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Jie Tang, Jiaqian Fei, Chunxia Gu, Weixia Liu, Minwei Li, Cheng Zhou
BACKGROUND/AIMS: B and T lymphocyte attenuator (BTLA) is an immune inhibitory receptor involved in the pathogenesis of chronic viral infections. Little is known about the effects of BTLA gene polymorphisms on chronic hepatitis B virus (HBV) infections. In this study, we investigated whether the polymorphisms of BTLA are associated with the progression of chronic HBV infection. METHODS: A total of 382 chronic HBV carriers and 170 healthy individuals in the same region were recruited for this study...
March 16, 2018: Cellular Physiology and Biochemistry
Jeonghwan Lee, Young Lee, Boram Park, Sungho Won, Jin Suk Han, Nam Ju Heo
Chronic kidney disease (CKD) is an important social health problem characterized by a decrease in the kidney glomerular filtration rate (GFR). In this study, we analyzed genome-wide association studies for kidney disease-related traits using data from a Korean adult health screening cohort comprising 7,064 participants. Kidney disease-related traits analyzed include blood urea nitrogen (BUN), serum creatinine, estimated GFR, and uric acid levels. We detected two genetic loci (SLC14A2 and an intergenic region) and 8 single nucleotide polymorphisms (SNPs) associated with BUN, 3 genetic loci (BCAS3, C17orf82, ALDH2) and 6 SNPs associated with serum creatinine, 3 genetic loci (BCAS3, C17orf82/TBX2, LRP2) and 7 SNPs associated with GFR, and 14 genetic loci (3 in ABCG2/PKD2, 2 in SLC2A9, 3 in intergenic regions on chromosome 4; OTUB1, NRXN2/SLC22A12, CDC42BPG, RPS6KA4, SLC22A9, and MAP4K2 on chromosome 11) and 84 SNPs associated with uric acid levels...
2018: PloS One
Ozlem Kurnaz-Gomleksiz, Ozlem Kucukhuseyin, Elif Ozkok, Zehra Bugra, Oguz Ozturk, Hulya Yilmaz-Aydogan
BACKGROUND: The OLR1 gene has been identified as a candidate gene for coronary artery disease (CAD). Six single-nucleotide polymorphisms (SNPs) of the OLR1 gene located within intron 4 (IVS4-27G>C, IVS4-73C>T, IVS4-14A>G), intron 5 (IVS5-70A>G, IVS5-27G>T) and 3'UTR (188C>T) comprise a linkage disequilibrium (LD) block, which is strongly associated with the elevated risk of CAD. OBJECTIVES: We aimed to investigate the effects of the OLR1 IVS4-14A>G and -73C>T SNPs on metabolic parameters in Turkish CAD patients, and the linkage between these 2 genetic variants...
March 20, 2018: Advances in Clinical and Experimental Medicine: Official Organ Wroclaw Medical University
Kenta Sakurai, Hiroko Kawasaki
Phenotypic and genetic changes during long-term preservation have been observed in microbial strains at culture collections (CCs). It is imperative to verify the effects of these changes on quality of the strains preserved at CCs. In this study, we performed genome-wide single-nucleotide polymorphism (SNP) analysis of different production lots, which had been derived from the same origin and preserved at the NITE Biological Resource Center (NBRC) for a 4-38-year period by the vacuum liquid drying method at 4 °C...
March 20, 2018: International Journal of Systematic and Evolutionary Microbiology
Tanja Čugura, Jakob Boh, Tomaž Zupanc, Peter Pregelj, Alja Videtič Paska
Dysregulations in serotonin neurotransmission can be a strong contributing factor in suicide and impulsive-aggressive personality traits. Victims of suicide form a heterogeneous group in terms of planning, lethality and number of used methods. In this study, we tested single nucleotide polymorphisms (SNPs) of the monoamine oxidase (MAO) A and B genes on the Slovenian population, which has one of the highest suicide rates in the world. Genotyping was performed on 77 victims of complex suicide, 406 victims of simple suicide and 289 controls...
March 20, 2018: International Journal of Legal Medicine
Marijke Linschoten, Arco J Teske, Maarten J Cramer, Elsken van der Wall, Folkert W Asselbergs
Chemotherapy-related cardiac dysfunction is a significant side effect of anticancer treatment. Risk stratification is based on clinical- and treatment-related risk factors that do not adequately explain individual susceptibility. The addition of genetic variants may improve risk assessment. We conducted a systematic literature search in PubMed and Embase, to identify studies investigating genetic risk factors for chemotherapy-related cardiac dysfunction. Included were articles describing genetic variants in humans altering susceptibility to chemotherapy-related cardiac dysfunction...
January 2018: Circ Genom Precis Med
Zusen Ye, Hao Zhang, Lingli Sun, Huan Cai, Yonggang Hao, Zongliang Xu, Zhizhong Zhang, Xinfeng Liu
Elevated C-reactive protein (CRP) levels increase the risk of poor functional disability in patients with ischemic stroke (IS). This study aimed to investigate the association between CRP gene polymorphisms and 3-month functional disability of large artery atherosclerotic (LAA) stroke in Han Chinese. Patients with first-ever LAA IS were prospectively enrolled in Nanjing Stroke Registry Program between August 2013 and October 2015. Five single-nucleotide polymorphisms (SNPs) (rs876537, rs2794520, rs3093059, rs7553007 and rs11265260) in CRP gene related to CRP levels in Asian by genome-wide association study were genotyped...
March 19, 2018: Neuromolecular Medicine
Muna Al-Asfi, Dennis McNevin, Bhavik Mehta, Daniel Power, Michelle E Gahan, Runa Daniel
AbstractThe ability to provide accurate DNA-based forensic intelligence requires analysis of multiple DNA markers to predict the biogeographical ancestry (BGA) and externally visible characteristics (EVCs) of the donor of biological evidence. Massively parallel sequencing (MPS) enables the analysis of hundreds of DNA markers in multiple samples simultaneously, increasing the value of the intelligence provided to forensic investigators while reducing the depletion of evidential material resulting from multiple analyses...
March 19, 2018: International Journal of Legal Medicine
Lehui Du, Wei Yu, Xiang Huang, Nana Zhao, Fang Liu, Fang Tong, Sujing Zhang, Baolong Niu, Xiaoliang Liu, Shouping Xu, Yurong Huang, Xiangkun Dai, Chuanbin Xie, Gaoxiang Chen, Xiaohu Cong, Baolin Qu
Background: Growing data suggest that DNA damage repair and detoxification pathways play crucial roles in radiation-induced toxicities. To determine whether common functional single-nucleotide polymorphisms (SNPs) in candidate genes from these pathways can be used as predictors of radiation pneumonitis (RP), we conducted a prospective study to evaluate the associations between functional SNPs and risk of RP. Methods: We recruited a total of 149 lung cancer patients who had received intensity modulated radiation therapy (IMRT)...
2018: Journal of Cancer
Ning Zhang, Jian Jia, Qiuju Ding, Huimei Chen, Xiaoman Ye, Haixia Ding, Yiyang Zhan
The CYP17A1 gene, which encodes17α-hydroxylase and 17,20-lyase, has been identified as a common hypertension susceptibility locus in a European population. However, the association between CYP17A1 polymorphisms and hypertension is unclear in the Chinese population as well as in the role of serum 25(OH) D levels. Six single nucleotide polymorphisms (SNPs) in CYP17A1 were genotyped in two stages in a Han Chinese population, and the serum 25(OH) D levels were measured. Analysis in stage 1 showed that the rs1004467 minor G-allele and rs11191548 minor C-allele in CYP17A1 were significantly associated with a decreased risk of hypertension and higher serum 25(OH) D levels (all P < 0...
March 19, 2018: Journal of Human Genetics
Donglei Zhang, Jieying Qin, Lin Li, Guannan Su, Guo Huang, Qingfeng Cao, Aize Kijlstra, Peizeng Yang
Fc receptors are known to have a pivotal role in the initiation and regulation of many immunological and inflammatory processes. This study aimed to investigate the association of Fc receptor family gene polymorphisms with ocular Behçet's disease (BD) in Han Chinese. A two stage case-control study was performed in 1022 BD cases and 1803 healthy controls. Twenty-three SNPs were genotyped using the MassARRAY system (Sequenom), TaqMan SNP Genotyping Assay and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method...
March 19, 2018: Scientific Reports
Lindsay A Holden, Kim H Brown
Common strains of wildtype zebrafish (Danio rerio) have unique genomic features including SNPs and CNV, but strain information often goes unreported in the literature. As a result, the confounding effects of interstrain variation makes repetition of studies in zebrafish challenging. Here we analyze hepatic mRNA expression patterns between three common zebrafish strains (AB, Tuebingen (TU), and WIK) using Agilent 4 × 44 K gene expression microarrays to establish baseline mRNA expression across strains and between sexes...
March 19, 2018: Scientific Reports
Daniel L McCartney, Rosie M Walker, Stewart W Morris, Susan M Anderson, Barbara J Duff, Riccardo E Marioni, J Kirsty Millar, Shane E McCarthy, Niamh M Ryan, Stephen M Lawrie, Andrew R Watson, Douglas H R Blackwood, Pippa A Thomson, Andrew M McIntosh, W Richard McCombie, David J Porteous, Kathryn L Evans
Recent work has highlighted a possible role for altered epigenetic modifications, including differential DNA methylation, in susceptibility to psychiatric illness. Here, we investigate blood-based DNA methylation in a large family where a balanced translocation between chromosomes 1 and 11 shows genome-wide significant linkage to psychiatric illness. Genome-wide DNA methylation was profiled in whole-blood-derived DNA from 41 individuals using the Infinium HumanMethylation450 BeadChip (Illumina Inc., San Diego, CA)...
March 19, 2018: NPJ Schizophrenia
Valérie Besnard, Alain Calender, Diane Bouvry, Yves Pacheco, Catherine Chapelon-Abric, Florence Jeny, Hilario Nunes, Carole Planès, Dominique Valeyre
BACKGROUND: Sarcoidosis is a systemic disease characterized by the formation of immune granulomas in various organs, mainly the lungs and the lymphatic system. Exaggerated granulomatous reaction might be triggered in response to unidentified antigens in individuals with genetic susceptibility. The present study aimed to determine the genetic variants implicated in a familial case of sarcoidosis. METHODS: Sarcoidosis presentation and history, NOD2 profile, NF-κB and cytokine production in blood monocytes/macrophages were evaluated in individuals from a family with late appearance of sarcoidosis...
March 20, 2018: Respiratory Research
Eva Pampouille, Cécile Berri, Simon Boitard, Christelle Hennequet-Antier, Stéphane A Beauclercq, Estelle Godet, Christophe Praud, Yves Jégo, Elisabeth Le Bihan-Duval
BACKGROUND: White striping (WS) is an emerging muscular defect occurring on breast and thigh muscles of broiler chickens. It is characterized by the presence of white striations parallel to the muscle fibers and has significant consequences for meat quality. The etiology of WS remains poorly understood, even if previous studies demonstrated that the defect prevalence is related to broiler growth and muscle development. Moreover, recent studies showed moderate to high heritability values of WS, which emphasized the role of genetics in the expression of the muscle defect...
March 20, 2018: BMC Genomics
Kashif Bashir, Romana Sarwar, Shazia Fatima, Soma Saeed, Ishrat Mahjabeen, Mahmood Akhtar Kayani
PURPOSE: Variants in DNA repair genes may alter the repair mechanisms that make the persons vulnerable to DNA damage. These polymorphic variants in the DNA repair pathway genes, such as XRCC1, have been associated with susceptibility of several types of cancer including thyroid cancer. This study was designed to explore the link between XRCC1 polymorphisms and modulation of thyroid cancer risk. METHODS: Our study consisted of 456 thyroid cancer patients and 400 controls...
January 2018: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
Ramon A Juste, Patricia Vazquez, Otsanda Ruiz-Larrañaga, Mikel Iriondo, Carmen Manzano, Mikel Agirre, Andone Estonba, Maria V Geijo, Elena Molina, Iker A Sevilla, Marta Alonso-Hearn, Nieves Gomez, Valentin Perez, Adoracion Cortes, Joseba M Garrido
Control of major mycobacterial diseases affecting livestock is a challenging issue that requires different approaches. The use of genetic markers for improving resistance to Mycobacterium avium subsp. paratuberculosis infection in cattle has been explored as a promising population strategy We performed paratuberculosis epidemiopathogenic phenotypic and genotypic characterization involving 24 SNPs in six candidate genes ( NOD2, CD209, SLC11A1, SP110, TLR2 and TLR4 ) on 502 slaughtered Friesian cows. In the current study, we investigate whether recently proposed paratuberculosis (PTB) epidemiopathogenic (EP) forms (apparently free-AF, latent-LAT and patent-PAT) could be associated with some combination of these 24 SNPs...
February 2018: Heliyon
Xingchun Peng, Jun Shi, Wanqun Sun, Xuzhi Ruan, Yang Guo, Lunhua Zhao, Jue Wang, Bin Li
IL-6 is critical for tumorigenesis. However, previous studies on the association of IL-6 promoter polymorphisms with predisposition to different cancer types are somewhat contradictory. Therefore, we performed this meta-analysis regarding the relationship between IL-6 promoter single nucleotide polymorphisms and cancer susceptibility and prognosis. Up to April 2017, 97 original publications were identified covering three IL-6 promoter SNPs. Our results showed statistically significant association between IL-6 promoter and cancer risk and prognosis...
February 23, 2018: Oncotarget
Nurgul Sikhayeva, Yerkebulan Talzhanov, Aisha Iskakova, Jarkyn Dzharmukhanov, Raushan Nugmanova, Elena Zholdybaeva, Erlan Ramanculov
Background: Ethnic differences exist in the frequencies of genetic variations that contribute to the risk of common disease. This study aimed to analyse the distribution of several genes, previously associated with susceptibility to type 2 diabetes and obesity-related phenotypes, in a Kazakh population. Methods: A total of 966 individuals belonging to the Kazakh ethnicity were recruited from an outpatient clinic. We genotyped 41 common single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes in other ethnic groups and 31 of these were in Hardy-Weinberg equilibrium...
2018: Clinical Interventions in Aging
Cheng-Hong Yang, Kuo-Chuan Wu, Li-Yeh Chuang, Hsueh-Wei Chang
DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination...
2018: Evolutionary Bioinformatics Online
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