Virginia A Fisher, Kristin Young, Llilda Barata, Xuan Deng, Jacek Czajkowski, David Hadley, Julius S Ngwa, Tarunveer S Ahluwalia, Audrey Y Chu, Nancy L Heard-Costa, Elise Lim, Jeremiah Perez, John D Eicher, Zoltán Kutalik, Luting Xue, Anubha Mahajan, Frida Renström, Joseph Wu, Qibin Qi, Shafqat Ahmad, Tamuno Alfred, Najaf Amin, Lawrence F Bielak, Amelie Bonnefond, Jennifer Bragg, Gemma Cadby, Martina Chittani, Scott Coggeshall, Tanguy Corre, Nese Direk, Joel Eriksson, Krista Fischer, Mathias Gorski, Marie Neergaard Harder, Momoko Horikoshi, Tao Huang, Jennifer E Huffman, Anne U Jackson, Johanne Marie Justesen, Stavroula Kanoni, Leena Kinnunen, Marcus E Kleber, Pirjo Komulainen, Meena Kumari, Unhee Lim, Jian'an Luan, Leo-Pekka Lyytikäinen, Massimo Mangino, Ani Manichaikul, Jonathan Marten, Rita P S Middelberg, Martina Müller-Nurasyid, Pau Navarro, Louis Pérusse, Natalia Pervjakova, Cinzia Sarti, Albert Vernon Smith, Jennifer A Smith, Alena Stančáková, Rona J Strawbridge, Heather M Stringham, Yun Ju Sung, Toshiko Tanaka, Alexander Teumer, Stella Trompet, Sander W van der Laan, Peter J van der Most, Jana V Van Vliet-Ostaptchouk, Sailaja L Vedantam, Niek Verweij, Jacqueline M Vink, Veronique Vitart, Ying Wu, Loic Yengo, Weihua Zhang, Jing Hua Zhao, Martina E Zimmermann, Niha Zubair, Gonçalo R Abecasis, Linda S Adair, Saima Afaq, Uzma Afzal, Stephan J L Bakker, Traci M Bartz, John Beilby, Richard N Bergman, Sven Bergmann, Reiner Biffar, John Blangero, Eric Boerwinkle, Lori L Bonnycastle, Erwin Bottinger, Daniele Braga, Brendan M Buckley, Steve Buyske, Harry Campbell, John C Chambers, Francis S Collins, Joanne E Curran, Gert J de Borst, Anton J M de Craen, Eco J C de Geus, George Dedoussis, Graciela E Delgado, Hester M den Ruijter, Gudny Eiriksdottir, Anna L Eriksson, Tõnu Esko, Jessica D Faul, Ian Ford, Terrence Forrester, Karl Gertow, Bruna Gigante, Nicola Glorioso, Jian Gong, Harald Grallert, Tanja B Grammer, Niels Grarup, Saskia Haitjema, Göran Hallmans, Anders Hamsten, Torben Hansen, Tamara B Harris, Catharina A Hartman, Maija Hassinen, Nicholas D Hastie, Andrew C Heath, Dena Hernandez, Lucia Hindorff, Lynne J Hocking, Mette Hollensted, Oddgeir L Holmen, Georg Homuth, Jouke Jan Hottenga, Jie Huang, Joseph Hung, Nina Hutri-Kähönen, Erik Ingelsson, Alan L James, John-Olov Jansson, Marjo-Riitta Jarvelin, Min A Jhun, Marit E Jørgensen, Markus Juonala, Mika Kähönen, Magnus Karlsson, Heikki A Koistinen, Ivana Kolcic, Genovefa Kolovou, Charles Kooperberg, Bernhard K Krämer, Johanna Kuusisto, Kirsti Kvaløy, Timo A Lakka, Claudia Langenberg, Lenore J Launer, Karin Leander, Nanette R Lee, Lars Lind, Cecilia M Lindgren, Allan Linneberg, Stephane Lobbens, Marie Loh, Mattias Lorentzon, Robert Luben, Gitta Lubke, Anja Ludolph-Donislawski, Sara Lupoli, Pamela A F Madden, Reija Männikkö, Pedro Marques-Vidal, Nicholas G Martin, Colin A McKenzie, Barbara McKnight, Dan Mellström, Cristina Menni, Grant W Montgomery, Aw Bill Musk, Narisu Narisu, Matthias Nauck, Ilja M Nolte, Albertine J Oldehinkel, Matthias Olden, Ken K Ong, Sandosh Padmanabhan, Patricia A Peyser, Charlotta Pisinger, David J Porteous, Olli T Raitakari, Tuomo Rankinen, D C Rao, Laura J Rasmussen-Torvik, Rajesh Rawal, Treva Rice, Paul M Ridker, Lynda M Rose, Stephanie A Bien, Igor Rudan, Serena Sanna, Mark A Sarzynski, Naveed Sattar, Kai Savonen, David Schlessinger, Salome Scholtens, Claudia Schurmann, Robert A Scott, Bengt Sennblad, Marten A Siemelink, Günther Silbernagel, P Eline Slagboom, Harold Snieder, Jan A Staessen, David J Stott, Morris A Swertz, Amy J Swift, Kent D Taylor, Bamidele O Tayo, Barbara Thorand, Dorothee Thuillier, Jaakko Tuomilehto, Andre G Uitterlinden, Liesbeth Vandenput, Marie-Claude Vohl, Henry Völzke, Judith M Vonk, Gérard Waeber, Melanie Waldenberger, R G J Westendorp, Sarah Wild, Gonneke Willemsen, Bruce H R Wolffenbuttel, Andrew Wong, Alan F Wright, Wei Zhao, M Carola Zillikens, Damiano Baldassarre, Beverley Balkau, Stefania Bandinelli, Carsten A Böger, Dorret I Boomsma, Claude Bouchard, Marcel Bruinenberg, Daniel I Chasman, Yii-DerIda Chen, Peter S Chines, Richard S Cooper, Francesco Cucca, Daniele Cusi, Ulf de Faire, Luigi Ferrucci, Paul W Franks, Philippe Froguel, Penny Gordon-Larsen, Hans-Jörgen Grabe, Vilmundur Gudnason, Christopher A Haiman, Caroline Hayward, Kristian Hveem, Andrew D Johnson, J Wouter Jukema, Sharon L R Kardia, Mika Kivimaki, Jaspal S Kooner, Diana Kuh, Markku Laakso, Terho Lehtimäki, Loic Le Marchand, Winfried März, Mark I McCarthy, Andres Metspalu, Andrew P Morris, Claes Ohlsson, Lyle J Palmer, Gerard Pasterkamp, Oluf Pedersen, Annette Peters, Ulrike Peters, Ozren Polasek, Bruce M Psaty, Lu Qi, Rainer Rauramaa, Blair H Smith, Thorkild I A Sørensen, Konstantin Strauch, Henning Tiemeier, Elena Tremoli, Pim van der Harst, Henrik Vestergaard, Peter Vollenweider, Nicholas J Wareham, David R Weir, John B Whitfield, James F Wilson, Jessica Tyrrell, Timothy M Frayling, Inês Barroso, Michael Boehnke, Panagiotis Deloukas, Caroline S Fox, Joel N Hirschhorn, David J Hunter, Tim D Spector, David P Strachan, Cornelia M van Duijn, Iris M Heid, Karen L Mohlke, Jonathan Marchini, Ruth J F Loos, Tuomas O Kilpeläinen, Ching-Ti Liu, Ingrid B Borecki, Kari E North, L Adrienne Cupples
Few genome-wide association studies (GWAS) account for environmental exposures, like smoking, potentially impacting the overall trait variance when investigating the genetic contribution to obesity-related traits. Here, we use GWAS data from 51,080 current smokers and 190,178 nonsmokers (87% European descent) to identify loci influencing BMI and central adiposity, measured as waist circumference and waist-to-hip ratio both adjusted for BMI. We identify 23 novel genetic loci, and 9 loci with convincing evidence of gene-smoking interaction (GxSMK) on obesity-related traits...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28443460/augmented-expression-of-runx1-deregulates-the-global-gene-expression-of-u87-glioblastoma-multiforme-cells-and-inhibits-tumor-growth-in-mice
#13
Yoel Bogoch, Gilgi Friedlander-Malik, Lior Lupu, Ekaterina Bondar, Nitzan Zohar, Sheila Langier, Zvi Ram, Ido Nachmany, Joseph M Klausner, Niv Pencovich
Glioblastoma multiforme is the most common and aggressive primary brain tumor in adults. A mesenchymal phenotype was associated with tumor aggressiveness and poor prognosis in glioblastoma multiforme patients. Recently, the transcription factor RUNX1 was suggested as a driver of the glioblastoma multiforme mesenchymal gene expression signature; however, its independent role in this process is yet to be described. Here, we assessed the role of RUNX1 in U87 glioblastoma multiforme cells in correspondence to its mediated transcriptome and genome-wide occupancy pattern...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28443200/epidemiology-of-ovarian-cancer-a-review
#14
Brett M Reid, Jennifer B Permuth, Thomas A Sellers
Ovarian cancer (OC) is the seventh most commonly diagnosed cancer among women in the world and the tenth most common in China. Epithelial OC is the most predominant pathologic subtype, with five major histotypes that differ in origination, pathogenesis, molecular alterations, risk factors, and prognosis. Genetic susceptibility is manifested by rare inherited mutations with high to moderate penetrance. Genome-wide association studies have additionally identified 29 common susceptibility alleles for OC, including 14 subtype-specific alleles...
February 2017: Cancer Biology & Medicine
https://www.readbyqxmd.com/read/28443016/genetics-of-aggression-in-alzheimer-s-disease-ad
#15
Walter J Lukiw, Evgeny I Rogaev
Alzheimer's disease (AD) is a terminal, age-related neurological syndrome exhibiting progressive cognitive and memory decline, however AD patients in addition exhibit ancillary neuropsychiatric symptoms (NPSs) and these include aggression. In this communication we provide recent evidence for the mis-regulation of a small family of genes expressed in the human hippocampus that appear to be significantly involved in expression patterns common to both AD and aggression. DNA array- and mRNA transcriptome-based gene expression analysis and candidate gene association and/or genome-wide association studies (CGAS, GWAS) of aggressive attributes in humans have revealed a surprisingly small subset of six brain genes that are also strongly associated with altered gene expression patterns in AD...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28442506/genome-wide-association-studies-of-chemotherapeutic-toxicities-genomics-of-inequality
#16
Brandon Mapes, Omar El Charif, Shereen Al-Sawwaf, M Eileen Dolan
With an estimated global population of cancer survivors exceeding 32 million and growing, there is a heightened awareness of the long-term toxicities resulting from cancer treatments and their impact on quality of life. Unexplained heterogeneity in the persistence and development of toxicities, as well as an incomplete understanding of their mechanisms have generated a growing need for the identification of predictive pharmacogenomic markers. Early studies addressing this need used a candidate gene approach; however, over the last decade, unbiased and comprehensive genome-wide association studies (GWAS) have provided markers of phenotypic risk and potential targets to explore the mechanistic and regulatory pathways of biological functions associated with chemotherapeutic toxicity...
April 25, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28442247/regional-enrichment-analyses-on-genetic-profiles-for-schizophrenia-and-bipolar-disorder
#17
Jingyu Liu, Jiayu Chen, Nora I Perrone-Bizzozero, Jessica A Turner, Vince D Calhoun
Both schizophrenia (SZ) and bipolar disorder (BD) are highly heritable psychiatric disorders. The significant genomic risk loci are of great importance but with no guarantee of known functional impact and they cannot totally explain the genetic inheritance. In this study we present regional enrichment analyses across the genome, aiming to strike a balance between individual risk loci and integrated regional effects. Chromosomes were partitioned into 2 million base-pair regions (indicated by an underscore sign in the cytogenetic bands) on which enrichment tests are performed...
April 22, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28442232/a-genetic-risk-score-predicts-cardiovascular-events-in-patients-with-stable-coronary-artery-disease
#18
Morten Krogh Christiansen, Mette Nyegaard, Sanne Bøjet Larsen, Erik Lerkevang Grove, Morten Würtz, Søs Neergaard-Petersen, Anne-Mette Hvas, Henrik Kjærulf Jensen, Steen Dalby Kristensen
BACKGROUND: Genetic risk scores (GRSs) may predict cardiovascular risk in community-based populations. However, studies investigating the association with recurrent cardiovascular events in patients with established coronary artery disease (CAD) are conflicting. METHODS: We genotyped 879 patients with high-risk stable CAD and created a GRS based on 45 single nucleotide polymorphisms previously reported to be associated with CAD in genome-wide association studies...
April 19, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28441938/mitors-a-method-for-high-throughput-sensitive-and-accurate-detection-of-mitochondrial-dna-heteroplasmy
#19
Julien Marquis, Gregory Lefebvre, Yiannis A I Kourmpetis, Mohamed Kassam, Frédéric Ronga, Umberto De Marchi, Andreas Wiederkehr, Patrick Descombes
BACKGROUND: Mitochondrial dysfunction is linked to numerous pathological states, in particular related to metabolism, brain health and ageing. Nuclear encoded gene polymorphisms implicated in mitochondrial functions can be analyzed in the context of classical genome wide association studies. By contrast, mitochondrial DNA (mtDNA) variants are more challenging to identify and analyze for several reasons. First, contrary to the diploid nuclear genome, each cell carries several hundred copies of the circular mitochondrial genome...
April 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28441456/genome-wide-association-study-of-facial-morphology-reveals-novel-associations-with-frem1-and-park2
#20
Myoung Keun Lee, John R Shaffer, Elizabeth J Leslie, Ekaterina Orlova, Jenna C Carlson, Eleanor Feingold, Mary L Marazita, Seth M Weinberg
Several studies have now shown evidence of association between common genetic variants and quantitative facial traits in humans. The reported associations generally involve simple univariate measures and likely represent only a small fraction of the genetic loci influencing facial morphology. In this study, we applied factor analysis to a set of 276 facial linear distances derived from 3D facial surface images of 2187 unrelated individuals of European ancestry. We retained 23 facial factors, which we then tested for genetic associations using a genome-wide panel of 10,677,593 single nucleotide polymorphisms (SNPs)...
2017: PloS One
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