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Single nucleotide polymorphism

J Woo, J E Kim, J J Im, J Lee, H S Jeong, S Park, S-Y Jung, H An, S Yoon, S M Lim, S Lee, J Ma, E Y Shin, Y-E Han, B Kim, E H Lee, L Feng, H Chun, B-E Yoon, I Kang, S R Dager, I K Lyoo, C J Lee
The role of astrocytes in brain plasticity has not been extensively studied compared with that of neurons. Here we adopted integrative translational and reverse-translational approaches to explore the role of an astrocyte-specific major water channel in the brain, aquaporin-4 (AQP4), in brain plasticity and learning. We initially identified the most prevalent genetic variant of AQP4 (single nucleotide polymorphism of rs162008 with C or T variation, which has a minor allele frequency of 0.21) from a human database (n=60 706) and examined its functionality in modulating the expression level of AQP4 in an in vitro luciferase reporter assay...
April 2018: Molecular Psychiatry
Veronica Ortega, Christina Mendiola, Gopalrao V N Velagaleti
One of the well-known hallmarks of cancer is genomic instability. Although gradualism is a well-established process of cancer evolution, recent studies have shown that chromothripsis or chromoanasynthesis can result in complex genomic rearrangements by a single catastrophic event rather than several incremental steps. These two novel phenomena suggest an evolutionary modality for cancer cells to circumvent individual mutational events with one simultaneous shattering of chromosomes or chromosome regions resulting in the random reassembling of shattered genetic material to form complex derivative chromosomes...
2018: Methods in Molecular Biology
Miganoosh Simonian, Meysam Mosallayi, Maryam Miraghajani, Awat Feizi, Sharifeh Khosravi, Ahmad Reza Salehi, Deniz Mortazavi, Farideh Saberi, Rasoul Salehi
Aim: In present study we have elucidated the role of 2758 A>G (rs696), in the recognition site of miR449a in the 3' UTR of NFKB inhibitor alpha (NFKBIA) gene, in development of sporadic colorectal cancer. Background: Colorectal cancer (CRC) is rated as second cause of cancer death. Genetic determinants are considered as driving forces in development of sporadic CRC. Single nucleotide polymorphisms (SNPs), are attributed as the main genetic factor in cancers susceptibility...
2018: Gastroenterology and Hepatology From Bed to Bench
Maryam Karkhane, Seyed Reza Mohebbi, Pedram Azimzadeh, Hasti Avarandeh, Shabnam Kazemian, Afsaneh Sharifian, Behzad Hatami, Hamid Asadzadeh Aghdaei
Aim: Our goal was to identify the putative association of rs4072111 variant in IL-16 gene and HCV susceptibility in an Iranian population. Background: Interleukin 16 (IL-16), a multifunctional cytokine, plays a vital role in modulation of immune system. Methods: In present case control and cross sectional study, IL-16 gene variant in 300 patients with hepatitis C (HCV) infection and 300 healthy individuals were analyzed. To evaluate this possible association, genomic DNA from venous blood was extracted and genotypes of IL-16 rs4072111 variant were determined by polymerase chain reaction- Fragments Length Polymorphism Technique (PCR-RFLP)...
2018: Gastroenterology and Hepatology From Bed to Bench
Giulia F Del Gobbo, E Magda Price, Courtney W Hanna, Wendy P Robinson
Background: 5,10-Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in one-carbon metabolism that ensures the availability of methyl groups for methylation reactions. Two single-nucleotide polymorphisms (SNPs) in the MTHFR gene, 677C>T and 1298A>C, result in a thermolabile enzyme with reduced function. These variants, in both the maternal and/or fetal genes, have been associated with pregnancy complications including miscarriage, neural tube defects (NTDs), and preeclampsia (PE), perhaps due to altered capacity for DNA methylation (DNAm)...
2018: Clinical Epigenetics
Duan Zeng, Shen He, Shunying Yu, Guanjun Li, Changlin Ma, Yi Wen, Yifeng Shen, Yimin Yu, Huafang Li
Background: Increasing evidence has indicated that dysfunction of miR-124 and target gene regulator of G protein signaling 4 ( RGS4 ) may be involved in the etiology and treatment of major depressive disorder (MDD). However, the molecular mechanisms are not fully understood. This study aimed to investigate whether common genetic variations in these two genes are associated with MDD and therapeutic response to antidepressants in the Chinese population. Methods: Three polymorphisms including rs531564 (a functional single-nucleotide polymorphism [SNP] in MIR124-1 ), rs10759 (a microRNA-binding site SNP in RGS4 ), and rs951436 (a promoter SNP in RGS4 ) were genotyped in 225 Chinese MDD patients and 436 controls...
2018: Neuropsychiatric Disease and Treatment
Harita Gogri, Sabita Ray, Snehal Agrawal, S Aruna, Kanjaksha Ghosh, Ajit Gorakshakar
BACKGROUND: Molecular genotyping of ABO blood group system has identified more than 60 "O" group alleles based on the single-nucleotide polymorphisms present in the ABO gene. Heterogeneity of O group alleles has been observed in various countries from South America, Europe, Middle East, and Asia. India is a vast country with more than 1300 million population which is divided into various ethnic and tribal groups. However, very little is known about the heterogeneity of O alleles in Indians...
January 2018: Asian Journal of Transfusion Science
Jun Muratsu, Masahiro Koseki, Daisaku Masuda, Yuji Yasuga, Satoki Tomoyama, Keiji Ataka, Yoshiki Yagi, Atsushi Nakagawa, Hidehumi Hamada, Shigeki Fujita, Hiroaki Hattori, Tohru Ohama, Makoto Nishida, Hisatoyo Hiraoka, Yuji Matsuzawa, Shizuya Yamashita
We report a case of Tangier disease with Leriche syndrome and bleeding tendency. In this male patient, nasal hemorrhage had been observed frequently throughout childhood. At 46 years old, he experienced effort angina, and coronary angiography demonstrated 75% stenosis in the right coronary artery. Orange-colored tonsils, mild hepatosplenomegaly and very low levels of serum high-density lipoprotein cholesterol (HDL-C) were observed, and the patient was diagnosed with Tangier disease. At 52 years old, effort angina recurred...
March 20, 2018: Journal of Atherosclerosis and Thrombosis
Xu Wang, Xiaochang Zhang, Lina Jin, Zhiguang Yang, Wei Li, Jiuwei Cui
OBJECTIVE: Early detection and diagnosis of lung cancer remain challenging but would improve patient prognosis. The goal of this study is to develop a model to estimate the risk of lung cancer for a given individual. METHODS: We conducted a case-control study to develop a predictive model to identify individuals at high risk for lung cancer. Clinical data from 500 lung cancer patients and 500 population-based age- and gender-matched controls were used to develop and evaluate the model...
February 28, 2018: Cancer Biomarkers: Section A of Disease Markers
Suresh Venkateswaran, Jarod Prince, David J Cutler, Urko M Marigorta, David T Okou, Sampath Prahalad, David Mack, Brendan Boyle, Thomas Walters, Anne Griffiths, Cary G Sauer, Neal LeLeiko, David Keljo, James Markowitz, Susan S Baker, Joel Rosh, Marian Pfefferkorn, Melvin B Heyman, Ashish Patel, Anthony Otley, Robert Baldassano, Joshua Noe, Paul Rufo, Maria Oliva-Hemker, Sonia Davis, Michael E Zwick, Greg Gibson, Lee A Denson, Jeffrey Hyams, Subra Kugathasan
Background: The genetic contributions to pediatric onset ulcerative colitis (UC), characterized by severe disease and extensive colonic involvement, are largely unknown. In adult onset UC, Genome Wide Association Study (GWAS) has identified numerous loci, most of which have a modest susceptibility risk (OR 0.84-1.14), with the exception of the human leukocyte antigen (HLA) region on Chromosome 6 (OR 3.59). Method: To study the genetic contribution to exclusive pediatric onset UC, a GWAS was performed on 466 cases with 2099 healthy controls using UK Biobank array...
March 19, 2018: Inflammatory Bowel Diseases
Xiaowei Wu, Changxin Li, Jinming Mao, Ling Li, Yan Liu, Yao Hou
The aim of this study was to find related pathogenic genes in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy in (CADASIL)-like patients. The direct sequencing and high-throughput multiplex polymerase chain reaction (PCR) was performed to screen for related genes. The clinical and imaging data of a CADASIL-like patient (the pro-band) and his family members were collected. At first, the known hereditary cerebral vascular genes of the pro-band were screened with direct sequencing to find candidate gene mutations...
March 15, 2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
Jian Zeng, Dorian Garrick, Jack Dekkers, Rohan Fernando
Genomic prediction exploits single nucleotide polymorphisms (SNPs) across the whole genome for predicting genetic merit of selection candidates. In most models for genomic prediction, e.g. BayesA, B, C, R and GBLUP, independence of SNP effects is assumed. However, SNP effects are expected to be locally dependent given the presence of a nearby QTL because SNPs surrounding the QTL do not segregate independently. A consequence of ignoring this dependence is that SNPs with small effects may be overly shrunk, e...
2018: PloS One
Lihong Wang, Chih-Hsin Tang, Tingting Lu, Yi Sun, Guohong Xu, Chien-Chung Huang, Shun-Fa Yang, Chen-Ming Su
Rheumatoid arthritis (RA) is a chronic systemic inflammatory disease. To date, the specific mechanisms that drive RA disease remain unknown and provide the impetus for genetic investigations into the development of RA. Researchers hope to identify gene polymorphisms that could serve as treatment targets in patients with RA. We have previously suggested that the gene encoding the pro-inflammatory adipokine resistin (RETN) may correlate with RA development. In this report, we sought to determine whether selected RETN single nucleotide polymorphisms (SNPs) are associated with RA susceptibility and clinicopathological characteristics...
March 2018: Medicine (Baltimore)
V N Shishkova, T V Adasheva, A Yu Remenik, V N Valyaeva, V M Shklovsky
AIM: To study the relationship between clinical-anthropometric, biochemical, metabolic, vascular-inflammatory, molecular-genetic parameters and the development of the first ischemic stroke, and to develop a prognostic model for determining the probability of its occurrence. MATERIAL AND METHODS: The study included 196 first ischemic stroke patients and 119 healthy people matched for age, place of residence and nationality to the group of patients. The main anthropometric, clinical, biochemical, metabolic parameters and markers of vascular inflammation and endothelial dysfunction were assessed...
2018: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
Ena Xiao, Qiang Chen, Aaron L Goldman, Hao Yang Tan, Kaitlin Healy, Brad Zoltick, Saumitra Das, Bhaskar Kolachana, Joseph H Callicott, Dwight Dickinson, Karen F Berman, Daniel R Weinberger, Venkata S Mattay
BACKGROUND: We explored the cumulative effect of several late-onset Alzheimer's disease (LOAD) risk loci using a polygenic risk profile score (RPS) approach on measures of hippocampal function, cognition, and brain morphometry. METHODS: In a sample of 231 healthy control subjects (19-55 years of age), we used an RPS to study the effect of several LOAD risk loci reported in a recent meta-analysis on hippocampal function (determined by its engagement with blood oxygen level-dependent functional magnetic resonance imaging during episodic memory) and several cognitive metrics...
November 2017: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
Xinwei Chen, Dominika Lewandowska, Miles R Armstrong, Katie Baker, Tze-Yin Lim, Micha Bayer, Brian Harrower, Karen McLean, Florian Jupe, Kamil Witek, Alison K Lees, Jonathan D Jones, Glenn J Bryan, Ingo Hein
A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes. We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis...
March 20, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Salpie Nowinski, Aida Santaolalla, Ben O'Leary, Massimo Loda, Ayesha Mirchandani, Mark Emberton, Mieke Van Hemelrijck, Anita Grigoriadis
Novel approaches for classification, including molecular features, are needed to direct therapy for men with low-grade prostate cancer (PCa), especially men on active surveillance. Risk alleles identified from genome-wide association studies (GWAS) could improve prognostication. Those risk alleles that coincided with genes and somatic copy number aberrations associated with progression of PCa were selected as the most relevant for prognostication. In a systematic literature review, a total of 698 studies were collated...
February 27, 2018: Oncotarget
Claire Hian Tzer Chan, Prabhakaran Munusamy, Sau Yeen Loke, Geok Ling Koh, Audrey Zhi Yi Yang, Hai Yang Law, Chui Sheun Yoon, Chow Yin Wong, Wei Sean Yong, Nan Soon Wong, Raymond Chee Hui Ng, Kong Wee Ong, Preetha Madhukumar, Chung Lie Oey, Gay Hui Ho, Puay Hoon Tan, Min Han Tan, Peter Ang, Yoon Sim Yap, Ann Siew Gek Lee
Genome-wide association studies (GWAS) have proven highly successful in identifying single nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk. The majority of these studies are on European populations, with limited SNP association data in other populations. We genotyped 51 GWAS-identified SNPs in two independent cohorts of Singaporean Chinese. Cohort 1 comprised 1294 BC cases and 885 controls and was used to determine odds ratios (ORs); Cohort 2 had 301 BC cases and 243 controls for deriving polygenic risk scores (PRS)...
February 27, 2018: Oncotarget
Chey Loveday, Kevin Litchfield, Max Levy, Amy Holroyd, Peter Broderick, Zsofia Kote-Jarai, Alison M Dunning, Kenneth Muir, Julian Peto, Rosalind Eeles, Douglas F Easton, Darshna Dudakia, Nick Orr, Nora Pashayan, Alison Reid, Robert A Huddart, Richard S Houlston, Clare Turnbull
Testicular germ cell tumor (TGCT), the most common cancer in men aged 18 to 45 years, has a strong heritable basis. Genome-wide association studies (GWAS) have proposed single nucleotide polymorphisms (SNPs) at a number of loci influencing TGCT risk. To further evaluate the association of recently proposed risk SNPs with TGCT at 2q14.2, 3q26.2, 7q36.3, 10q26.13 and 15q21.3, we analyzed genotype data on 3,206 cases and 7,422 controls. Our analysis provides independent replication of the associations for risk SNPs at 2q14...
February 27, 2018: Oncotarget
Luis Varona, Andres Legarra, Miguel A Toro, Zulma G Vitezica
In the last decade, genomic selection has become a standard in the genetic evaluation of livestock populations. However, most procedures for the implementation of genomic selection only consider the additive effects associated with SNP (Single Nucleotide Polymorphism) markers used to calculate the prediction of the breeding values of candidates for selection. Nevertheless, the availability of estimates of non-additive effects is of interest because: (i) they contribute to an increase in the accuracy of the prediction of breeding values and the genetic response; (ii) they allow the definition of mate allocation procedures between candidates for selection; and (iii) they can be used to enhance non-additive genetic variation through the definition of appropriate crossbreeding or purebred breeding schemes...
2018: Frontiers in Genetics
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