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Genome wide association study

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https://www.readbyqxmd.com/read/29220677/a-powerful-approach-to-estimating-annotation-stratified-genetic-covariance-via-gwas-summary-statistics
#1
Qiongshi Lu, Boyang Li, Derek Ou, Margret Erlendsdottir, Ryan L Powles, Tony Jiang, Yiming Hu, David Chang, Chentian Jin, Wei Dai, Qidu He, Zefeng Liu, Shubhabrata Mukherjee, Paul K Crane, Hongyu Zhao
Despite the success of large-scale genome-wide association studies (GWASs) on complex traits, our understanding of their genetic architecture is far from complete. Jointly modeling multiple traits' genetic profiles has provided insights into the shared genetic basis of many complex traits. However, large-scale inference sets a high bar for both statistical power and biological interpretability. Here we introduce a principled framework to estimate annotation-stratified genetic covariance between traits using GWAS summary statistics...
December 7, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29220643/polygenic-risk-for-alcohol-consumption-and-its-association-with-alcohol-related-phenotypes-do-stress-and-life-satisfaction-moderate-these-relationships
#2
Gabry W Mies, Karin J H Verweij, Jorien L Treur, Lannie Ligthart, Iryna O Fedko, Jouke Jan Hottenga, Gonneke Willemsen, Meike Bartels, Dorret I Boomsma, Jacqueline M Vink
BACKGROUND: Genetic and environmental factors contribute about equally to alcohol-related phenotypes in adulthood. In the present study, we examined whether more stress at home or low satisfaction with life might be associated with heavier drinking or more alcohol-related problems in individuals with a high genetic susceptibility to alcohol use. METHODS: Information on polygenic scores and drinking behavior was available in 6705 adults (65% female; 18-83 years) registered with the Netherlands Twin Register...
December 2, 2017: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/29220522/meta-analysis-of-genome-wide-association-studies-identifies-8-novel-loci-involved-in-shape-variation-of-human-head-hair
#3
Fan Liu, Yan Chen, Gu Zhu, Pirro G Hysi, Sijie Wu, Kaustubh Adhikari, Krystal Breslin, Ewelina Pospiech, Merel A Hamer, Fuduan Peng, Charanya Muralidharan, Victor Acuna-Alonzo, Samuel Canizales-Quinteros, Gabriel Bedoya, Carla Gallo, Giovanni Poletti, Francisco Rothhammer, Maria Catira Bortolini, Rolando Gonzalez-Jose, Changqing Zeng, Shuhua Xu, Li Jin, André G Uitterlinden, M Arfan Ikram, Cornelia M van Duijn, Tamar Nijsten, Susan Walsh, Wojciech Branicki, Sijia Wang, Andrés Ruiz-Linares, Timothy D Spector, Nicholas G Martin, Sarah E Medland, Manfred Kayser
Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28,964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21...
December 6, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29220501/combination-of-247-genome-wide-association-studies-reveals-high-cancer-risk-as-a-result-of-evolutionary-adaptation
#4
Konstantinos Voskarides
Analysis of GLOBOCAN-2012 data shows clearly here that cancer incidence worldwide is highly related with low average annual temperatures and extreme low temperatures. This applies for all cancers together or separately for many frequent or rare cancer types (all cancers P = 9.49 x 10-18). Supporting fact is that Inuit people, living at extreme low temperatures, have the highest cancer rates today. Hypothesizing an evolutionary explanation, 240 cancer genome-wide association studies (GWAS) and seven GWAS for cold and high-altitude adaptation were combined...
December 5, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29218375/genetic-analysis-of-multi-environmental-spring-wheat-trials-identifies-genomic-regions-for-locus-specific-trade-offs-for-grain-weight-and-grain-number
#5
Sivakumar Sukumaran, Marta Lopes, Susanne Dreisigacker, Matthew Reynolds
GWAS on multi-environment data identified genomic regions associated with trade-offs for grain weight and grain number. Grain yield (GY) can be dissected into its components thousand grain weight (TGW) and grain number (GN), but little has been achieved in assessing the trade-off between them in spring wheat. In the present study, the Wheat Association Mapping Initiative (WAMI) panel of 287 elite spring bread wheat lines was phenotyped for GY, GN, and TGW in ten environments across different wheat growing regions in Mexico, South Asia, and North Africa...
December 7, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29218031/crispr-cas-systems-in-bacteroides-fragilis-an-important-pathobiont-in-the-human-gut-microbiome
#6
Mehrdad Tajkarimi, Hannah M Wexler
Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29217827/genome-wide-association-study-of-male-sexual-orientation
#7
Alan R Sanders, Gary W Beecham, Shengru Guo, Khytam Dawood, Gerulf Rieger, Judith A Badner, Elliot S Gershon, Ritesha S Krishnappa, Alana B Kolundzija, Jubao Duan, Pablo V Gejman, J Michael Bailey, Eden R Martin
Family and twin studies suggest that genes play a role in male sexual orientation. We conducted a genome-wide association study (GWAS) of male sexual orientation on a primarily European ancestry sample of 1,077 homosexual men and 1,231 heterosexual men using Affymetrix single nucleotide polymorphism (SNP) arrays. We identified several SNPs with p < 10-5, including regions of multiple supporting SNPs on chromosomes 13 (minimum p = 7.5 × 10-7) and 14 (p = 4.7 × 10-7). The genes nearest to these peaks have functions plausibly relevant to the development of sexual orientation...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29217820/longitudinal-exome-wide-association-study-to-identify-genetic-susceptibility-loci-for-hypertension-in-a-japanese-population
#8
Yoshiki Yasukochi, Jun Sakuma, Ichiro Takeuchi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Yoshiji Yamada
Genome-wide association studies have identified various genetic variants associated with complex disorders. However, these studies have commonly been conducted in a cross-sectional manner. Therefore, we performed a longitudinal exome-wide association study (EWAS) in a Japanese cohort. We aimed to identify genetic variants that confer susceptibility to hypertension using ~244 000 single-nucleotide variants (SNVs) and physiological data from 6026 Japanese individuals who underwent annual health check-ups for several years...
December 8, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29217731/genome-wide-analysis-of-grain-yield-stability-and-environmental-interactions-in-a-multiparental-soybean-population
#9
Alencar Xavier, Diego Jarquin, Reka Howard, Vishnu Ramasubramanian, James E Specht, George L Graef, William D Beavis, Brian W Diers, Qijian Song, Perry Cregan, Randall Nelson, Rouf Mian, J G Shannon, Leah McHale, Dechun Wang, William Schapaugh, Aaron J Lorenz, Shizhong Xu, William Muir, Katy M Rainey
Genetic improvement towards optimized and stable agronomic performance of soybean genotypes is desirable for food security. Understanding how genotypes perform in different environmental conditions helps breeders develop sustainable cultivars adapted to target regions. Complex traits of importance are known to be controlled by a large number of genomic regions with small effects whose magnitude and direction are modulated by environmental factors. Knowledge of the constraints and undesirable effects resulting from genotype by environmental interactions is a key objective in improving selection procedures in soybean breeding programs...
December 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29217450/cadm2-regulates-body-weight-and-energy-homeostasis-in-mice
#10
Xin Yan, Zhen Wang, Vanessa Schmidt, Anton Gauert, Thomas E Willnow, Matthias Heinig, Matthew N Poy
OBJECTIVE: Obesity is strongly linked to genes regulating neuronal signaling and function, implicating the central nervous system in the maintenance of body weight and energy metabolism. Genome-wide association studies identified significant associations between body mass index (BMI) and multiple loci near Cell adhesion molecule2 (CADM2), which encodes a mediator of synaptic signaling enriched in the brain. Here we sought to further understand the role of Cadm2 in the pathogenesis of hyperglycemia and weight gain...
November 22, 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/29216827/comparative-genomic-analysis-of-brevibacterium-strains-insights-into-key-genetic-determinants-involved-in-adaptation-to-the-cheese-habitat
#11
Nguyen-Phuong Pham, Séverine Layec, Eric Dugat-Bony, Marie Vidal, Françoise Irlinger, Christophe Monnet
BACKGROUND: Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains. RESULTS: The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses...
December 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29216378/melonet-db-a-grand-rna-seq-gene-expression-atlas-in-melon-cucumis-melo-l
#12
Ryoichi Yano, Satoko Nonaka, Hiroshi Ezura
Melon (Cucumis melo L.) is an important Cucurbitaceae crop produced world-wide, exhibiting wide genetic variations and comprising both climacteric and non-climacteric fruit types. The muskmelon cultivar "Earl's favorite Harukei-3 (Harukei-3)" known for its sweetness and rich aroma is used for breeding of high-grade muskmelon in Japan. We conducted RNA-seq transcriptome studies in 30 different tissues of the 'Harukei-3' melon. These included root, stems, leaves, flowers, regenerating callus, and ovaries, in addition to the flesh and peel sampled at 7 stages of fruit development...
December 4, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#13
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29215398/a-genetic-risk-score-for-fasting-plasma-glucose-is-independently-associated-with-arterial-stiffness-a-mendelian-randomization-study
#14
Mikael Gottsäter, George Hindy, Marju Orho-Melander, Peter M Nilsson, Olle Melander
BACKGROUND: Arterial stiffness is known to be associated with a number of clinical conditions including hypertension, diabetes and dyslipidemia, and may predict cardiovascular events and mortality. However, causal links are hard to establish. Results from genome-wide association studies have identified only a few single nucleotide polymorphisms associated with arterial stiffness, the results have been inconsistent between studies and overlap with other clinical conditions is lacking. Our aim was to investigate a potential shared set of risk single nucleotide polymorphisms between relevant cardiometabolic traits and arterial stiffness...
December 5, 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/29215096/exome-sequencing-revealed-a-novel-nonsense-variant-in-alx3-gene-underlying-frontorhiny
#15
Asmat Ullah, Muhammad Umair, Umm E-Kalsoom, Shaheen Shahzad, Sulman Basit, Wasim Ahmad
Frontorhiny is one of the two forms of mid-facial malformations characterized by ocular hypertelorism, wide and short nasal ridge, bifid nasal tip, broad columella, widely separated nares, long and wide philtrum and V-shaped hairline. Sometimes these phenotypes are associated with ptosis and midline dermoid cysts. Frontorhiny inherits in an autosomal recessive pattern. Sequence variants in the Aristaless-like homeobox 3 (ALX3) gene underlying frontorhiny have been reported previously. Here, in the present study, we have investigated four patients in a consanguineous family of Pakistani origin segregating frontorhiny in autosomal recessive manner...
November 16, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29214346/comparative-genomics-reveals-the-presence-of-putative-toxin-antitoxin-system-in-wolbachia-genomes
#16
Kopal Singhal, Sujata Mohanty
Multiple toxin-antitoxin (TA) systems are housed in different locations within the bacterial genome and are known to be associated with various cellular processes and stress-related adaptation. In endosymbionts, although, the TA system has scarce occurrence but studies have highlighted its presence in enhancing host-symbiont interactions. Wolbachia, an obligate endosymbiont, has recently been proposed as a biocontrol agent which may be helpful in controlling vector-borne diseases. There are reports suggesting the role of TA system in inducing cytoplasmic incompatibility in case of Wolbachia, however, the underlying mechanism is still not known...
December 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29214033/lupus-related-single-nucleotide-polymorphisms-and-risk-of-diffuse-large-b-cell-lymphoma
#17
Sasha Bernatsky, Héctor A Velásquez García, John J Spinelli, Patrick Gaffney, Karin E Smedby, Rosalind Ramsey-Goldman, Sophia S Wang, Hans-Olov Adami, Demetrius Albanes, Emanuele Angelucci, Stephen M Ansell, Yan W Asmann, Nikolaus Becker, Yolanda Benavente, Sonja I Berndt, Kimberly A Bertrand, Brenda M Birmann, Heiner Boeing, Paolo Boffetta, Paige M Bracci, Paul Brennan, Angela R Brooks-Wilson, James R Cerhan, Stephen J Chanock, Jacqueline Clavel, Lucia Conde, Karen H Cotenbader, David G Cox, Wendy Cozen, Simon Crouch, Anneclaire J De Roos, Silvia de Sanjose, Simonetta Di Lollo, W Ryan Diver, Ahmet Dogan, Lenka Foretova, Hervé Ghesquières, Graham G Giles, Bengt Glimelius, Thomas M Habermann, Corinne Haioun, Patricia Hartge, Henrik Hjalgrim, Theodore R Holford, Elizabeth A Holly, Rebecca D Jackson, Rudolph Kaaks, Eleanor Kane, Rachel S Kelly, Robert J Klein, Peter Kraft, Anne Kricker, Qing Lan, Charles Lawrence, Mark Liebow, Tracy Lightfoot, Brian K Link, Marc Maynadie, James McKay, Mads Melbye, Thierry J Molina, Alain Monnereau, Lindsay M Morton, Alexandra Nieters, Kari E North, Anne J Novak, Kenneth Offit, Mark P Purdue, Marco Rais, Jacques Riby, Eve Roman, Nathaniel Rothman, Gilles Salles, Gianluca Severi, Richard K Severson, Christine F Skibola, Susan L Slager, Alex Smith, Martyn T Smith, Melissa C Southey, Anthony Staines, Lauren R Teras, Carrie A Thompson, Hervé Tilly, Lesley F Tinker, Anne Tjonneland, Jenny Turner, Claire M Vajdic, Roel C H Vermeulen, Joseph Vijai, Paolo Vineis, Jarmo Virtamo, Zhaoming Wang, Stephanie Weinstein, Thomas E Witzig, Andrew Zelenetz, Anne Zeleniuch-Jacquotte, Yawei Zhang, Tongzhang Zheng, Mariagrazia Zucca, Ann E Clarke
Objective: Determinants of the increased risk of diffuse large B-cell lymphoma (DLBCL) in SLE are unclear. Using data from a recent lymphoma genome-wide association study (GWAS), we assessed whether certain lupus-related single nucleotide polymorphisms (SNPs) were also associated with DLBCL. Methods: GWAS data on European Caucasians from the International Lymphoma Epidemiology Consortium (InterLymph) provided a total of 3857 DLBCL cases and 7666 general-population controls...
2017: Lupus Science & Medicine
https://www.readbyqxmd.com/read/29213072/characterization-of-large-copy-number-variation-in-mexican-type-2-diabetes-subjects
#18
Iván de Jesús Ascencio-Montiel, Dalila Pinto, Esteban J Parra, Adán Valladares-Salgado, Miguel Cruz, Stephen W Scherer
The effect of Copy Number Variants (CNVs) on Type 2 Diabetes (T2D) remains little explored. The present study characterized large rare CNVs in 686 T2D and 194 non-T2D subjects of Mexican ancestry genotyped using the Affymetrix Genome-Wide Human SNP array 5.0. Rare CNVs with ≥ 100 kb length were identified using a stringent strategy based on merging CNVs calls generated using Birdsuit, iPattern and PennCNV algorithms. We applied three different strategies to evaluate the distribution of CNVs in the T2D and non-T2D samples: 1) Burden analysis, 2) Identification of CNVs in loci previously associated to T2D, and 3) Identification of CNVs observed only in the T2D group...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29213071/gwas-of-the-electrocardiographic-qt-interval-in-hispanics-latinos-generalizes-previously-identified-loci-and-identifies-population-specific-signals
#19
Raúl Méndez-Giráldez, Stephanie M Gogarten, Jennifer E Below, Jie Yao, Amanda A Seyerle, Heather M Highland, Charles Kooperberg, Elsayed Z Soliman, Jerome I Rotter, Kathleen F Kerr, Kelli K Ryckman, Kent D Taylor, Lauren E Petty, Sanjiv J Shah, Matthew P Conomos, Nona Sotoodehnia, Susan Cheng, Susan R Heckbert, Tamar Sofer, Xiuqing Guo, Eric A Whitsel, Henry J Lin, Craig L Hanis, Cathy C Laurie, Christy L Avery
QT interval prolongation is a heritable risk factor for ventricular arrhythmias and can predispose to sudden death. Most genome-wide association studies (GWAS) of QT were performed in European ancestral populations, leaving other groups uncharacterized. Herein we present the first QT GWAS of Hispanic/Latinos using data on 15,997 participants from four studies. Study-specific summary results of the association between 1000 Genomes Project (1000G) imputed SNPs and electrocardiographically measured QT were combined using fixed-effects meta-analysis...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29212897/genetic-variants-contributing-to-circulating-matrix-metalloproteinase-8-levels-and-their-association-with-cardiovascular-diseases-a-genome-wide-analysis
#20
Aino Salminen, Efthymia Vlachopoulou, Aki S Havulinna, Taina Tervahartiala, Wolfgang Sattler, Marja-Liisa Lokki, Markku S Nieminen, Markus Perola, Veikko Salomaa, Juha Sinisalo, Seppo Meri, Timo Sorsa, Pirkko J Pussinen
BACKGROUND: Matrix metalloproteinase 8 (MMP-8) is a proinflammatory enzyme expressed mainly by neutrophils. Elevated serum and plasma concentrations of MMP-8 are associated with the risk for and outcome of cardiovascular diseases (CVDs). The origin of circulating MMP-8 is not completely clear. METHODS AND RESULTS: We performed a genome-wide association study of serum MMP-8 levels in 2 populations comprising altogether 6049 individuals. Moreover, we studied whether MMP-8-associated variants are linked to increased risk of CVDs and overall mortality in >20 000 subjects...
December 2017: Circulation. Cardiovascular Genetics
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