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Single nucleotide polymorphisms (SNPs)

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https://www.readbyqxmd.com/read/29777939/variation-of-genes-encoding-kat1-aadat-and-ido1-as-a-potential-risk-of-depression-development
#1
Paulina Wigner, Piotr Czarny, Ewelina Synowiec, Michał Bijak, Monika Talarowska, Piotr Galecki, Janusz Szemraj, Tomasz Sliwinski
Numerous data suggests that the disorders of tryptophan catabolites (TRYCATs) pathway, including a decreased level of tryptophan or evaluated concentration of harmful TRYCATs -kynurenine, quinolinic acid, 3-hydroxyanthranilic acid, 3-hydroxytryptophan - may cause the occurrence of DD symptoms. In this work, we assessed the relationship between single-nucleotide polymorphisms (SNPs) of KAT1, KAT2 and IDO1 gene encoding, and the risk of depression development. Our study was performed on the DNA isolated from peripheral blood of 281 depressed patients and 236 controls...
May 16, 2018: European Psychiatry: the Journal of the Association of European Psychiatrists
https://www.readbyqxmd.com/read/29777907/novel-snps-of-wnk1-and-akr1c3-are-associated-with-preeclampsia
#2
Cheng-Juan Sun, Lin Li, Xueyan Li, Wei-Yuan Zhang, Xiao-Wei Liu
Preeclampsia is a hypertensive disorder of pregnancy and is one of the most common causes of poor perinatal outcomes. Preeclampsia increases the risk of hypertension in the future. Variants of WNK1 (lysine deficient protein kinase 1), ADRB2 (β2 adrenergic receptor), NEDD4L (ubiquitin-protein ligase NEDD4-like), KLK1 (kallikrein 1) contribute to hypertension, and AKR1C3 (aldo-keto reductase family1 member C3), is associated with preeclampsia. The association of single nucleotide polymorphisms (SNPs) in these five candidate preeclampsia susceptibility genes and the related traits in Chinese individuals were investigated...
May 16, 2018: Gene
https://www.readbyqxmd.com/read/29777226/genetic-contribution-to-waist-to-hip-ratio-in-mexican-children-and-adolescents-based-on-12-loci-validated-in-european-adults
#3
Michelle Turcotte, Arkan Abadi, Jesus Peralta-Romero, Fernando Suarez, Hudson Reddon, Jaime Gomez-Zamudio, Ana I Burguete-Garcia, Miguel Cruz, David Meyre
BACKGROUND/OBJECTIVES: The prevalence of abdominal obesity in Mexican children has risen dramatically in the past decade. Genome-wide association studies (GWAS) for waist-to-hip ratio (WHR) performed predominantly in European descent adult  populations have identified multiple single-nucleotide polymorphisms (SNPs) with larger effects in women. The contribution of these SNPs to WHR in non-European children is unknown. SUBJECTS/METHODS: Mexican children and adolescents (N = 1421, 5-17 years) were recruited in Mexico City...
March 13, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29777116/genetic-risk-score-of-common-genetic-variants-for-impaired-fasting-glucose-and-newly-diagnosed-type-2-diabetes-influences-oxidative-stress
#4
Minjoo Kim, Minkyung Kim, Limin Huang, Sun Ha Jee, Jong Ho Lee
We tested the hypothesis that the cumulative effects of common genetic variants related to elevated fasting glucose are collectively associated with oxidative stress. Using 25 single nucleotide polymorphisms (SNPs), a weighted genetic risk score (wGRS) was constructed by summing nine risk alleles based on nominal significance and a consistent effect direction in 1,395 controls and 718 patients with impaired fasting glucose (IFG) or newly diagnosed type 2 diabetes. All the participants were divided into the following three groups: low-wGRS, middle-wGRS, and high-wGRS groups...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29776379/development-of-a-rapid-field-applicable-molecular-diagnostic-for-knockdown-resistance-kdr-markers-in-an-gambiae
#5
Vera T Unwin, Shaun Ainsworth, Emily J Rippon, El Hadji Amadou Niang, Mark J I Paine, David Weetman, Emily R Adams
BACKGROUND: The spread of insecticide resistance (IR) is a major threat to vector control programmes for mosquito-borne diseases. Early detection of IR using diagnostic markers could help inform these programmes, especially in remote locations where gathering reliable bioassay data is challenging. Most current molecular tests for genetic IR markers are only suitable for use in well-equipped laboratory settings. There is an unmet need for field-applicable diagnostics. METHODS: A single-cartridge test was designed to detect key IR mutations in the major African vector of malaria, Anopheles gambiae...
May 18, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29776335/using-genomic-relationship-likelihood-for-parentage-assignment
#6
Kim E Grashei, Jørgen Ødegård, Theo H E Meuwissen
BACKGROUND: Parentage assignment is usually based on a limited number of unlinked, independent genomic markers (microsatellites, low-density single nucleotide polymorphisms (SNPs), etc.). Classical methods for parentage assignment are exclusion-based (i.e. based on loci that violate Mendelian inheritance) or likelihood-based, assuming independent inheritance of loci. For true parent-offspring relations, genotyping errors cause apparent violations of Mendelian inheritance. Thus, the maximum proportion of such violations must be determined, which is complicated by variable call- and genotype error rates among loci and individuals...
May 18, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29775696/tph2-polymorphisms-across-the-spectrum-of-psychiatric-morbidity-a-systematic-review-and-meta-analysis
#7
REVIEW
Koen Willem Ottenhof, Mari Sild, Mélissa Luce Lévesque, Henricus Gerardus Ruhé, Linda Booij
Tryptophan hydroxylase 2 (TPH2) is the rate-limiting enzyme in brain serotonin synthesis. The TPH2 gene has frequently been investigated in relation to psychiatric morbidity. The aim of the present review is to integrate results from association studies between TPH2 single nucleotide polymorphisms (SNPs) and various psychiatric disorders, which we furthermore quantified with meta-analysis. We reviewed 166 studies investigating 69 TPH2 SNPs in a broad range of psychiatric disorders, including over 30,000 patients...
May 15, 2018: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/29774466/rs2227982-and-rs2227981-in-pdcd1-gene-are-functional-snps-associated-with-t1d-risk-in-east-asian
#8
Yong Gu, Lei Xiao, Wei Gu, Shu Chen, Yingjie Feng, Jian Wang, Zhixiao Wang, Yun Cai, Heng Chen, Xinyu Xu, Yun Shi, Mei Zhang, Kuanfeng Xu, Tao Yang
AIMS: To investigate whether PDCD1 gene polymorphisms are functional, and their associations with T1D risk and related clinical characteristics. METHODS: A total of 3060 Chinese Han individuals (1019 T1D patients and 2041 healthy controls) were genotyped for 4 tag single nucleotide polymorphisms (SNPs) within the PDCD1 region (rs2227982, rs7421861, rs10204525, and rs6710479) and another most studied synonymous SNP, rs2227981. In addition, 251 healthy individuals underwent an oral glucose tolerance test (OGTT); measures of insulin release and sensitivity were estimated from insulinogenic, BIGTT, Matsuda...
May 17, 2018: Acta Diabetologica
https://www.readbyqxmd.com/read/29774036/the-pattern-and-distribution-of-induced-mutations-in-j-curcas-using-reduced-representation-sequencing
#9
Fatemeh Maghuly, Stephan Pabinger, Julie Krainer, Margit Laimer
Mutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonate (EMS) induced mutants and 14 wild-type accessions of Jatropha curcas for the detection of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels) by two different approaches (nGBS and ddGBS) on an Illumina HiSeq 2000 sequencer...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29773897/fine-scale-temperature-associated-genetic-structure-between-inshore-and-offshore-populations-of-sea-scallop-placopecten-magellanicus
#10
Sarah J Lehnert, Claudio DiBacco, Mallory Van Wyngaarden, Nicholas W Jeffery, J Ben Lowen, Emma V A Sylvester, Brendan F Wringe, Ryan R E Stanley, Lorraine C Hamilton, Ian R Bradbury
In the northwest Atlantic Ocean, sea scallop (Placopecten magellanicus) has been characterized by a latitudinal genetic cline with a breakpoint between northern and southern genetic clusters occurring at ~45°N along eastern Nova Scotia, Canada. Using 96 diagnostic single-nucleotide polymorphisms (SNPs) capable of discriminating between northern and southern clusters, we examined fine-scale genetic structure of scallops among 27 sample locations, spanning the largest geographic range evaluated in this species to date (~37-51°N)...
May 17, 2018: Heredity
https://www.readbyqxmd.com/read/29773828/single-nucleotide-polymorphisms-in-the-g-protein-coupled-receptor-kinase-5-grk5-gene-are-associated-with-plasma-ldl-cholesterol-levels-in-humans
#11
Stefan Z Lutz, Mathias Falcenberg, Fausto Machicao, Andreas Peter, Martin Kächele, Elko Randrianarisoa, Angela Lehn-Stefan, Robert Wagner, Jürgen Machann, Fritz Schick, Martin Heni, Axel Ullrich, Andreas Fritsche, Norbert Stefan, Hans-Ulrich Häring, Harald Staiger, Konstantinos Kantartzis
Genetically modified mice models suggest an important role for G-protein-coupled receptor kinase 5 (GRK5) in the pathophysiology of obesity and related disorders. We investigated whether single nucleotide polymorphisms (SNPs) in the gene encoding GRK5 affect cardiometabolic traits in humans. We genotyped 3 common SNPs in intron 1 (rs1980030, rs10466210, rs9325562) and one SNP in intron 3 (rs10886471) of GRK5 in 2332 subjects at risk for type 2 diabetes. Total- and visceral fat mass were measured by magnetic resonance (MR) tomography and liver fat content by 1 H-MR spectroscopy...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773352/the-anril-genetic-variants-and-their-interactions-with-environmental-risk-factors-on-atherothrombotic-stroke-in-a-han-chinese-population
#12
Li Xiong, Wei Liu, Li Gao, Qiwen Mu, Xindong Liu, Yuhuan Feng, Zhi Tang, Huanyu Tang, Hua Liu
BACKGROUND: Ischemic stroke (IS) is considered to be a heterogeneous, multifactorial disease with a strong genetic background. This study aims to determine whether variants in the antisense noncoding RNA in the INK4 locus (ANRIL) gene are associated with IS in Han Chinese, as well as whether there is evidence of a gene-environment interactions. MATERIALS AND METHODS: A case-controlled association study was conducted in which only patients with atherothrombotic stroke (ATS) were enrolled...
May 14, 2018: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
https://www.readbyqxmd.com/read/29773097/polymorphism-in-rs2229783-of-the-alpha-1-xi-collagen-gene-is-associated-with-susceptibility-to-but-not-severity-of-kashin-beck-disease-in-a-northwest-chinese-han-population
#13
Xiao Wei Shi, Feng Zhang, Zhi Yan Li, Ai Li Lyu, Xiong Guo
A case-control study was conducted to investigate associations between organophosphate pesticide (OP) exposure, aggression, impulsivity, and attempted suicide. The purpose of this study was to explore whether genomic polymorphisms in the alpha 1(XI) collagen gene (COL11A1) were associated with the risk and severity of Kashin-Beck disease (KBD). Twenty-two single nucleotide polymorphisms (SNPs) in COL11A1 were genotyped in 274 KBD cases and 249 healthy controls using the Sequenom MassARRAY system. The expression of type XI collagen (COL11A) in the knee articular cartilage of 22 KBD patients and 21 controls was analyzed by immunohistochemistry...
April 2018: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/29772088/predicting-genotypes-environmental-range-from-genome-environment-associations
#14
Stéphanie Manel, Marco Andrello, Karine Henry, Daphné Verdelet, Aude Darracq, Pierre-Edouard Guerin, Bruno Desprez, Pierre Devaux
Genome-environment association methods aim to detect genetic markers associated with environmental variables. The detected associations are usually analysed separately to identify the genomic regions involved in local adaptation. However, a recent study suggests that single-locus associations can be combined and used in a predictive way to estimate environmental variables for new individuals on the basis of their genotypes. Here, we introduce an original approach to predict the environmental range (values and upper and lower limits) of species genotypes from the genetic markers significantly associated with those environmental variables in an independent set of individuals...
May 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29771920/maternal-human-telomerase-reverse-transcriptase-variants-are-associated-with-preterm-labor-and-preterm-premature-rupture-of-membranes
#15
Caroline Marrs, Kevin Chesmore, Ramkumar Menon, Scott Williams
OBJECTIVE: Premature aging and short telomere lengths of fetal tissues are associated with spontaneous preterm labor (PTL) and preterm premature rupture of membranes (pPROM). Maintenance of telomere length is performed by the enzyme telomerase. Human telomerase reverse transcriptase (hTERT) is a subunit of telomerase, and its dysfunction affects telomere shortening. This study assessed whether maternal or fetal genetic variations in the hTERT gene are associated with PTL or pPROM. METHODS: A case (PTL or pPROM) control (term birth) genetic association study was conducted in 654 non-Hispanic white mothers (438 term, 162 PTL, 54 pPROM) and 502 non-Hispanic white newborns (346 term, 116 PTB, 40 pPROM)...
2018: PloS One
https://www.readbyqxmd.com/read/29771169/associations-between-skin-rash-treatment-outcome-and-single-nucleotide-polymorphisms-in-head-and-neck-cancer-patients-receiving-the-egfr-inhibitor-zalutumumab-results-from-the-dahanca-19-trial
#16
Line Brøndum, Jan Alsner, Brita Singers Sørensen, Christian Maare, Jørgen Johansen, Hanne Primdahl, Jan Folkvard Evensen, Claus Andrup Kristensen, Lisbeth Juhler Andersen, Jens Overgaard, Jesper Grau Eriksen
PURPOSE: To study the associations between development of moderate to severe skin rash, clinical outcome, and single nucleotide polymorphisms (SNPs) in candidate genes in head and neck cancer patients from the DAHANCA 19 trial receiving the EGFR-inhibitor zalutumumab concurrently with radiation treatment. MATERIAL AND METHODS: 310 patients were included from the zalutumumab-arm of the DAHANCA 19 study. Nine SNPs in the candidate genes EGFR, EGF, AREG, FCGR2A, FCGR3A, and CCND1 were successfully determined in 294 patients...
May 17, 2018: Acta Oncologica
https://www.readbyqxmd.com/read/29770990/pool-based-genome-wide-association-study-identified-novel-candidate-regions-on-bta9-and-14-for-oleic-acid-percentage-in-japanese-black-cattle
#17
Fuki Kawaguchi, Hiroto Kigoshi, Ayaka Nakajima, Yuta Matsumoto, Yoshinobu Uemoto, Moriyuki Fukushima, Emi Yoshida, Eiji Iwamoto, Takayuki Akiyama, Namiko Kohama, Eiji Kobayashi, Takeshi Honda, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki
Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1...
May 17, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/29770529/genome-wide-association-studies-identified-variants-for-taurine-concentration-in-japanese-black-beef
#18
Nanae Sasago, Masayuki Takeda, Tsuyoshi Ohtake, Tsuyoshi Abe, Hironori Sakuma, Takatoshi Kojima, Shinji Sasaki, Yoshinobu Uemoto
We performed genome-wide association studies (GWAS) using the BovineSNP50 array to detect significant single nucleotide polymorphisms (SNPs) that may affect the concentration of 22 free amino acids and three peptides in Japanese Black beef cattle. A total of 574 Japanese Black cattle and 40,657 SNPs from the array were used for this study. Genome-wide significant SNPs were detected for β-alanine (three SNPs on chromosomes 22 and 29) and taurine (26 SNPs on chromosome 22). Importantly, the top two SNPs for taurine were highly significant (p = 6...
May 16, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/29769702/fine-mapping-of-98-obesity-loci-in-mexican-children
#19
Hsin Yen Liu, Akram Alyass, Arkan Abadi, Jesus Peralta-Romero, Fernando Suarez, Jaime Gomez-Zamudio, Astride Audirac, Esteban J Parra, Miguel Cruz, David Meyre
BACKGROUND/OBJECTIVES: Mexico has one of the highest prevalence of childhood obesity in the world. Genome-wide association studies (GWAS) for obesity have identified multiple single-nucleotide polymorphisms (SNPs) in populations of European, East Asian, and African descent. The contribution of these loci to obesity in Mexican children is unclear. We assessed the transferability of 98 obesity loci in Mexican children and fine-mapped the association signals. SUBJECTS/METHODS: The study included 405 and 390 Mexican children with normal weight and obesity...
March 12, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29769357/evolution-of-genomic-variation-in-the-burrowing-owl-in-response-to-recent-colonization-of-urban-areas
#20
Jakob C Mueller, Heiner Kuhl, Stefan Boerno, Jose L Tella, Martina Carrete, Bart Kempenaers
When a species successfully colonizes an urban habitat it can be expected that its population rapidly adapts to the new environment but also experiences demographic perturbations. It is, therefore, essential to gain an understanding of the population structure and the demographic history of the urban and neighbouring rural populations before studying adaptation at the genome level. Here, we investigate populations of the burrowing owl ( Athene cunicularia ), a species that colonized South American cities just a few decades ago...
May 16, 2018: Proceedings. Biological Sciences
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