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Genome wide association studies

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https://www.readbyqxmd.com/read/29471430/gwas-identifies-two-novel-colorectal-cancer-loci-at-16q24-1-and-20q13-12
#1
Chizu Tanikawa, Yoichiro Kamatani, Atsushi Takahashi, Yukihide Momozawa, Karine Leveque, Satoshi Nagayama, Koshi Mimori, Masaki Mori, Hideshi Ishii, Johji Inazawa, Jun Yasuda, Akito Tsuboi, Atsushi Shimizu, Makoto Sasaki, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Shoichiro Tsugane, Mariko Naito, Kenji Wakai, Teruhide Koyama, Toshiro Takezaki, Koichiro Yuji, Yoshinori Murakami, Yusuke Nakamura, Michiaki Kubo, Koichi Matsuda
Colorectal cancer is the fourth leading cause of cancer mortality worldwide. Genome-wide association studies (GWAS) identified more than 50 colorectal cancer loci. However, most of the previous studies were conducted in European populations, and host genetic factors among Japanese population are largely remained to be identified. To identify novel loci in the Japanese population, here, we performed a large-scale GWAS using 6,692 cases and 27,178 controls followed by a replication analysis using more than 11,000 case-control samples...
February 17, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29471399/from-genome-wide-association-studies-to-mendelian-randomization-novel-opportunities-for-understanding-cardiovascular-disease-causality-pathogenesis-prevention-and-treatment
#2
Marianne Benn, Børge G Nordestgaard
The Mendelian randomization approach is an epidemiologic study design incorporating genetic information into traditional epidemiologic studies to infer causality of biomarkers, risk factors, or lifestyle factors on disease risk. Mendelian randomization studies often draw on novel information generated in genome-wide association studies on causal associations between genetic variants and a risk factor or lifestyle factor. Such information can then be used in a largely unconfounded study design free of reverse causation to understand if and how risk factors and lifestyle factors cause cardiovascular disease...
February 19, 2018: Cardiovascular Research
https://www.readbyqxmd.com/read/29471369/genome-wide-association-study-of-stayability-and-heifer-pregnancy-in-red-angus-cattle
#3
S E Speidel, B A Buckley, R J Boldt, R M Enns, J Lee, M L Spangler, M G Thomas
Reproductive performance is the most important component of cattle production from the standpoint of economic sustainability of commercial beef enterprises. Heifer Pregnancy (HPG) and Stayability (STAY) genetic predictions are two selection tools published by the Red Angus Association of America (RAAA) to assist with improvements in reproductive performance. Given the importance of HPG and STAY to the profitability of commercial beef enterprises, the objective of this study was to identify QTL associated with both HPG and STAY in Red Angus cattle...
February 19, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29471259/functional-genomics-and-assays-of-regulatory-activity-detect-mechanisms-at-loci-for-lipid-traits-and-coronary-artery-disease
#4
REVIEW
Tamara S Roman, Karen L Mohlke
Many genome-wide association studies (GWAS) have identified signals located in non-coding regions, and an increasing number of functional genomics annotations of regulatory elements and assays of regulatory activity have been used to investigate mechanisms. Genome-wide datasets that characterize chromatin structure help detect potential regulatory elements. Assays to experimentally assess candidate variants include transcriptional reporter assays, and recently, massively parallel reporter assays (MPRAs). Additionally, the effect of candidate regulatory elements and variants on gene expression and function can be evaluated using genomic editing with the CRISPR-Cas9 technology...
February 19, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29470622/genetic-dissection-of-wheat-panicle-traits-using-linkage-analysis-and-a-genome-wide-association-study
#5
Kai Liu, Xiaoxiao Sun, Tangyuan Ning, Xixian Duan, Qiaoling Wang, Tongtong Liu, Yuling An, Xin Guan, Jichun Tian, Jiansheng Chen
Coincident regions on chromosome 4B for GW, on 5A for SD and TSS, and on 3A for SL and GNS were detected through an integration of a linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A and 6A were identified with high PVE% on a composite map. The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding...
February 22, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29470621/novel-sources-of-resistance-to-septoria-nodorum-blotch-in-the-vavilov-wheat-collection-identified-by-genome-wide-association-studies
#6
Huyen T T Phan, Kasia Rybak, Stefania Bertazzoni, Eiko Furuki, Eric Dinglasan, Lee T Hickey, Richard P Oliver, Kar-Chun Tan
The fungus Parastagonospora nodorum causes Septoria nodorum blotch (SNB) of wheat. A genetically diverse wheat panel was used to dissect the complexity of SNB and identify novel sources of resistance. The fungus Parastagonospora nodorum is the causal agent of Septoria nodorum blotch (SNB) of wheat. The pathosystem is mediated by multiple fungal necrotrophic effector-host sensitivity gene interactions that include SnToxA-Tsn1, SnTox1-Snn1, and SnTox3-Snn3. A P. nodorum strain lacking SnToxA, SnTox1, and SnTox3 (toxa13) retained wild-type-like ability to infect some modern wheat cultivars, suggesting evidence of other effector-mediated susceptibility gene interactions or the lack of host resistance genes...
February 22, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29470286/genetic-variants-associated-with-obesity-and-insulin-resistance-in-hispanic-boys-with-nonalcoholic-fatty-liver-disease
#7
John C Rausch, Joel E Lavine, Naga Chalasani, Xiuqing Guo, Soonil Kwon, Jeffrey B Schwimmer, Jean P Molleston, Rohit Loomba, Elizabeth M Brunt, Yii-Der Ida Chen, Mark O Goodarzi, Kent D Taylor, Katherine P Yates, Jerome I Rotter
BACKGROUND AND OBJECTIVES: Nonalcoholic fatty liver disease (NAFLD) disproportionately affects Hispanic boys. Further, obesity and insulin resistance are major risk factors for NAFLD. No gene localization studies had been performed on children with biopsy-proven NAFLD. This study aims to identify genomic variants associated with increased adiposity and insulin resistance in a population of children with varying histologic severity of NAFLD. METHODS: We conducted a genome-wide association scan (GWAS) including 624,297 single-nucleotide polymorphisms (SNPs) distributed among all 22 autosomal chromosomes in 234 Hispanic boys (up to 18 years of age) who were consecutively recruited in a prospective cohort study in the Nonalcoholic Steatohepatitis Clinical Research Network Studies...
February 21, 2018: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/29468687/genome-wide-association-mapping-of-the-architecture-of-susceptibility-to-the-root-knot-nematode-meloidogyne-incognita-in-arabidopsis-thaliana
#8
Sonja Warmerdam, Mark G Sterken, Casper van Schaik, Marian E P Oortwijn, Octavina C A Sukarta, Jose L Lozano-Torres, Marcel Dicke, Johannes Helder, Jan E Kammenga, Aska Goverse, Jaap Bakker, Geert Smant
Susceptibility to the root-knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focused on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance. To study the genetic architecture of susceptibility to M. incognita, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome-wide association mapping...
February 22, 2018: New Phytologist
https://www.readbyqxmd.com/read/29467776/genome-wide-association-analyses-identify-qtl-hotspots-for-yield-and-component-traits-in-durum-wheat-grown-under-yield-potential-drought-and-heat-stress-environments
#9
Sivakumar Sukumaran, Matthew P Reynolds, Carolina Sansaloni
Understanding the genetic bases of economically important traits is fundamentally important in enhancing genetic gains in durum wheat. In this study, a durum panel of 208 lines (comprised of elite materials and exotics from the International Maize and Wheat Improvement Center gene bank) were subjected to genome wide association study (GWAS) using 6,211 DArTseq single nucleotide polymorphisms (SNPs). The panel was phenotyped under yield potential (YP), drought stress (DT), and heat stress (HT) conditions for 2 years...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29467742/genetic-diversity-and-phylogenetic-relationships-of-coevolving-symbiont-harboring-insect-trypanosomatids-and-their-neotropical-dispersal-by-invader-african-blowflies-calliphoridae
#10
Tarcilla C Borghesan, Marta Campaner, Tania E Matsumoto, Omar A Espinosa, Victor Razafindranaivo, Fernando Paiva, Julio C Carranza, Nestor Añez, Luis Neves, Marta M G Teixeira, Erney P Camargo
This study is about the inter- and intra-specific genetic diversity of trypanosomatids of the genus Angomonas , and their association with Calliphoridae (blowflies) in Neotropical and Afrotropical regions. Microscopic examination of 3,900 flies of various families, mostly Calliphoridae, revealed that 31% of them harbored trypanosomatids. Small subunit rRNA (SSU rRNA) barcoding showed that Angomonas predominated (46%) over the other common trypanosomatids of blowflies of genera Herpetomonas and Wallacemonas ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29467655/atherosclerosis-is-an-inflammatory-disease-which-lacks-a-common-anti-inflammatory-therapy-how-human-genetics-can-help-to-this-issue-a-narrative-review
#11
REVIEW
Cristiano Fava, Martina Montagnana
Atherosclerosis is a multifactorial disease triggered and sustained by different risk factors such as dyslipidemia, arterial hypertension, diabetes mellitus, smoke, etc. Since a couple of decades, a pivotal role for inflammation in its pathogenesis has been recognized and proved at molecular levels, and already described in many animal models. Despite all this knowledge, due to the complexity of the specific inflammatory process subtending atherosclerosis and to the fact that inflammation is also a protective response against microorganisms, no anti-inflammatory therapy has been rendered available in the therapeutic armamentarium against atherosclerosis and vascular events till 2017 when canakinumab in the first ad-hoc randomized clinical trial (RCT) proved for the first time that targeting specifically inflammation lowers cardiovascular (CV) events...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29467471/network-analysis-of-coronary-artery-disease-risk-genes-elucidates-disease-mechanisms-and-druggable-targets
#12
Harri Lempiäinen, Ingrid Brænne, Tom Michoel, Vinicius Tragante, Baiba Vilne, Tom R Webb, Theodosios Kyriakou, Johannes Eichner, Lingyao Zeng, Christina Willenborg, Oscar Franzen, Arno Ruusalepp, Anuj Goel, Sander W van der Laan, Claudia Biegert, Stephen Hamby, Husain A Talukdar, Hassan Foroughi Asl, Gerard Pasterkamp, Hugh Watkins, Nilesh J Samani, Timo Wittenberger, Jeanette Erdmann, Heribert Schunkert, Folkert W Asselbergs, Johan L M Björkegren
Genome-wide association studies (GWAS) have identified over two hundred chromosomal loci that modulate risk of coronary artery disease (CAD). The genes affected by variants at these loci are largely unknown and an untapped resource to improve our understanding of CAD pathophysiology and identify potential therapeutic targets. Here, we prioritized 68 genes as the most likely causal genes at genome-wide significant loci identified by GWAS of CAD and examined their regulatory roles in 286 metabolic and vascular tissue gene-protein sub-networks ("modules")...
February 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29467456/genome-wide-crispr-screen-reveals-sgol1-as-a-druggable-target-of-sorafenib-treated-hepatocellular-carcinoma
#13
Weijian Sun, Bin He, Beng Yang, Wendi Hu, Shaobing Cheng, Heng Xiao, Zhengjie Yang, Xiaoyu Wen, Lin Zhou, Haiyang Xie, Xian Shen, Jian Wu, Shusen Zheng
The genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen is a powerful tool used to identify therapeutic targets that can be harnessed for cancer treatment. This study aimed to assess the efficacy of genome-wide CRISPR screening to identify druggable genes associated with sorafenib-treated hepatocellular carcinoma (HCC). A genome-scale CRISPR knockout (GeCKO v2) library containing 123,411 single guide RNAs (sgRNAs) was used to identify loss-of-function mutations conferring sorafenib resistance upon HCC cells...
February 21, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29467291/epigenetic-alterations-in-longevity-regulators-reduced-life-span-and-exacerbated-aging-related-pathology-in-old-father-offspring-mice
#14
Kan Xie, Devon P Ryan, Brandon L Pearson, Kristin S Henzel, Frauke Neff, Ramon O Vidal, Magali Hennion, Isabelle Lehmann, Melvin Schleif, Susanne Schröder, Thure Adler, Birgit Rathkolb, Jan Rozman, Anna-Lena Schütz, Cornelia Prehn, Michel E Mickael, Marco Weiergräber, Jerzy Adamski, Dirk H Busch, Gerhard Ehninger, Anna Matynia, Walker S Jackson, Eckhard Wolf, Helmut Fuchs, Valerie Gailus-Durner, Stefan Bonn, Martin Hrabě de Angelis, Dan Ehninger
Advanced age is not only a major risk factor for a range of disorders within an aging individual but may also enhance susceptibility for disease in the next generation. In humans, advanced paternal age has been associated with increased risk for a number of diseases. Experiments in rodent models have provided initial evidence that paternal age can influence behavioral traits in offspring animals, but the overall scope and extent of paternal age effects on health and disease across the life span remain underexplored...
February 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29466359/cdk-activity-provides-temporal-and-quantitative-cues-for-organizing-genome-duplication
#15
Anthony Perrot, Christopher Lee Millington, Blanca Gómez-Escoda, Diane Schausi-Tiffoche, Pei-Yun Jenny Wu
In eukaryotes, the spatial and temporal organization of genome duplication gives rise to distinctive profiles of replication origin usage along the chromosomes. While it has become increasingly clear that these programs are important for cellular physiology, the mechanisms by which they are determined and modulated remain elusive. Replication initiation requires the function of cyclin-dependent kinases (CDKs), which associate with various cyclin partners to drive cell proliferation. Surprisingly, although we possess detailed knowledge of the CDK regulators and targets that are crucial for origin activation, little is known about whether CDKs play a critical role in establishing the genome-wide pattern of origin selection...
February 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29464080/effects-of-interactions-between-common-genetic-variants-and-alcohol-consumption-on-colorectal-cancer-risk
#16
Nan Song, Aesun Shin, Jae Hwan Oh, Jeongseon Kim
Background: Genome-wide association studies (GWAS) have identified approximately 40 common genetic loci associated with colorectal cancer risk. To investigate possible gene-environment interactions (GEIs) between GWAS-identified single-nucleotide polymorphisms (SNPs) and alcohol consumption with respect to colorectal cancer, a hospital-based case-control study was conducted. Results: Higher levels of alcohol consumption as calculated based on a standardized definition of a drink (1 drink=12...
January 19, 2018: Oncotarget
https://www.readbyqxmd.com/read/29463994/the-homeotic-protein-six3-suppresses-carcinogenesis-and-metastasis-through-recruiting-the-lsd1-nurd-mta3-complex
#17
Yu Zheng, Yi Zeng, Rongfang Qiu, Ruiqiong Liu, Wei Huang, Yongqiang Hou, Shuang Wang, Shuai Leng, Dandan Feng, Yang Yang, Yan Wang
The homeodomain transcription factor SIX3 was recently reported to be a negative regulator of the Wnt pathway and has an emerging role in cancer. However, how SIX3 contributes to tumorigenesis and metastasis is poorly understood. METHODS: We employed affinity purification and mass spectrometry (MS) to identify the proteins physically associated with SIX3. Genome-wide analysis of the SIX3/LSD1/NuRD(MTA3) complex using a chromatin immunoprecipitation-on-chip approach identified a cohort of target genes including WNT1 and FOXC2 , which are critically involved in cell proliferation and epithelial-to-mesenchymal transition...
2018: Theranostics
https://www.readbyqxmd.com/read/29463654/emergence-of-an-extensively-drug-resistant-salmonella-enterica-serovar-typhi-clone-harboring-a-promiscuous-plasmid-encoding-resistance-to-fluoroquinolones-and-third-generation-cephalosporins
#18
Elizabeth J Klemm, Sadia Shakoor, Andrew J Page, Farah Naz Qamar, Kim Judge, Dania K Saeed, Vanessa K Wong, Timothy J Dallman, Satheesh Nair, Stephen Baker, Ghazala Shaheen, Shahida Qureshi, Mohammad Tahir Yousafzai, Muhammad Khalid Saleem, Zahra Hasan, Gordon Dougan, Rumina Hasan
Antibiotic resistance is a major problem in Salmonella enterica serovar Typhi, the causative agent of typhoid. Multidrug-resistant (MDR) isolates are prevalent in parts of Asia and Africa and are often associated with the dominant H58 haplotype. Reduced susceptibility to fluoroquinolones is also widespread, and sporadic cases of resistance to third-generation cephalosporins or azithromycin have also been reported. Here, we report the first large-scale emergence and spread of a novel S Typhi clone harboring resistance to three first-line drugs (chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole) as well as fluoroquinolones and third-generation cephalosporins in Sindh, Pakistan, which we classify as extensively drug resistant (XDR)...
February 20, 2018: MBio
https://www.readbyqxmd.com/read/29463506/fetal-genotype-and-maternal-glucose-have-independent-and-additive-effects-on-birth-weight
#19
Alice E Hughes, Michael Nodzenski, Robin N Beaumont, Octavious Talbot, Beverley M Shields, Denise M Scholtens, Bridget A Knight, William L Lowe, Andrew T Hattersley, Rachel M Freathy
Maternal glycemia is a key determinant of birth weight but recent large-scale genome wide-association studies demonstrated an important contribution of fetal genetics. It is not known whether fetal genotype modifies the impact of maternal glycemia, or whether it acts through insulin-mediated growth. We tested the effects of maternal fasting plasma glucose (FPG) and a fetal genetic score for birth weight on birth weight and fetal insulin in 2,051 European mother-child pairs from the Exeter Family Study of Childhood Health (EFSOCH) and Hyperglycemia and Adverse Pregnancy Outcome (HAPO) Study...
February 20, 2018: Diabetes
https://www.readbyqxmd.com/read/29462091/distinct-genomic-copy-number-alterations-distinguish-mucinous-tubular-and-spindle-cell-carcinoma-of-the-kidney-from-papillary-renal-cell-carcinoma-with-overlapping-histologic-features
#20
Qinghu Ren, Lu Wang, Hikmat A Al-Ahmadie, Samson W Fine, Anuradha Gopalan, Sahussapont J Sirintrapun, Satish K Tickoo, Victor E Reuter, Ying-Bei Chen
Mucinous tubular and spindle cell carcinoma (MTSCC) of the kidney is a rare type of renal cell carcinoma that frequently exhibits histologic and immunophenotypic features overlapping with type 1 papillary renal cell carcinoma (PRCC). To clarify molecular attributes that can be used for this difficult differential diagnosis, we sought to delineate the genome-wide copy number alterations in tumors displaying classic histologic features of MTSCC in comparison to the solid variant of type 1 PRCC and indeterminate cases with overlapping histologic features...
February 16, 2018: American Journal of Surgical Pathology
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