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https://www.readbyqxmd.com/read/29352517/mirna-binding-site-variants-of-type-2-diabetes-candidate-loci-predispose-to-gestational-diabetes-mellitus-in-chinese-han-women
#1
Xiaojing Wang, Wei Li, Liangkun Ma, Fan Ping, Juntao Liu, Xueyan Wu, Jiangfeng Mao, Xi Wang, Min Nie
AIMS/INTRODUCTION: Emerging evidence suggested that the genetic background of GDM was analogous to T2DM. In contrast to T2DM, the genetic studies for GDM were limited. Accordingly, the aim of this study was to extensively explore the influence of miR-binding-SNPs in T2DM candidate loci on GDM susceptibility in Chinese. METERIALS AND METHODS: A total of 839 GDM and 900 controls were enrolled. Six miR-binding-SNPs were selected from 30 T2DM susceptibility loci and genotyped using TaqMan allelic discrimination assays...
January 20, 2018: Journal of Diabetes Investigation
https://www.readbyqxmd.com/read/29352395/association-between-crp-genetic-diversity-and-bipolar-disorder-comorbid-complications
#2
Wahid Boukouaci, José Oliveira, Bruno Etain, Meriem Bennabi, Christina Mariaselvam, Nora Hamdani, Céline Manier, Djaouida Bengoufa, Frank Bellivier, Chantal Henry, Jean-Pierre Kahn, Dominique Charron, Rajagopal Krishnamoorthy, Marion Leboyer, Ryad Tamouza
BACKGROUND: Chronic low-grade inflammation is believed to contribute, at least in a subset of patients, to the development of bipolar disorder (BD). In this context, the most investigated biological marker is the acute phase response molecule, C-reactive protein (CRP). While the genetic diversity of CRP was amply studied in various pathological settings, little is known in BD. METHODS: 568 BD patients along with 163 healthy controls (HC) were genotyped for the following single-nucleotide polymorphisms (SNPs) on the CRP gene: intron rs1417938 (+ 29) T/A, 3'-UTR rs1130864 (+ 1444) G/A, and downstream rs1205 (+ 1846) (C/T)...
January 20, 2018: International Journal of Bipolar Disorders
https://www.readbyqxmd.com/read/29352323/identification-of-a-molecular-marker-tightly-linked-to-bacterial-wilt-resistance-in-tomato-by-genome-wide-snp-analysis
#3
Boyoung Kim, In Sun Hwang, Hyung Jin Lee, Je Min Lee, Eunyoung Seo, Doil Choi, Chang-Sik Oh
Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29352185/genetic-fingerprinting-of-salmon-louse-lepeophtheirus-salmonis-populations-in-the-north-east-atlantic-using-a-random-forest-classification-approach
#4
A Jacobs, M De Noia, K Praebel, Ø Kanstad-Hanssen, M Paterno, D Jackson, P McGinnity, A Sturm, K R Elmer, M S Llewellyn
Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352173/maize-chlorotic-mottle-virus-exhibits-low-divergence-between-differentiated-regional-sub-populations
#5
Luke Braidwood, Diego F Quito-Avila, Darlene Cabanas, Alberto Bressan, Anne Wangai, David C Baulcombe
Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of maize chlorotic mottle virus with Potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352099/smoking-and-parkinson-disease-evidence-for-gene-by-smoking-interactions
#6
Pei-Chen Lee, Ismaïl Ahmed, Marie-Anne Loriot, Claire Mulot, Kimberly C Paul, Jeff M Bronstein, Beate Ritz, Alexis Elbaz
OBJECTIVE: To investigate whether cigarette smoking interacts with genes involved in individual susceptibility to xenobiotics for the risk of Parkinson disease (PD). METHODS: Two French population-based case-control studies (513 patients, 1,147 controls) were included as a discovery sample to examine gene-smoking interactions based on 3,179 single nucleotide polymorphisms (SNPs) in 289 genes involved in individual susceptibility to xenobiotics. SNP-by-cigarette smoking interactions were tested in the discovery sample through an empirical Bayes (EB) approach...
January 19, 2018: Neurology
https://www.readbyqxmd.com/read/29352079/identification-and-validation-of-a-new-source-of-low-grain-cadmium-accumulation-in-durum-wheat
#7
Atena Oladzad Abbasabadi, Ajay Kumar, Seyed Pirseyedi, Evan Salsman, Marina Dobrydina, Roshan Sharma Poudel, Wesam A AbuHammad, Shiaoman Chao, Justin D Faris, Elias M Elias
Cadmium (Cd) is a heavy metal that has no known biological function and is toxic for many living organisms. The maximum level of Cd concentration allowed in the international market for wheat grain is 0.2 mg kg-1. Because phenotyping for Cd uptake is expensive and time consuming, molecular markers associated with genes conferring low Cd uptake would expedite selection and lead to the development of durum cultivars with reduced Cd concentrations. Here, we identified single nucleotide polymorphisms (SNPs) associated with a novel low Cd uptake locus in the durum experimental line D041735, which has hexaploid common wheat in its pedigree...
January 19, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29351800/drug-resistance-genes-pvcrt-o-and-pvmdr-1-polymorphism-in-patients-from-malaria-endemic-south-western-coastal-region-of-india
#8
Shiny Joy, Benudhar Mukhi, Susanta K Ghosh, Rajeshwara N Achur, D Channe Gowda, Namita Surolia
BACKGROUND: Malaria is highly prevalent in many parts of India and is mostly caused by the parasite species Plasmodium vivax followed by Plasmodium falciparum. Chloroquine (CQ) is the first-line treatment for blood stage P. vivax parasites, but cases of drug resistance to CQ have been reported from India. One of the surveillance strategies which is used to monitor CQ drug resistance, is the analysis of single nucleotide polymorphisms (SNPs) of the associated gene markers. Susceptibility to CQ can also be determined by copy number assessment of multidrug resistant gene (mdr-1)...
January 19, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29351603/the-unexpected-function-of-a-flavin-dependent-oxidoreductase-fox-from-variovorax-paradoxus-tbea6
#9
Christina Meinert, Marc Schürmann, Jan-Eike Domeyer, Anja Poehlein, Rolf Daniel, Alexander Steinbüchel
3,3'-Thiodipropionic acid (TDP) is used as an additive in food and cosmetic industry and as precursor substrate for biotechnical polythioester production. Its catabolism was investigated in Variovorax paradoxus TBEA6 previous to this study. It was reported that the insertion of the transposon Tn5::mob into a gene showing high homology to flavin-dependent oxidoreductases (fox) resulted in impaired growth with TDP. Therefore, it was assumed that the initial cleavage of TDP is catalyzed by an FAD-dependent oxidoreductase (Fox, VPARA_05580)...
January 17, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29351600/gtc-how-to-maintain-huge-genotype-collections-in-a-compressed-form
#10
Agnieszka Danek, Sebastian Deorowicz
Motivation: Nowadays, genome sequencing is frequently used in many research centers. In projects, such as the Haplotype Reference Consortium or the Exome Aggregation Consortium, huge databases of genotypes in large populations are determined. Together with the increasing size of these collections, the need for fast and memory frugal ways of representation and searching in them becomes crucial. Results: We present GTC, a novel compressed data structure for representation of huge collections of genetic variation data...
January 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29350248/natural-variation-and-genetic-make-up-of-leaf-blade-area-in-spring-barley
#11
Ahmad M Alqudah, Helmy M Youssef, Andreas Graner, Thorsten Schnurbusch
GWAS analysis for leaf blade area (LA) revealed intriguing genomic regions associated with putatively novel QTL and known plant stature-related phytohormone and sugar-related genes. Despite long-standing studies in the morpho-physiological characters of leaf blade area (LA) in cereal crops, advanced genetic studies to explore its natural variation are lacking. The importance of modifying LA in improving cereal grain yield and the genes controlling leaf traits have been well studied in rice but not in temperate cereals...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29349811/genetic-analysis-of-interleukin-18-gene-polymorphisms-in-alopecia-areata
#12
Sumeyya Deniz Celik, Omer Ates
BACKGROUND: Alopecia areata (AA), which appears as nonscarring hair shedding on any hair-bearing area, is a common organ-specific autoimmune condition. Cytokines have important roles in the development of AA. Interleukin (IL) 18 is a significant proinflammatory cytokine that was found higher in the patients with AA. We aimed to investigate whether the IL-18 (rs187238 and rs1946518) single nucleotide polymorphisms (SNPs) may be associated with AA and/or clinical outcome of patients with AA in Turkish population...
January 18, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29348888/the-association-analysis-of-tlr2-and-tlr4-gene-with-tuberculosis-in-the-tibetan-chinese-population
#13
Xin Xue, Yi Qiu, Dong Jiang, Tianbo Jin, Mengdan Yan, Xikang Zhu, Yonglie Chu
Background: The present study was undertaken to explore the relationship of Toll-like receptor (TLR) 2, TLR4 genes polymorphisms with Pulmonary tuberculosis (PTB) risk in a sample of Chinese population. Methods: For this study, we recruited 467 subjects with PTB and 504 healthy subjects from a Tibetan population living in near or in Xi'an, China. Association analyses of single-nucleotide polymorphisms (SNPs) in TLR2 and TLR4 were performed with SPSS Statistics (version 17...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348838/single-nucleotide-polymorphisms-in-znf208-are-associated-with-increased-risk-for-hbv-in-chinese-people
#14
Hengxin Li, Jun Chen, RuiZhi Zhang, Ran Xu, Zhe Zhang, Le Ren, Qi Yang, Yumei Tian, Daxu Li
Single nucleotide polymorphisms (SNPs) in ZNF208 may be associated with susceptibility to Hepatitis B virus (HBV). In the current study, we analyzed the association between ZNF208 SNPs and risk of HBV in 242 HBV patients and 300 healthy subjects from the Xi'an area of Chinese Han Population. Of the five SNPs examined, rs2188971 (OR: 1.36, 95% CI: 1.04-1.76, P = 0.022), rs8103163 (OR: 1.40, 95% CI: 1.08-1.82, P = 0.010) and rs7248488 (OR: 1.38, 95% CI: 1.07-1.79, P = 0.014) were correlated with HBV susceptibility based on Chi-square tests...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348692/genome-wide-search-for-higher-order-epistasis-as-modifiers-of-treatment-effects-on-bone-mineral-density-in-childhood-cancer-survivors
#15
Cindy Im, Kirsten K Ness, Sue C Kaste, Wassim Chemaitilly, Wonjong Moon, Yadav Sapkota, Russell J Brooke, Melissa M Hudson, Leslie L Robison, Yutaka Yasui, Carmen L Wilson
Single-nucleotide polymorphisms (SNPs) contributing to interactions between regulatory elements that modulate gene transcription may explain some of the uncharacterized variation for complex traits. We explored this hypothesis among 856 adult survivors of pediatric cancer exposed to curative treatments that adversely affect bone mineral density (BMD). To restrict our search to interactions among SNPs in regulatory elements, our analysis considered 75523 SNPs mapped to putative promoter or enhancer regions. In anticipation that power to detect higher order epistasis would be low using an exhaustive search and a Bonferroni-corrected threshold for genome-wide significance (e...
January 18, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29348398/association-study-of-polymorphisms-in-genes-relevant-to-vitamin-b12-and-folate-metabolism-with-childhood-autism-spectrum-disorder-in-a-han-chinese-population
#16
Zengyu Zhang, Lianfang Yu, Sufang Li, Jun Liu
BACKGROUND Both genetic and environmental factors play a role in the development of autism spectrum disorder (ASD). This case-control study examined the association between childhood ASD and single-nucleotide polymorphisms (SNPs) in genes involved with vitamin B12 and folate metabolism. MATERIAL AND METHODS Genotypes of transcobalamin 2 (TCN2) rs1801198, methionine synthase (MTR) rs1805087, methionine synthase reductase (MTRR) rs1801394, and methylene tetrahydrofolate reductase (MTHFR) rs1801133 were examined in 201 children with ASD and 200 healthy controls from the Han Chinese population...
January 19, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29346646/the-evolutionary-history-of-nebraska-deer-mice-local-adaptation-in-the-face-of-strong-gene-flow
#17
Susanne P Pfeifer, Stefan Laurent, Vitor C Sousa, Catherine R Linnen, Matthieu Foll, Laurent Excoffier, Hopi E Hoekstra, Jeffrey D Jensen
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29346588/genome-sequencing-of-museum-specimens-reveals-rapid-changes-in-the-genetic-composition-of-honey-bees-in-california
#18
Julie M Cridland, Santiago R Ramirez, Cheryl A Dean, Amber Sciligo, Neil D Tsutsui
The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years...
January 15, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29346564/genome-wide-comparison-of-allele-specific-gene-expression-between-african-and-european-populations
#19
Lei Tian, Asifullah Khan, Zhilin Ning, Kai Yuan, Chao Zhang, Haiyi Lou, Yuan Yuan, Shuhua Xu
Transcriptomic diversity across human populations reflects differential regulatory mechanisms. Allelic-imbalanced gene expression is a genetic regulatory mechanism that contributes to human phenotypic variation. To systematically investigate genome-wide allele-specific expression (ASE), we analyzed RNA-Seq data from European and African populations provided by the Geuvadis project. We identified 17 sites in 13 genes showing ASE in both Europeans and Africans, and 19 sites in 18 genes showing population-specific ASE, including both novel and known ASE signals...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29346471/use-of-single-nucleotide-polymorphisms-and-mammographic-density-plus-classic-risk-factors-for-breast-cancer-risk-prediction
#20
Elke M van Veen, Adam R Brentnall, Helen Byers, Elaine F Harkness, Susan M Astley, Sarah Sampson, Anthony Howell, William G Newman, Jack Cuzick, D Gareth R Evans
Importance: Single-nucleotide polymorphisms (SNPs) have demonstrated an association with breast cancer susceptibility, but there is limited evidence on how to incorporate them into current breast cancer risk prediction models. Objective: To determine whether a panel of 18 SNPs (SNP18) may be used to predict breast cancer in combination with classic risk factors and mammographic density. Design, Setting, and Participants: This cohort study enrolled a subcohort of 9363 women, aged 46 to 73 years, without a previous breast cancer diagnosis from the larger prospective cohort of the PROCAS study (Predicting Risk of Cancer at Screening) specifically to evaluate breast cancer risk-assessment methods...
January 18, 2018: JAMA Oncology
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