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Genome wide association study

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https://www.readbyqxmd.com/read/29454095/an-esophageal-adenocarcinoma-susceptibility-locus-at-9q22-also-confers-risk-to-esophageal-squamous-cell-carcinoma-by-regulating-the-function-of-barx1
#1
Caiwang Yan, Yong Ji, Tongtong Huang, Fei Yu, Yong Gao, Yayun Gu, Qi Qi, Jiangbo Du, Juncheng Dai, Hongxia Ma, Guangfu Jin
Genome wide association studies (GWAS) have identified a series of genetic variants associated with the risk of esophageal adenocarcinoma (EAC)/Barrett's esophagus (BE), which was different from those loci for esophageal squamous cell carcinoma (ESCC). It is important to evaluate whether these susceptibility loci for EAC/BE are also implicated in ESCC development. In the current study, we analyzed genetic variants at 3p13, 9q22, 16q24 and 19p13 in a case-control study including 2139 ESCC patients and 2463 cancer-free controls in a Chinese population, and further characterized the biological relevance of genetic variants by functional assays...
February 14, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29453864/-lpcat1-controls-phosphate-homeostasis-in-a-zinc-dependent-manner
#2
Mushtak Kisko, Nadia Bouain, Alaeddine Safi, Anna Medici, Robert C Akkers, David Secco, Gilles Fouret, Gabriel Krouk, Mark Gm Aarts, Wolfgang Busch, Hatem Rouached
All living organisms require a variety of essential elements for their basic biological functions. While the homeostasis of nutrients is highly intertwined, the molecular and genetic mechanisms of these dependencies remains poorly understood. Here, we report a discovery of a molecular pathway that control phosphate (Pi) accumulation plants in Zn deficiency. Using genome-wide association studies we first identified allelic variation of the Lyso-PhosphatidylCholine (PC) AcylTransferase 1 ( LPCAT1 ) gene as the key determinant of shoot Pi accumulation under Zn deficiency...
February 17, 2018: ELife
https://www.readbyqxmd.com/read/29453822/full-genome-sequencing-of-porcine-circovirus-3-field-strains-from-denmark-italy-and-spain-demonstrates-a-high-within-europe-genetic-heterogeneity
#3
G Franzo, M Legnardi, C K Hjulsager, F Klaumann, L E Larsen, J Segales, M Drigo
Porcine circovirus 3 (PCV3) is a new species of the Circovirus genus, which has recently been associated with different clinical syndromes. Its presence has been reported in different countries of North and South America, Asia and recently also Europe (Poland). However, different from the other continents, no European PCV3 sequence is currently available in public databases. There is a strong need of epidemiological data and full-genome sequences from Europe because of its relevance in the understanding of PCV3 molecular epidemiology and control...
February 16, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29453460/development-and-initial-characterization-of-a-novel-ghrelin-receptor-crispr-cas9-knockout-wistar-rat-model
#4
L J Zallar, B J Tunstall, C T Richie, Y J Zhang, Z B You, E L Gardner, M Heilig, J Pickel, G F Koob, L F Vendruscolo, B K Harvey, L Leggio
BACKGROUND/OBJECTIVES: Ghrelin, a stomach-derived hormone implicated in numerous behaviors including feeding, reward, stress, and addictive behaviors, acts by binding to the growth hormone secretagogue receptor (GHSR). Here, we present the development, verification, and initial characterization of a novel GHSR knockout (KO) Wistar rat model created with CRISPR genome editing. METHODS: Using CRISPR/Cas9, we developed a GHSR KO in a Wistar background. Loss of GHSR mRNA expression was histologically verified using RNAscope in wild-type (WT; n = 2) and KO (n = 2) rats...
January 30, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29453348/abcg2-contributes-to-the-development-of-gout-and-hyperuricemia-in-a-genome-wide-association-study
#5
Chung-Jen Chen, Chia-Chun Tseng, Jeng-Hsien Yen, Jan-Gowth Chang, Wen-Cheng Chou, Hou-Wei Chu, Shun-Jen Chang, Wei-Ting Liao
Although many genome-wide association studies (GWASs) of hyperuricemia or gout have been reported, the related genetic factors and the mechanisms from hyperuricemia to gouty attack remain unclear. This study aimed to identify genetic factors and pathogenesis of gout from hyperuricemia by genome-wide association study (GWAS). 747 gout patients, 747 hyperuricemia and 2071 age-matched controls were recruited and analyzed with Affymetrix 650 K chip to find the related genetic variants. The functions of the related genes were investigated in an endothelial cell (EC) with urate crystal stimulation...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453196/genome-wide-association-study-identifies-erbb4-on-2q34-as-a-novel-locus-associated-with-sperm-motility-in-japanese-men
#6
Youichi Sato, Atsushi Tajima, Takehiro Sato, Shiari Nozawa, Miki Yoshiike, Issei Imoto, Aiko Yamauchi, Teruaki Iwamoto
BACKGROUND: The decrease in sperm motility has a potent influence on fertilisation. Sperm motility, represented as the percentage of motile sperm in ejaculated sperms, is influenced by lifestyle habits or environmental factors and by inherited factors. However, genetic factors contributing to individual differences in sperm motility remain unclear. To identify genetic factors that influence human sperm motility, we performed a genome-wide association study (GWAS) of sperm motility. METHODS: A two-stage GWAS was conducted using 811 Japanese men in a discovery stage, followed by a replication study using an additional 779 Japanese men...
February 16, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29453109/genetic-basis-of-diabetic-kidney-disease-and-other-diabetic-complications
#7
REVIEW
Niina Sandholm, Per-Henrik Groop
Diabetic kidney disease and other long-term complications are common in diabetes, and comprise the main cause of co-morbidity and premature mortality in individuals with diabetes. While familial clustering and heritability have been reported for all diabetic complications, the genetic background and the molecular mechanisms remain poorly understood. In recent years, genome-wide association studies have identified a few susceptibility loci for the renal complications as well as for diabetic retinopathy, diabetic cardiovascular disease and mortality...
February 13, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29452776/women-specific-risk-factors-for-heart-failure-a-genetic-approach
#8
REVIEW
Jet van der Kemp, Yvonne T van der Schouw, Folkert W Asselbergs, N Charlotte Onland-Moret
Heart failure is a complex disease, which is presented differently by men and women. Several studies have shown that reproductive factors, such as age at natural menopause, parity and polycystic ovarian syndrome (PCOS), may play a role in the development of heart failure. Shared genetics may provide clues to underlying mechanisms; however, this has never been examined. Therefore, the aim of the current study was to explore whether any reproductive factor is potentially related to heart failure in women, based on genetic similarities...
March 2018: Maturitas
https://www.readbyqxmd.com/read/29452408/genome-wide-association-study-identifies-seven-novel-susceptibility-loci-for-primary-open-angle-glaucoma
#9
Yukihiro Shiga, Masato Akiyama, Koji M Nishiguchi, Kota Sato, Nobuhiro Shimozawa, Atsushi Takahashi, Yukihide Momozawa, Makoto Hirata, Matsuda Koichi, Taiki Yamaji, Motoki Iwasaki, Shoichiro Tsugane, Isao Oze, Haruo Mikami, Mariko Naito, Kenji Wakai, Munemitsu Yoshikawa, Masahiro Miyake, Kenji Yamashiro, Kenji Kashiwagi, Takeshi Iwata, Fumihiko Mabuchi, Mitsuko Takamoto, Mineo Ozaki, Kazuhide Kawase, Makoto Aihara, Makoto Araie, Tetsuya Yamamoto, Yoshiaki Kiuchi, Makoto Nakamura, Yasuhiro Ikeda, Koh-Hei Sonoda, Tatsuro Ishibashi, Koji Nitta, Aiko Iwase, Shiroaki Shirato, Yoshitaka Oka, Mamoru Satoh, Makoto Sasaki, Nobuo Fuse, Yoichi Suzuki, Ching-Yu Cheng, Chiea Chuen Khor, Mani Baskaran, Shamira Perera, Tin Aung, Eranga N Vithana, Jessica N Cooke Bailey, Jae H Kang, Louis R Pasquale, Jonathan L Haines, Janey L Wiggs, Kathryn P Burdon, Puya Gharahkhani, Alex W Hewitt, David A Mackey, Stuart MacGregor, Jamie E Craig, R Rand Allingham, Micheal Hauser, Adeyinka Ashaye, Donald L Budenz, Stephan Akafo, Susan E I Williams, Yoichiro Kamatani, Toru Nakazawa, Michiaki Kubo
Primary open-angle glaucoma (POAG) is the leading cause of irreversible blindness worldwide for which 15 disease-associated loci had been discovered. Among them, only 5 loci have been associated with POAG in Asians. We carried out a genome-wide association study and a replication study that included a total of 7,378 POAG cases and 36,385 controls from a Japanese population. After combining the GWAS and the two replication sets, we identified 11 POAG-associated loci, including 4 known (CDKN2B-AS1, ABCA1, SIX6 and AFAP1) and 7 novel loci (FNDC3B, ANKRD55-MAP3K1, LMX1B, LHPP, HMGA2, MEIS2 and LOXL1) at a genome-wide significance level (p < 5...
February 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29452120/quantifying-the-polygenic-contribution-to-cutaneous-squamous-cell-carcinoma-risk
#10
Joanne E Sordillo, Peter Kraft, Ann Chen Wu, Maryam M Asgari
Genetic factors play an important role in cutaneous squamous cell carcinoma (cSCC) risk. Genome-wide association studies have identified 21 single nucleotide polymorphisms (SNPs) associated with cSCC risk. Yet no studies have attempted to quantify the contribution of heritability to cSCC risk by calculating the population attributable risk (PAR) using a combination of all discovered genetic variants. Using an additive multi-locus linear logistic model, we determined the cumulative association of these 21 genetic regions to cSCC PAR...
February 13, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29451423/replication-of-type-2-diabetes-associated-variants-in-a-saudi-arabian-population
#11
Ruifang Li-Gao, Salma Majid Wakil, Brian F Meyer, Nduna Dzimiri, Dennis O Mook-Kanamori
Over 120 type 2 diabetes (T2D) loci have been identified from genome-wide association analysis (GWAS), mainly from Caucasian populations. Very limited knowledge is available on the Saudi Arabian population. In this study, 122 previously reported T2D related variants from 84 loci were examined in a Saudi Arabian cohort of 1,578 individuals (659 T2D cases and 919 controls). Eleven SNPs corresponding to 9 independent loci had a p-value <0.05. If a more stringent Bonferroni threshold of p=4.1×10 -4 (=0.05/122) was applied, none of the SNPs would have reached the significance level...
February 16, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29451311/impaired-phloem-loading-in-zmsweet13a-b-c-sucrose-transporter-triple-knock-out-mutants-in-zea-mays
#12
Margaret Bezrutczyk, Thomas Hartwig, Marc Horshman, Si Nian Char, Jinliang Yang, Bing Yang, Wolf B Frommer, Davide Sosso
Crop yield depends on efficient allocation of sucrose from leaves to seeds. In Arabidopsis, phloem loading is mediated by a combination of SWEET sucrose effluxers and subsequent uptake by SUT1/SUC2 sucrose/H + symporters. ZmSUT1 is essential for carbon allocation in maize, but the relative contribution to apoplasmic phloem loading and retrieval of sucrose leaking from the translocation path is not known. Here we analysed the contribution of SWEETs to phloem loading in maize. We identified three leaf-expressed SWEET sucrose transporters as key components of apoplasmic phloem loading in Zea mays L...
February 16, 2018: New Phytologist
https://www.readbyqxmd.com/read/29450768/cc398-staphylococcus-aureus-subpopulations-in-belgian-patients
#13
M Angeles Argudín, A Deplano, S Vandendriessche, M Dodémont, C Nonhoff, O Denis, S Roisin
Studies based on genome-wide single nucleotide polymorphisms (SNPs) supported the existence of two subpopulations in clonal complex (CC) 398 Staphylococcus aureus: an ancestral human-adapted clade (HC) and an animal-associated clade (AC). In this study, we have investigated the occurrence of genetic markers that allow discrimination of these subpopulations among CC398 isolates collected during 2014 to 2016 from human patients in Belgium. A collection of isolates was investigated by means of spa-typing and 16S-mecA-nuc PCR...
February 15, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29450669/association-of-tert-clptm1l-and-8q24-common-genetic-variants-with-gallbladder-cancer-susceptibility-and-prognosis-in-north-indian-population
#14
Saurabh Yadav, Abhijit Chandra, Ashok Kumar, Balraj Mittal
Gallbladder carcinoma (GBC) is one of the common malignancy of the biliary tract. Several genome wide and candidate gene studies have reported associations between multiple cancer types and single-nucleotide polymorphisms on 5p15.33 and 8q24.21 loci. However, predisposition potential of these genetic variants has not been assessed in GBC. We performed the present study to assess the potential of five polymorphisms on 5p15.33 and one on 8q24.21 locus in GBC risk and treatment response in patients undergoing chemoradiotherapy...
February 15, 2018: Biochemical Genetics
https://www.readbyqxmd.com/read/29450541/induction-of-ocular-complement-activation-by-inflammatory-stimuli-and-intraocular-inhibition-of-complement-factor-d-in-animal-models
#15
Maura A Crowley, Omar Delgado, Adrian Will-Orrego, Natasha M Buchanan, Karen Anderson, Bruce D Jaffee, Thaddeus P Dryja, Sha-Mei Liao
Purpose: Genome-wide association studies suggest a role for the complement system in age-related macular degeneration (AMD). We characterized ocular complement activation and evaluated a complement factor D (FD) neutralizing antibody. Methods: Mice were treated with toll-like receptor (TLR) ligands, intravitreal injection (IVT), or corneal debridement. Levels of complement proteins and mRNA were measured. A FD neutralizing antibody was administered IVT into eyes of rabbits that were challenged with LPS (lipopolysaccharide) administered intravenously...
February 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29450147/lemongrass-cymbopogon-flexuosus-essential-oil-demonstrated-anti-inflammatory-effect-in-pre-inflamed-human-dermal-fibroblasts
#16
Xuesheng Han, Tory L Parker
Lemongrass ( Cymbopogon flexuosus ) essential oil (LEO), which has citral as its main component, has exhibited anti-inflammatory effect in both animal and human cells. In this study, we evaluated the anti-inflammatory activity of a commercially available LEO in pre-inflamed human dermal fibroblasts. We first studied the impact of LEO on 17 protein biomarkers that are critically associated with inflammation and tissue remodeling. LEO significantly inhibited production of the inflammatory biomarkers vascular cell adhesion molecule 1 (VCAM-1), interferon gamma-induced protein 10 (IP-10), interferon-inducible T-cell alpha chemoattractant (I-TAC), and monokine induced by gamma interferon (MIG); decreased levels of the tissue remodeling biomarkers collagen-I and III, epidermal growth factor receptor (EGFR), and plasminogen activator inhibitor (PAI-1); and inhibited the immunomodulatory biomarker macrophage colony-stimulating factor (M-CSF)...
June 2017: Biochimie Open
https://www.readbyqxmd.com/read/29449860/adaptive-genetic-divergence-despite-significant-isolation-by-distance-in-populations-of-taiwan-cow-tail-fir-keteleeria-davidiana-var-formosana
#17
Kai-Ming Shih, Chung-Te Chang, Jeng-Der Chung, Yu-Chung Chiang, Shih-Ying Hwang
Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana , disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29449654/analysis-combining-correlated-glaucoma-traits-identifies-five-new-risk-loci-for-open-angle-glaucoma
#18
Puya Gharahkhani, Kathryn P Burdon, Jessica N Cooke Bailey, Alex W Hewitt, Matthew H Law, Louis R Pasquale, Jae H Kang, Jonathan L Haines, Emmanuelle Souzeau, Tiger Zhou, Owen M Siggs, John Landers, Mona Awadalla, Shiwani Sharma, Richard A Mills, Bronwyn Ridge, David Lynn, Robert Casson, Stuart L Graham, Ivan Goldberg, Andrew White, Paul R Healey, John Grigg, Mitchell Lawlor, Paul Mitchell, Jonathan Ruddle, Michael Coote, Mark Walland, Stephen Best, Andrea Vincent, Jesse Gale, Graham RadfordSmith, David C Whiteman, Grant W Montgomery, Nicholas G Martin, David A Mackey, Janey L Wiggs, Stuart MacGregor, Jamie E Craig
Open-angle glaucoma (OAG) is a major cause of blindness worldwide. To identify new risk loci for OAG, we performed a genome-wide association study in 3,071 OAG cases and 6,750 unscreened controls, and meta-analysed the results with GWAS data for intraocular pressure (IOP) and optic disc parameters (the overall meta-analysis sample size varying between 32,000 to 48,000 participants), which are glaucoma-related traits. We identified and independently validated four novel genome-wide significant associations within or near MYOF and CYP26A1, LINC02052 and CRYGS, LMX1B, and LMO7 using single variant tests, one additional locus (C9) using gene-based tests, and two genetic pathways - "response to fluid shear stress" and "abnormal retina morphology" - in pathway-based tests...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29448938/comparative-genomic-analysis-of-ten-clinical-streptococcus-pneumoniae-collected-from-a-malaysian-hospital-reveal-31-new-unique-drug-resistant-snps-using-whole-genome-sequencing
#19
Hassan Mahmood Jindal, Babu Ramanathan, Cheng Foh Le, Ranganath Gudimella, Rozaimi Razali, Rishya Manikam, Shamala Devi Sekaran
BACKGROUND: Streptococcus pneumoniae or pneumococcus is a leading cause of morbidity and mortality worldwide, specifically in relation to community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs. METHODS: In this study, whole genome sequencing (WGS) was performed for 10 clinical strains of S. pneumoniae with different levels of sensitivity to standard antibiotics...
February 15, 2018: Journal of Biomedical Science
https://www.readbyqxmd.com/read/29448039/development-of-sirna-mediated-rna-interference-and-functional-analysis-of-novel-parasitic-nematode-specific-protein-of-setaria-digitata
#20
M B C L Somarathne, Y I N S Gunawardena, N V Chandrasekharan, R S Dassanayake
Despite the differences of the host, parasitic nematodes may share commonalities in their parasitizing genes. Setaria digitata novel protein (SDNP) is such an entity which is parasitic nematode-specific and having sequence similarities with those of W. bancrofti, B. malayi, Loa loa and Onchocerca volvulus. Post-transcriptional gene silencing by siRNA mediated RNA interference (RNAi) is a widely used technique in functional genomics. Though the technique has been used in several free-living, plant and animal parasitic nematodes, it has not yet been tried out for the filarial worm S...
February 12, 2018: Experimental Parasitology
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