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Single nucleotide polymorphisms (SNPs)

Antonino Rapisarda, Nicoletta Giamblanco, Giovanni Marletta
Clinical application of DNA microarrays used for screening of single nucleotide polymorphisms (SNPs) are very important for diagnosis of diseases and appropriate treatment of patients. In this paper localized surface plasmon resonance (LSPR) technique has been used to study the DNA hybridization process for binary solutions of respectively perfectly matching (PM) and single base mismatching (MM) 93-mer ssDNA from KRAS codon 12. 5'-thiol modified 35-mer ssDNA has been linked to the Au nanodisks array as probe with a surface coverage of 2...
October 14, 2016: Journal of Colloid and Interface Science
Qiang Xu, Yang Shi, Ting Yu, Xuewen Xu, Yali Yan, Xiaohua Qi, Xuehao Chen
Cucumber is an economically important vegetable crop worldwide. Powdery mildew (PM) is one of the most severe diseases that can affect cucumber crops. There have been several research efforts to isolate PM resistance genes for breeding PM-resistant cucumber. In the present study, we used a chromosome segment substitution line, SSL508-28, which carried PM resistance genes from the donor parent, JIN5-508, through twelve generations of backcrossing with a PM-susceptible inbred line, D8. We performed whole-genome resequencing of SSL508-28 and D8 to identify single nucleotide polymorphisms (SNPs), and insertions and deletions (indels)...
2016: PloS One
Wei He, Peng Huang, Dinghua Liu, Lingling Zhong, Rongbin Yu, Jianan Li
Background: Base excision repair (BER) is the primary DNA repair system with the ability to fix base lesions caused by oxidative damage. Genetic variants influencing the BER pathway may affect the susceptibility and the outcomes of ischemic stroke. Here, we examined how single nucleotide polymorphisms (SNPs) associated with BER impact susceptibility and short-term recovery of ischemic stroke. Methods: We selected 320 ischemic stroke patients and 303 controls. Then we genotyped SNPs of NEIL1 rs4462560, NEIL3 rs12645561 and XRCC1 rs25487 in both groups...
October 17, 2016: International Journal of Environmental Research and Public Health
Asami Fujii, Naoya Inoue, Mikio Watanabe, Chisa Kawakami, Yoh Hidaka, Yoshihide Hayashizaki, Yoshinori Iwatani
BACKGROUND: Graves' disease (GD) and Hashimoto's disease (HD) are autoimmune thyroid diseases distinguished by the presence or absence of an anti-thyroid stimulating hormone receptor (TSHR) antibody (TRAb). TSHR gene polymorphisms determine the amount of TSHR expressed, which may in turn influence TRAb production. The FANTOM5 project identified six GD-associated SNPs within the enhancer regions of TSHR and unknown genes. In this study, we examined the association of 11 TSHR and unknown gene polymorphisms, 5 of which are located in TSHR enhancer regions, with the development and prognosis of GD and HD...
October 20, 2016: Thyroid: Official Journal of the American Thyroid Association
Gamal Allam, Imad A A Mohamed, Khaled A Alswat, Said H Abbadi, Raad Nassif, Bader J Alharthi, Amre Nasr
Tuberculosis (TB) considers one of the most common infectious diseases all over the world. IL-37, a novel member of the IL-1 family, exhibits anti-inflammatory activities. Various cytokine genes polymorphisms have been reported to be associated with susceptibility to TB infection. However, association between genetic variations in the IL-37 gene with susceptibility to TB infection is not known. Therefore, the aim of this investigation was to identify the association of IL-37 genetic polymorphisms with TB infection in Saudi population...
October 20, 2016: Microbiology and Immunology
Kai Song, Li Li, Guofan Zhang
Next-generation sequencing (NGS) technology is being applied to an increasing number of non-model species and has been used as the primary approach for accurate genotyping in genetic and evolutionary studies. However, inferring genotypes from sequencing data is challenging, particularly for organisms with a high degree of heterozygosity. This is because genotype calls from sequencing data are often inaccurate due to low sequencing coverage, and if this is not accounted for, genotype uncertainty can lead to serious bias in downstream analyses, such as quantitative trait locus mapping and genome-wide association studies...
October 20, 2016: Scientific Reports
Hanne Gro Olsen, Tim Martin Knutsen, Anna M Lewandowska-Sabat, Harald Grove, Torfinn Nome, Morten Svendsen, Mariann Arnyasi, Marte Sodeland, Kristil K Sundsaasen, Sandra Rinne Dahl, Bjørg Heringstad, Hanne H Hansen, Ingrid Olsaker, Matthew Peter Kent, Sigbjørn Lien
BACKGROUND: Clinical mastitis is an inflammation of the mammary gland and causes significant costs to dairy production. It is unfavourably genetically correlated to milk production, and, thus, knowledge of the mechanisms that underlie these traits would be valuable to improve both of them simultaneously through breeding. A quantitative trait locus (QTL) that affects both clinical mastitis and milk production has recently been fine-mapped to around 89 Mb on bovine chromosome 6 (BTA6), but identification of the gene that underlies this QTL was not possible due to the strong linkage disequilibrium between single nucleotide polymorphisms (SNPs) within this region...
October 19, 2016: Genetics, Selection, Evolution: GSE
Zongze Zhang, Robin B Gasser, Xin Yang, Fangyuan Yin, Guanghui Zhao, Min Bao, Baoliang Pan, Weiyi Huang, Chunren Wang, Fengcai Zou, Yanqin Zhou, Junlong Zhao, Rui Fang, Min Hu
Haemonchus contortus is one of the most important parasitic nematodes of small ruminants around the world, particularly in tropical and subtropical regions. The control of haemonchosis relies mainly on anthelmintics, but the excessive and prolonged use of anthelmintics is causing serious drug resistance issues in many countries. As benzimidazole (BZ) anthelmintics have been broadly used in China, we hypothesized that resistance is widespread. Given the link between three known single nucleotide polymorphisms (SNPs, designated F167Y, E198A and F200Y) in the isotype-1 β-tubulin gene and BZ resistance, our goal here was to explore the presence of these mutations in H...
October 5, 2016: International Journal for Parasitology, Drugs and Drug Resistance
Christian Rellstab, Stefan Zoller, Lorenz Walthert, Isabelle Lesur, Andrea R Pluess, René Graf, Catherine Bodénès, Christoph Sperisen, Antoine Kremer, Felix Gugerli
Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested if >3'500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate, and soil characteristics...
October 19, 2016: Molecular Ecology
Ou Liu, Wuxiang Xie, Yanwen Qin, Lixin Jia, Jing Zhang, Yi Xin, Xinliang Guan, Haiyang Li, Ming Gong, Yuyong Liu, Xiaolong Wang, Jianrong Li, Feng Lan, Hongjia Zhang
Matrix metalloproteinases-2 (MMP-2) plays an important role in the pathogenesis of type A aortic dissection (AD). The aim of this study was to evaluate the association of 3 single nucleotide polymorphisms (SNPs) in the MMP-2 gene with type A AD risk and aortic diameters in patients. We performed a case-control study with 172 unrelated type A AD patients and 439 controls. Three SNPs rs11644561, rs11643630, and rs243865 were genotyped through the MassARRAY platform. Allelic associations of SNPs and SNP haplotypes with type A AD and aortic diameters in patients were evaluated...
October 2016: Medicine (Baltimore)
Suzanne Gonzalez, Jayanta Gupta, Erika Villa, Indika Mallawaarachchi, Marco Rodriguez, Mercedes Ramirez, Juan Zavala, Regina Armas, Albana Dassori, Javier Contreras, Deborah Flores, Alvaro Jerez, Alfonso Ontiveros, Humberto Nicolini, Michael Escamilla
OBJECTIVES: Recent genome-wide association studies (GWASs) have identified numerous putative genetic polymorphisms associated with bipolar disorder (BD) and/or schizophrenia (SC). We hypothesized that a portion of these polymorphisms would also be associated with BD in the Latino American population. To identify such regions, we tested previously identified genetic variants associated with BD and/or SC and ancestral haploblocks containing these single nucleotide polymorphisms (SNPs) in a sample of Latino subjects with BD...
September 2016: Bipolar Disorders
James N Ingle, Fang Xie, Matthew J Ellis, Paul E Goss, Lois E Shepherd, Judith-Anne W Chapman, Bingshu E Chen, Michiaki Kubo, Yoichi Furukawa, Yukihide Momozawa, Vered Stearns, Kathleen I Pritchard, Poulami Barman, Erin E Carlson, Matthew P Goetz, Richard M Weinshilboum, Krishna R Kalari, Liewei Wang
Genetic risks in breast cancer remain only partly understood. Here we report the results of a genome-wide association study of germline DNA from 4,658 women, including 252 women experiencing a breast cancer recurrence, who were entered on the MA.27 adjuvant trial comparing the aromatase inhibitors (AI) anastrozole and exemestane. Single nucleotide polymorphisms (SNP) of top significance were identified in the gene encoding MIR2052HG, a long noncoding RNA of unknown function. Heterozygous or homozygous individuals for variant alleles exhibited a ~40% or ~63% decrease, respectively, in the hazard of breast cancer recurrence relative to homozygous wild-type individuals...
October 10, 2016: Cancer Research
Paul J Martin, Wenhong Fan, Barry E Storer, David M Levine, Lue Ping Zhao, Edus H Warren, Mary E D Flowers, Stephanie J Lee, Paul A Carpenter, Michael Boeckh, Sangeeta Hingorani, Li Yan, Qiang Hu, Leah Preus, Song Liu, Stephen Spellman, Xiaochun Zhu, Marcelo Pasquini, Philip McCarthy, Daniel Stram, Xin Sheng, Loreall Pooler, Christopher A Haiman, Lara Sucheston-Campbell, Theresa Hahn, John A Hansen
Previous studies have identified single-nucleotide polymorphisms (SNPs) associated with the risk of chronic graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (HCT). The current study determined whether these associations could be replicated in large cohorts of donors and recipients. Each SNP was tested with cohorts of patients having the same donor type (HLA-matched related, unrelated or both) reported in the original publication, and testing was limited to the same genome (recipient or donor) and genetic model (dominant, recessive or allelic) reported in the original study...
October 6, 2016: Blood
Vendula Bartáková, Katarína Kuricová, Filip Zlámal, Jana Bělobrádková, Katetřina Kaňková
PURPOSE: Gestational diabetes mellitus (GDM) represents the most frequent metabolic disorder in pregnancy. Since dietary intake plays an important role in obesity and type 2 diabetes development, it is likely to be for the susceptibility to GDM too. Food preferences, driving partly the diet composition, are changing during pregnancy. Taste and genetic variability in taste receptors is an important factor in determining food preferences. Aims of our study were (1) to characterize dietary habits of pregnant women and to find possible differences in food preferences between healthy pregnant women and those with GDM and (2) to ascertain possible association of several single nucleotide polymorphisms (SNPs) in taste receptor (TR) genes with GDM...
October 18, 2016: European Journal of Nutrition
Rui Zhang, Yan Bi, Weibo Niu, Xiaoye Huang, Shiqing Chen, Xingwang Li, Xi Wu, Yanfei Cao, Fengping Yang, Lu Wang, Weidong Li, Yifeng Xu, Lin He, Tao Yu, Guang He
Schizophrenia (SZ) and major depressive disorder (MDD) are two common severe mental disorders that have arisen to public awareness in recent years. Serotonin (5-HT) receptors have been implicated in the pathophysiology of psychiatric disorders especially in MDD and SZ. The aim of this study is to explore whether the variants in the 5-HT1A and 5-HT2A gene are susceptible to SZ or MDD in the Chinese Han population. Five SNPs (Single Nucleotide Polymorphisms) (rs1364043, rs10042486, rs6313, rs6311, rs17289304) in these genes were genotyped from 752 SZ patients, 568 MDD patients, and 846 normal controls of Chinese Han origin...
October 15, 2016: Neuroscience Letters
M A Rosales-Reynoso, A R Arredondo-Valdez, C I Juárez-Vázquez, L I Wence-Chavez, P Barros-Núñez, M P Gallegos-Arreola, S E Flores-Martínez, M C Morán-Moguel, J Sánchez-Corona
Accumulative evidence suggests that alterations due to mutations or genetic polymorphisms in the TCF7L2 and CCND1 genes, which are components of the Wnt signaling pathway, contributes to carcinogenesis. The present study was designated to clarify whether common single nucleotide polymorphisms (SNPs) of the transcription factor 7- like 2 (TCF7L2) and cyclin D1 (CCND1) genes are associated with colorectal cancer risk in Mexican patients. A case-control study including 197 colorectal cancer patients and 100 healthy subjects was conducted in a Mexican population...
September 30, 2016: Cellular and Molecular Biology
Silvia Mahmood, Andrea Evinová, Mária Škereňová, Igor Ondrejka, Ján Lehotský
BACKGROUND: Major depressive disorder (MDD) is a main public health concern worldwide. Despite extensive investigations, the exact mechanisms responsible for MDD have not been identified. Epidermal growth factor (EGF) and insulin growth factor binding protein-3 (IGFBP-3) are involved in brain function. Tumour suppressor protein p53 is widely involved in neuronal death in response to different forms of acute insults and neurological disorders. The present study focuses on the possible associations of the single-nucleotide polymorphisms (SNP) of EGF A61G (rs4444903), IGFBP-3 C32G (rs2854746) and TP53 G72C (rs1042522) genes with MDD risk in the Slovak population...
September 2016: Central European Journal of Public Health
Isabel Rodríguez-Quilón, Luis Santos-Del-Blanco, María Jesús Serra-Varela, Jarkko Koskela, Santiago C González-Martínez, Ricardo Alía
Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
Yoichiro Otaki, Tetsu Watanabe, Satoshi Nishiyama, Hiroki Takahashi, Takanori Arimoto, Tetsuro Shishido, Takuya Miyamoto, Tsuneo Konta, Yoko Shibata, Hidenori Sato, Ryo Kawasaki, Makoto Daimon, Yoshiyuki Ueno, Takeo Kato, Takamasa Kayama, Isao Kubota
BACKGROUND: Oxidative stress is a major cause of cardiovascular disease. Superoxide dismutase-1 (SOD1) is an antioxidant that protects against oxidative stress. Deoxyribonucleic acid (DNA) variations such as single nucleotide polymorphism (SNP) or haplotypes within the SOD gene are reportedly associated with the development of cardiovascular disease. However, it remains to be determined whether SOD1 variability is associated with cardiovascular or all-cause mortality in the general population...
2016: PloS One
Laura Pöyhönen, Liisa Kröger, Heini Huhtala, Johanna Mäkinen, Kirsi Nuolivirta, Jussi Mertsola, Qiushui He, Matti Korppi
BACKGROUND: Interferon-gamma (IFN-γ) is a key cytokine in defense against mycobacteria, including Bacillus Calmette-Guérin (BCG). Mannose-binding lectin (MBL) and Toll-like receptors (TLRs) are pattern-recognizing molecules of innate immunity. The aim of the present study was to investigate the relationship between polymorphisms in MBL, TLR1, TLR2, and TLR6 encoding genes and stimulated IFN-γ and interleukin-12 (IL-12) ex vivo production in BCG osteitis survivors. METHODS: Data on single nucleotide polymorphisms (SNPs) in the MBL2 gene and TLR1, TLR2, and TLR6 genes were available from 132 former BCG osteitis patients, and data on ex vivo IFN-γ and IL-12 production were available from 115 and 118 patients, respectively...
October 17, 2016: Pediatric Infectious Disease Journal
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