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Single nucleotide polymorphism

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https://www.readbyqxmd.com/read/28931241/association-of-a-novel-mutation-in-the-plasmodium-falciparum-chloroquine-resistance-transporter-with-decreased-piperaquine-sensitivity
#1
Sonia Agrawal, Kara A Moser, Lindsay Morton, Michael P Cummings, Ankita Parihar, Ankit Dwivedi, Amol C Shetty, Elliott F Drabek, Christopher G Jacob, Philipp P Henrich, Christian M Parobek, Krisada Jongsakul, Rekol Huy, Michele D Spring, Charlotte A Lanteri, Suwanna Chaorattanakawee, Chanthap Lon, Mark M Fukuda, David L Saunders, David A Fidock, Jessica T Lin, Jonathan J Juliano, Christopher V Plowe, Joana C Silva, Shannon Takala-Harrison
Background: Amplified copy number in the plasmepsin II/III genes within Plasmodium falciparum has been associated with decreased sensitivity to piperaquine. To examine this association and test whether additional loci might also contribute, we performed a genome-wide association study of ex vivo P. falciparum susceptibility to piperaquine. Methods: Plasmodium falciparum DNA from 183 samples collected primarily from Cambodia was genotyped at 33716 genome-wide single nucleotide polymorphisms (SNPs)...
August 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28931071/the-origin-of-multiple-clones-in-the-parthenogenetic-lizard-species-darevskia-rostombekowi
#2
Alexey P Ryskov, Fedor A Osipov, Andrey V Omelchenko, Seraphima K Semyenova, Anastasiya E Girnyk, Vitaly I Korchagin, Andrey A Vergun, Robert W Murphy
The all-female Caucasian rock lizard Darevskia rostombekowi and other unisexual species of this genus reproduce normally via true parthenogenesis. Typically, diploid parthenogenetic reptiles exhibit some amount of clonal diversity. However, allozyme data from D. rostombekowi have suggested that this species consists of a single clone. Herein, we test this hypothesis by evaluating variation at three variable microsatellite loci for 42 specimens of D. rostombekowi from four populations in Armenia. Analyses based on single nucleotide polymorphisms of each locus reveal five genotypes or presumptive clones in this species...
2017: PloS One
https://www.readbyqxmd.com/read/28930911/an-enrichment-strategy-yields-seven-novel-single-nucleotide-polymorphisms-associated-with-mortality-and-altered-th17-responses-following-blunt-trauma
#3
Lukas Schimunek, Rami A Namas, Jinling Yin, Dongmei Liu, Derek Barclay, Fayten El-Dehaibi, Andrew Abboud, Haley Lindberg, Ruben Zamora, R Billiar Timothy, Yoram Vodovotz
Trauma is the leading cause of death worldwide for individuals under the age of 55. Interpatient genomic differences, in the form of candidate single nucleotide polymorphisms (SNPs), have been associated previously with adverse outcomes after trauma. However, the utility of these SNPs to predict outcomes based on a meaningful endpoint such as survival is as yet undefined. We hypothesized that specific SNP haplotypes could segregate trauma survivors from non-survivors. Genomic DNA samples were obtained from 453 blunt trauma patients, for whom complete daily clinical and biomarker data were available for 397...
September 19, 2017: Shock
https://www.readbyqxmd.com/read/28930629/large-scale-replication-study-identified-multiple-independent-snps-in-ret-synergistically-associated-with-hirschsprung-disease-in-southern-chinese-population
#4
Yan Zhang, Qiuming He, Ruizhong Zhang, Hong Zhang, Wei Zhong, Huimin Xia
Hischsprung disease (HSCR) is an intestinal disorder with strong genetic components. RET was considered as the strongest contributor. Multiple single nucleotide polymorphisms (SNP) were demonstrated as associated with HSCR in different populations. However, whether the associations of reported SNPs derived from one causal variants or congregations of multiple variants were still not clear. In this study, we successfully genotyped 16 SNPs in RET with a largest case-control study to date, totaling 1470 HSCR and 1473 control subjects in South Chinese population...
September 20, 2017: Aging
https://www.readbyqxmd.com/read/28930538/snps-and-other-polymorhisms-associated-with-acaricide-resistance-in-rhipicephalus-microplus
#5
Gabriela Aguilar, Andrea Margarita Olvera, Bertha Isabel Carvajal, Juan Mosqueda
Ixodicides resistance of ticks is one of the most important problems for the livestock industry in tropical and subtropical regions, mainly due to the increase in cases of multiple resistance in all families of the ixodicides used. Molecular markers such as single nucleotide polymorphisms (SNPs) has been proposed to identify the resistance to ixodicides in Rhipicephalus microplus. Many studies have recently been conducted using SNPs and other types of molecular markers to determine if they are associated with resistance to different products in many parts of the world...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930377/epigenetics-the-future-direction-in-systemic-sclerosis
#6
REVIEW
M Walczyk, A Paradowska-Gorycka, M Olesinska
Systemic sclerosis (SSc) is an immune-mediated connective tissue disease of which the aetiology is still unclear. Previous genetic studies including candidate-gene studies and genomewide association studies have identified a number of genetic variations that confer risk to SSc. However, these variants, such as single nucleotide polymorphisms, cannot completely explain the SSc susceptibility and the diversity in the clinical symptoms of SSc patients. The contribution of epigenetic mechanisms as a link between genetics and environmental triggers represents promising field in understanding the pathogenesis of SSc...
August 21, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/28930110/cytokine-single-nucleotide-polymorphisms-and-risk-of-non-small-cell-lung-cancer
#7
Cristina Pérez-Ramírez, Ahmed Alnatsha, Marisa Cañadas-Garre, Eduardo Villar, Javier Valdivia-Bautista, María J Faus-Dáder, Miguel Á Calleja-Hernández
OBJECTIVE: Lung cancer, particularly the non-small-cell lung cancer (NSCLC) subtype, is the leading cause of cancer-related death worldwide. Several functional polymorphisms in inflammatory cytokine genes, such as IL1B, IL6, IL12A, IL13 and IL16, have been associated with the risk of NSCLC. The aim of this study was to evaluate the association between ILs gene polymorphisms and the risk of developing NSCLC. PARTICIPANTS AND METHODS: A retrospective case-control study was carried out, including 174 NSCLC cases and 298 controls of Spanish origin...
September 18, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28930109/abcg2-regulatory-single-nucleotide-polymorphisms-alter-in-vivo-enhancer-activity-and-expression
#8
Rachel J Eclov, Mee J Kim, Aparna Chhibber, Robin P Smith, Nadav Ahituv, Deanna L Kroetz
OBJECTIVES: The expression and activity of the breast cancer resistance protein (ABCG2) contributes toward the pharmacokinetics of endogenous and xenobiotic substrates. The effect of genetic variation on the activity of cis-regulatory elements and nuclear response elements in the ABCG2 locus and their contribution toward ABCG2 expression have not been investigated systematically. In this study, the effect of genetic variation on the in-vitro and in-vivo enhancer activity of six previously identified liver enhancers in the ABCG2 locus was examined...
September 18, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28930056/developmentally-specific-associations-between-cnr1-genotype-and-cannabis-use-across-emerging-adulthood
#9
James R Ashenhurst, K Paige Harden, Travis T Mallard, William R Corbin, Kim Fromme
OBJECTIVE: Previous studies have found preliminary evidence for associations between common single-nucleotide polymorphisms (SNPs) in the cannabinoid receptor gene CNR1 and cannabis use and dependence. The present study examined a set of eight independent SNPs in or near CNR1 in relation to cannabis use measured longitudinally across emerging adulthood. METHOD: Using latent growth curve modeling of 10 waves of longitudinal data spanning mean ages 18.4-23.8 years in a sample of non-Hispanic White individuals (n = 334), we tested if genotype at each CNR1 SNP was associated with both level and growth of cannabis use over time...
September 2017: Journal of Studies on Alcohol and Drugs
https://www.readbyqxmd.com/read/28930002/investigation-of-outbreaks-of-salmonella-enterica-serovar-typhimurium-and-its-monophasic-variants-using-whole-genome-sequencing-denmark
#10
Pernille Gymoese, Gitte Sørensen, Eva Litrup, John Elmerdal Olsen, Eva Møller Nielsen, Mia Torpdahl
Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases...
October 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28929626/association-of-human-platelet-antigens-polymorphisms-with-susceptibility-to-hepatitis-c-virus-infection-in-chinese-population
#11
S-H Zhou, X-H Liang, L-N Shao, W-J Yu, C Zhao, M Liu
Hepatitis C virus (HCV) is a major cause of chronic hepatitis. Previous studies have identified a number of single nucleotide polymorphisms that are associated with HCV infection. Human platelet antigens (HPAs) polymorphisms play an important role in several diseases. Here, we demonstrated the association of the HPA-2, HPA-3, HPA-5 and HPA-15 polymorphisms with susceptibility to HCV infection in Chinese population. Overall, 118 patients with HCV and 167 controls were genotyped for HPAs. There were no significant differences in the allele and genotype frequency distribution for the HPA-3, HPA-5 and HPA-15 systems between the patients with chronic HCV infection and the healthy controls (p > ...
September 20, 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28929400/can-polymorphisms-in-the-fatty-acid-desaturase-fads-gene-cluster-alter-the-effects-of-fish-oil-supplementation-on-plasma-and-erythrocyte-fatty-acid-profiles-an-exploratory-study
#12
Suzanne J Meldrum, Yuchun Li, Guicheng Zhang, Alexandra E M Heaton, Nina D'Vaz, Judith Manz, Eva Reischl, Berthold V Koletzko, Susan L Prescott, Karen Simmer
PURPOSE: The enzymes encoded by fatty acid desaturases (FADS) genes determine the desaturation of long-chain polyunsaturated fatty acids (LCPUFA). We investigated if haplotype and single nucleotide polymorphisms (SNPs) in FADS gene cluster can influence LCPUFA status in infants who received either fish oil or placebo supplementation. METHODS: Children enrolled in the Infant Fish Oil Supplementation Study (IFOS) were randomly allocated to receive either fish oil or placebo from birth to 6 months of age...
September 19, 2017: European Journal of Nutrition
https://www.readbyqxmd.com/read/28929114/association-between-adam12-single-nucleotide-polymorphisms-and-knee-osteoarthritis-a-meta-analysis
#13
REVIEW
Zheng-Tao Lv, Shuang Liang, Xiao-Jian Huang, Peng Cheng, Wen-Tao Zhu, An-Min Chen
OBJECTIVE: ADAM12 polymorphisms may be associated with the risk of knee osteoarthritis (KOA), but currently available evidence remains controversial. We performed this meta-analysis to confirm whether ADAM12 polymorphisms were associated with susceptibility of KOA. METHODS: A comprehensive literature search in PubMed, EMBASE, and ISI Web of Science was conducted to identify observational studies assessing the association between ADAM12 polymorphisms and susceptibility of KOA...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28929106/common-expression-quantitative-trait-loci-shared-by-histone-genes
#14
Hanseol Kim, Yujin Suh, Chaeyoung Lee
A genome-wide association study (GWAS) was conducted to examine expression quantitative trait loci (eQTLs) for histone genes. We examined common eQTLs for multiple histone genes in 373 European lymphoblastoid cell lines (LCLs). A linear regression model was employed to identify single-nucleotide polymorphisms (SNPs) associated with expression of the histone genes, and the number of eQTLs was determined by linkage disequilibrium analysis. Additional associations of the identified eQTLs with other genes were also examined...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28929029/association-of-rs1801157-single-nucleotide-polymorphism-of-cxcl12-gene-in-breast-cancer-in-pakistan-and-in-silico-expression-analysis-of-cxcl12-cxcr4-associated-biological-regulatory-network
#15
Samra Khalid, Rumeza Hanif
BACKGROUND: C-X-C chemokine ligand 12 (CXCL12) has important implications in breast cancer (BC) pathogenesis. It is selectively expressed on B and T lymphocytes and is involved in hematopoiesis, thymocyte trafficking, stem cell motility, neovascularization, and tumorigenesis. The single nucleotide polymorphism (SNP) rs1801157 of CXCL12 gene has been found to be associated with higher risk of BC. METHODS: Our study focuses on the genotypic and allelic distribution of SNP (rs1801157; G/A) in Pakistani population as well as its association with the clinico-pathological features...
2017: PeerJ
https://www.readbyqxmd.com/read/28928994/foxe1-mutation-screening-in-a-case-with-cleft-lip-hypothyroidism-and-thyroid-carcinoma-a-new-syndrome
#16
Hugo Mendieta-Zerón, Angélica Jiménez-Rosales, Carlos Jhovani Pérez-Amado, Silvia Jiménez-Morales
A 26-year-old woman is referred to the Internal Medicine consultation due to increases in laboratory studies associated with Papillary Thyroid Carcinoma (PTC) that was confirmed by histopathological studies. Her clinical history revealed that, at 3 months of age, she was successfully treated with surgery for cleft lip (CL) and at the age of 24 years was diagnosed with hypothyroidism. Single nucleotide polymorphisms (SNPs) in FOXE1 and its promoter regions have been associated with various etiologies related to the thyroid, including orofacial clefting, specially cleft palate (CP) and CL, hypothyroidism (HT), and thyroid cancer...
2017: Case Reports in Genetics
https://www.readbyqxmd.com/read/28928973/prospective-replication-study-implicates-the-catechol-o-methyltransferase-val-158-met-polymorphism-as-a-biomarker-for-the-response-to-morphine-in-patients-with-cancer
#17
Hiromichi Matsuoka, Chihiro Makimura, Atsuko Koyama, Yoshihiko Fujita, Junji Tsurutani, Kiyohiro Sakai, Ryo Sakamoto, Kazuto Nishio, Kazuhiko Nakagawa
Genetic differences in humans cause clinical difficulties in opioid treatment. Previous studies indicate that a single nucleotide polymorphism in the catechol-O-methyltransferase (COMT) gene (rs4680; p.Val(158)Met) may present as a predictive biomarker for the response to morphine treatment. In our previous pilot exploratory study, patients with a G/G genotype were demonstrated to require a higher dose of morphine, compared with patients with A/A and A/G genotypes. In the present study, the aim was to replicate the findings in an independent cohort of opioid-treatment-naïve patients exhibiting various types of cancer...
October 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28928764/exploring-and-harnessing-haplotype-diversity-to-improve-yield-stability-in-crops
#18
REVIEW
Lunwen Qian, Lee T Hickey, Andreas Stahl, Christian R Werner, Ben Hayes, Rod J Snowdon, Kai P Voss-Fels
In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928763/comparative-mapping-and-candidate-gene-analysis-of-ssiia-associated-with-grain-amylopectin-content-in-barley-hordeum-vulgare-l
#19
Xiangyun Fan, Juan Zhu, Wenbin Dong, Yuandong Sun, Chao Lv, Baojian Guo, Rugen Xu
Amylopectin concentration in barley endosperm has important effects on grain quality and end-use. In this study, quantitative trait locus (QTL) analysis together with genome-wide association studies (GWAS) were performed to identify markers linked to grain amylopectin content respectively using a doubled haploid (DH) population of 178 lines and a collection of 185 diverse barley germplasms both genotyped by genotyping-by-sequencing (GBS). A stable QTL on chromosome 7H and 11 associated single nucleotide polymorphisms (SNPs) were detected...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928752/climate-clever-clovers-new-paradigm-to-reduce-the-environmental-footprint-of-ruminants-by-breeding-low-methanogenic-forages-utilizing-haplotype-variation
#20
Parwinder Kaur, Rudi Appels, Philipp E Bayer, Gabriel Keeble-Gagnere, Jiankang Wang, Hideki Hirakawa, Kenta Shirasawa, Philip Vercoe, Katia Stefanova, Zoey Durmic, Phillip Nichols, Clinton Revell, Sachiko N Isobe, David Edwards, William Erskine
Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H(2) = 0.4) and allelic variation in a region of Chr 8 accounted for 7...
2017: Frontiers in Plant Science
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