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https://www.readbyqxmd.com/read/28222519/genetic-stratification-to-identify-risk-groups-for-alzheimer-s-disease
#1
Riccardo E Marioni, Archie Campbell, Saskia P Hagenaars, Reka Nagy, Carmen Amador, Caroline Hayward, David J Porteous, Peter M Visscher, Ian J Deary
Stratification by genetic risk factors for Alzheimer's disease (AD) may help identify groups with the greatest disease risk. Biological changes that cause late-onset AD are likely to occur years, if not decades prior to diagnosis. Here, we select a subset of the Generation Scotland: Scottish Family Health Study cohort in a likely preclinical age-range of 60-70 years (subset n = 3,495 with cognitive and genetic data). We test for cognitive differences by polygenic risk scores for AD. The polygenic scores are constructed using all available SNPs, excluding those within a 500 kb distance of the APOE locus...
February 10, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28222201/linkage-and-mapping-of-quantitative-trait-loci-associated-with-angular-leaf-spot-and-powdery-mildew-resistance-in-common-beans
#2
Denis Bassi, Boris Briñez, Juliana Santa Rosa, Paula Rodrigues Oblessuc, Caléo Panhoca de Almeida, Stella Maris Nucci, Larissa Chariel Domingos da Silva, Alisson Fernando Chiorato, Rosana Pereira Vianello, Luis Eduardo Aranha Camargo, Matthew Wohlgemuth Blair, Luciana Lasry Benchimol-Reis
Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis...
February 20, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28222154/a-non-synonymous-snp-with-the-allele-frequency-correlated-with-the-altitude-may-contribute-to-the-hypoxia-adaptation-of-tibetan-chicken
#3
Sichen Li, Diyan Li, Xiaoling Zhao, Yan Wang, Huadong Yin, Lanyun Zhou, Chengling Zhong, Qing Zhu
The hypoxia adaptation to high altitudes is of considerable interest in the biological sciences. As a breed with adaptability to highland environments, the Tibetan chicken (Gallus gallus domestics), provides a biological model to search for genetic differences between high and lowland chickens. To address mechanisms of hypoxia adaptability at high altitudes for the Tibetan chicken, we focused on the Endothelial PAS domain protein 1 (EPAS1), a key regulatory factor in hypoxia responses. Detected were polymorphisms of EPAS1 exons in 157 Tibetan chickens from 8 populations and 139 lowland chickens from 7 breeds...
2017: PloS One
https://www.readbyqxmd.com/read/28222112/genome-wide-study-of-resistant-hypertension-identified-from-electronic-health-records
#4
Logan Dumitrescu, Marylyn D Ritchie, Joshua C Denny, Nihal M El Rouby, Caitrin W McDonough, Yuki Bradford, Andrea H Ramirez, Suzette J Bielinski, Melissa A Basford, High Seng Chai, Peggy Peissig, David Carrell, Jyotishman Pathak, Luke V Rasmussen, Xiaoming Wang, Jennifer A Pacheco, Abel N Kho, M Geoffrey Hayes, Martha Matsumoto, Maureen E Smith, Rongling Li, Rhonda M Cooper-DeHoff, Iftikhar J Kullo, Christopher G Chute, Rex L Chisholm, Gail P Jarvik, Eric B Larson, David Carey, Catherine A McCarty, Marc S Williams, Dan M Roden, Erwin Bottinger, Julie A Johnson, Mariza de Andrade, Dana C Crawford
Resistant hypertension is defined as high blood pressure that remains above treatment goals in spite of the concurrent use of three antihypertensive agents from different classes. Despite the important health consequences of resistant hypertension, few studies of resistant hypertension have been conducted. To perform a genome-wide association study for resistant hypertension, we defined and identified cases of resistant hypertension and hypertensives with treated, controlled hypertension among >47,500 adults residing in the US linked to electronic health records (EHRs) and genotyped as part of the electronic MEdical Records & GEnomics (eMERGE) Network...
2017: PloS One
https://www.readbyqxmd.com/read/28222097/a-genome-wide-association-study-identifies-a-lncrna-as-risk-factor-for-pathological-inflammatory-responses-in-leprosy
#5
Vinicius M Fava, Jeremy Manry, Aurélie Cobat, Marianna Orlova, Nguyen Van Thuc, Milton O Moraes, Carolinne Sales-Marques, Mariane M A Stefani, Ana Carla P Latini, Andrea F Belone, Vu Hong Thai, Laurent Abel, Alexandre Alcaïs, Erwin Schurr
Leprosy Type-1 Reactions (T1Rs) are pathological inflammatory responses that afflict a sub-group of leprosy patients and result in peripheral nerve damage. Here, we employed a family-based GWAS in 221 families with 229 T1R-affect offspring with stepwise replication to identify risk factors for T1R. We discovered, replicated and validated T1R-specific associations with SNPs located in chromosome region 10p21.2. Combined analysis across the three independent samples resulted in strong evidence of association of rs1875147 with T1R (p = 4...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28221857/listeria-monocytogenes-isolates-carrying-virulence-attenuating-mutations-in-internalin-a-are-commonly-isolated-from-ready-to-eat-food-processing-plant-and-retail-environments
#6
A VAN Stelten, A R Roberts, C S Manuel, K K Nightingale
Listeria monocytogenes is a human foodborne pathogen that may cause an invasive disease known as listeriosis in susceptible individuals. Internalin A (InlA; encoded by inlA) is a virulence factor that facilitates crossing of host cell barriers by L. monocytogenes . At least 19 single nucleotide polymorphisms (SNPs) in inlA that result in a premature stop codon (PMSC) have been described worldwide. SNPs leading to a PMSC in inlA have been shown to be causally associated with attenuated virulence. L. monocytogenes pathogens carrying virulence-attenuating (VA) mutations in inlA have been commonly isolated from ready-to-eat (RTE) foods but rarely have been associated with human disease...
October 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28220806/on-the-long-term-stability-of-clines-in-some-metabolic-genes-in-drosophila-melanogaster
#7
Rodrigo Cogni, Kate Kuczynski, Spencer Koury, Erik Lavington, Emily L Behrman, Katherine R O'Brien, Paul S Schmidt, Walter F Eanes
Very little information exists for long-term changes in genetic variation in natural populations. Here we take the unique opportunity to compare a set of data for SNPs in 15 metabolic genes from eastern US collections of Drosophila melanogaster that span a large latitudinal range and represent two collections separated by 12 to 13 years. We also expand this to a 22-year interval for the Adh gene and approximately 30 years for the G6pd and Pgd genes. During these intervals, five genes showed a statistically significant change in average SNP allele frequency corrected for latitude...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220744/burden-genotype-and-phenotype-profiles-of-adult-patients-with-sickle-cell-disease-in-cape-town-south-africa
#8
G D Pule, K Mnica, M Joubert, S Mowla, N Novitsky, A Wonkam
BACKGROUND: An exponential increase in the number of sickle cell disease (SCD) patients in paediatric services in Cape Town, South Africa, has been reported. The trend in adult/adolescent services has not been investigated. OBJECTIVES: To evaluate epidemiological trends of SCD and the profile of patients affected by SCD attending the Haematology Clinic at Groote Schuur Hospital (GSH), Cape Town. METHODS: (i) A retrospective review of the number of SCD patients over the past 20 years; (ii) a cross-sectional analysis of clinical and haematological characteristics of SCD patients; and (iii) molecular analysis of the haemoglobin S mutation, the haplotype in the β-globin-like genes cluster, the 3...
January 30, 2017: South African Medical Journal, Suid-Afrikaanse Tydskrif Vir Geneeskunde
https://www.readbyqxmd.com/read/28220687/environmental-factors-seven-gwas-identified-susceptibility-loci-and-risk-of-gastric-cancer-and-its-precursors-in-a-chinese-population
#9
Meng Cai, Shuyang Dai, Wanqing Chen, Changfa Xia, Lingeng Lu, Shuguang Dai, Jun Qi, Minjie Wang, Meilin Wang, Lanping Zhou, Fuhua Lei, Tingting Zuo, Hongmei Zeng, Xiaohang Zhao
Gene-environment interactions may increase gastric cancer (GC) risk. Seven susceptibility loci identified by genome-wide association studies (GWASs) suggest that genetic factors play a role in gastric carcinogenesis. Meanwhile, Helicobacter pylori (H. pylori) infection, smoking, and alcohol drinking are also important environmental factors for gastric cancer. However, studies to explore the role of gene-environment interactions in gastric carcinogenesis, and particularly the relationship between the seven susceptibility loci and their potential interactions with H...
February 21, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28220389/polymorphisms-in-key-bone-modulator-cytokines-genes-influence-bisphosphonates-therapy-in-postmenopausal-women
#10
C A D Lima, N R Javorski, A P O Souza, A D Barbosa, A P M C Valença, S Crovella, P R E Souza, J De Azevedo Silva, P Sandrin-Garcia
Osteoporosis is a multifactorial and debilitating disease resulting from decreased bone mineral density (BMD) and loss of tissue microarchitecture. Ineffective therapies may lead to bone fractures and subsequent death. Single nucleotide polymorphisms (SNPs) in key immune regulator genes have been associated with therapeutic response to bisphosphonates, which are the first therapeutic line of choice for osteoporosis. However, cytokine pathways and their relation with therapeutic adhesion remain to be fully elucidated...
February 21, 2017: Inflammopharmacology
https://www.readbyqxmd.com/read/28220208/abcb4-missense-mutations-d243a-k435t-g535d-i490t-r545c-and-s978p-significantly-impair-the-lipid-floppase-and-likely-predispose-to-secondary-pathologies-in-the-human-population
#11
Edward J Andress, Michael Nicolaou, Farrell McGeoghan, Kenneth J Linton
Bile salts are natural detergents required to solubilise dietary fat and lipid soluble vitamins. They are synthesised in hepatocytes and secreted into the luminal space of the biliary tree by the bile salt export pump (BSEP), an ATP-binding cassette (ABC) transporter in the canalicular membrane. BSEP deficiency causes cytotoxic accumulation of bile salts in the hepatocyte that results in mild-to-severe forms of cholestasis. The resulting inflammation can also progress to hepatocellular cancer via a novel mechanism involving upregulation of proliferative signalling pathways...
February 20, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28220206/a-user-guide-to-the-brassica-60k-illumina-infinium%C3%A2-snp-genotyping-array
#12
REVIEW
Annaliese S Mason, Erin E Higgins, Rod J Snowdon, Jacqueline Batley, Anna Stein, Christian Werner, Isobel A P Parkin
The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies...
February 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28220155/specificity-of-snp-detection-with-molecular-beacons-is-improved-by-stem-and-loop-separation-with-spacers
#13
Valentina M Farzan, Mikhail L Markelov, Alexander Yu Skoblov, German A Shipulin, Timofei S Zatsepin
Molecular beacons (MBs) are valuable tools in molecular biology, clinical diagnostics and analytical chemistry. Here we describe a novel approach for the design of MBs with nucleotide or non-nucleotide linkers between the stem and loop regions. Such modified MBs have significantly improved specificity and performance for single nucleotide polymorphism (SNP) detection. These advantages are especially distinct, when compared to the classic MBs, in the case of possible interactions between the stem and loop regions...
February 21, 2017: Analyst
https://www.readbyqxmd.com/read/28220139/genome-wide-single-nucleotide-polymorphism-discovery-and-the-construction-of-a-high-density-genetic-map-for-melon-cucumis-melo-l-using-genotyping-by-sequencing
#14
Che-Wei Chang, Yu-Hua Wang, Chih-Wei Tung
Although genotyping-by-sequencing (GBS) enables the efficient and low-cost generation of large numbers of markers, the utility of resultant genotypes are limited, because they are enormously error-prone and contain high proportions of missing data. In this study, we generated single nucleotide polymorphism (SNP) markers for 109 recombinant inbred lines of melon (Cucumis melo L.) using the GBS approach and ordered them according to their physical position on the draft double haploid line DHL92 genome. Next, by investigating associations between these SNPs, we discovered that some segments on the physical map conflict with linkage relationships...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28219832/the-role-of-single-nucleotide-polymorphisms-contained-in-proinflammatory-cytokine-genes-in-the-development-of-congenital-infection-with-human-cytomegalovirus-in-fetuses-and-neonates
#15
Wioletta Wujcicka, Jan Wilczyński, Dorota Nowakowska
PURPOSE: The research project targeted the distribution of genotypes, alleles and haplotypes in single nucleotide polymorphisms (SNPs) within the interleukin (IL) 1A, IL1B, IL6, IL12B and TNFA genes, in fetuses and neonates, congenitally infected with human cytomegalovirus (HCMV), and among uninfected controls. METHODS: The study included 20 fetuses and neonates with congenital HCMV infection and 31 control individuals. The presence and amount of viral DNA was determined by real-time PCR assay for UL55 gene...
February 17, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28219716/genetic-regulation-of-differentially-methylated-genes-in-visceral-adipose-tissue-of-severely-obese-men-discordant-for-the-metabolic-syndrome
#16
Frédéric Guénard, André Tchernof, Yves Deshaies, Simon Biron, Odette Lescelleur, Laurent Biertho, Simon Marceau, Louis Pérusse, Marie-Claude Vohl
A genetic influence on methylation levels has been reported and methylation quantitative trait loci (meQTL) have been identified in various tissues. The contribution of genetic and epigenetic factors in the development of the metabolic syndrome (MetS) has also been noted. To pinpoint candidate genes for testing the association of SNPs with MetS and its components, we aimed to evaluate the contribution of genetic variations to differentially methylated CpG sites in severely obese men discordant for MetS. A genome-wide differential methylation analysis was conducted in visceral adipose tissue (VAT) of 31 severely obese men discordant for MetS (16 with and 15 without MetS) and identified ∼17,800 variable CpG sites...
February 2, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28219444/a-functional-snp-associated-with-atopic-dermatitis-controls-cell-type-specific-methylation-of-the-vstm1-gene-locus
#17
Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H A Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun, Astrid Irwanto, Benjamin P Fairfax, Vivek Naranbhai, John E A Common, Mark Tang, Chin Keh Chuang, Marjo-Riitta Jarvelin, Julian C Knight, Xuejun Zhang, Fook Tim Chew, Shyam Prabhakar, Liu Jianjun, De Yun Wang, Francesca Zolezzi, Michael Poidinger, E Birgitte Lane, Linde Meyaard, Olaf Rötzschke
BACKGROUND: Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under investigation. We previously identified signal inhibitory receptor on leukocytes-1 (SIRL-1) as a powerful regulator of human innate immune cell function. While it is constitutively high expressed on neutrophils, on monocytes the SIRL-1 surface expression varies strongly between individuals...
February 20, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28218639/genetic-variations-as-modifying-factors-to-dietary-zinc-requirements-a-systematic-review
#18
REVIEW
Kaitlin J Day, Melissa M Adamski, Aimee L Dordevic, Chiara Murgia
Due to reduced cost and accessibility, the use of genetic testing has appealed to health professionals for personalising nutrition advice. However, translation of the evidence linking polymorphisms, dietary requirements, and pathology risk proves to be challenging for nutrition and dietetic practitioners. Zinc status and polymorphisms of genes coding for zinc-transporters have been associated with chronic diseases. The present study aimed to systematically review the literature to assess whether recommendations for zinc intake could be made according to genotype...
February 17, 2017: Nutrients
https://www.readbyqxmd.com/read/28218607/tet2-asxl1-idh1-and-idh2-single-nucleotide-polymorphisms-in-turkish-patients-with-chronic-myeloproliferative-neoplasms
#19
Nur Soyer, Burçin Tezcanlı Kaymaz, Melda Cömert Özkan, Çağdaş Aktan, Ali Şahin Küçükaslan, Fahri Şahin, Buket Kosova, Güray Saydam
We aimed to determine the genotype distribution, allele frequency and prognostic impact of IDH1/2(Isocitrate dehydrogenase), TET2(Ten-Eleven-Translocation2) and ASXL1(Additional Sex Combs-Like 1) single nucleotide polymorphisms (SNPs) in MPNs. TET2(rs763480), ASXL1(rs2208131) and IDH1(rs11554137) variant homozygous genotype frequencies were 1.5%, 9.2% and 2.3%, respectively. No IDH2 SNP was identified. IDH1 and TET2 frequencies were 5% in ET and 1.7% in ET, 5% in PMF, respectively. ASXL1 frequencies were 8...
February 20, 2017: Turkish Journal of Haematology: Official Journal of Turkish Society of Haematology
https://www.readbyqxmd.com/read/28217939/pitx2-dependent-gene-regulation-in-atrial-fibrillation-and-rhythm-control
#20
Fahima Syeda, Paulus Kirchhof, Larissa Fabritz
Atrial fibrillation (AF) is a common arrhythmia. Better prevention and treatment of AF are needed to reduce AF-associated morbidity and mortality. There are several major mechanisms that cause AF in patients, including a genetic predisposition to develop AF. Genome-wide association studies (GWAS) have identified genetic variants associated with AF populations, with the strongest hits clustering on chromosome 4q25, close to the gene for the homeobox transcription factor PITX2. The effect of these common gene variants on cardiac PITX2 mRNA is currently under study...
February 19, 2017: Journal of Physiology
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