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https://www.readbyqxmd.com/read/29166655/how-well-do-you-know-your-mutation-complex-effects-of-genetic-background-on-expressivity-complementation-and-ordering-of-allelic-effects
#1
Christopher H Chandler, Sudarshan Chari, Alycia Kowalski, Lin Choi, David Tack, Michael DeNieu, William Pitchers, Anne Sonnenschein, Leslie Marvin, Kristen Hummel, Christian Marier, Andrew Victory, Cody Porter, Anna Mammel, Julie Holms, Gayatri Sivaratnam, Ian Dworkin
For a given gene, different mutations influence organismal phenotypes to varying degrees. However, the expressivity of these variants not only depends on the DNA lesion associated with the mutation, but also on factors including the genetic background and rearing environment. The degree to which these factors influence related alleles, genes, or pathways similarly, and whether similar developmental mechanisms underlie variation in the expressivity of a single allele across conditions and among alleles is poorly understood...
November 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29166619/extensive-homeostatic-t-cell-phenotypic-variation-within-the-collaborative-cross
#2
Jessica B Graham, Jessica L Swarts, Michael Mooney, Gabrielle Choonoo, Sophia Jeng, Darla R Miller, Martin T Ferris, Shannon McWeeney, Jennifer M Lund
The Collaborative Cross (CC) is a panel of reproducible recombinant inbred mouse strains with high levels of standing genetic variation, affording an unprecedented opportunity to perform experiments in a small animal model containing controlled genetic diversity while allowing for genetic replicates. Here, we advance the utility of this unique mouse resource for immunology research because it allows for both examination and genetic dissection of mechanisms behind adaptive immune states in mice with distinct and defined genetic makeups...
November 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/29165854/mmp-3-1171-5a-6a-lys45glu-variants-affect-serum-levels-of-matrix-metalloproteinase-mmp-3-and-correlate-with-severity-of-copd-a-study-of-mmp-3-mmp-7-and-mmp-12-in-a-tunisian-population
#3
Sarra Bchir, Hela Ben Nasr, Abdelhamid Garrouch, Amel Ben Anes, Ammar Abbassi, Zouhair Tabka, Karim Chahed
OBJECTIVE: The goal of this study was to examine the role of MMP-3 (-1171 5A/6A; Lys45Glu (A/G)), MMP-7 (-181) A/G and MMP-12 (-82 A/G; Asn357Ser (A/G)) variants in the development and severity of chronic obstructive pulmonary disease (COPD) in Tunisians. METHODS: Plethysmography was performed in all participants to measure FEV1, FVC and FEV1/FVC parameters. Genotyping of MMP-3, MMP-7 and MMP-12 polymorphisms was carried out in 138 patients with COPD and 216 healthy controls using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)...
November 22, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/29165714/blood-lipid-genetic-scores-the-hmgcr-gene-and-cancer-risk-a-mendelian-randomization-study
#4
Marju Orho-Melander, George Hindy, Signe Borgquist, Christina-Alexandra Schulz, Jonas Manjer, Olle Melander, Tanja Stocks
Background: It is unclear whether there are causal associations between blood lipids, statin use and cancer risks. Under certain assumptions, Mendelian randomization analysis of a genetic marker for an exposure eliminates reverse causation and confounding. Methods: We applied Mendelian randomization analysis to genetic scores, comprising 26-41 single-nucleotide polymorphisms (SNPs), as instrumental variables (IVs) for triglycerides and low- and high-density lipoprotein cholesterol (LDLC, HDLC), using a prospective cohort of 26 904 individuals in which there were 6607 incident cancers...
November 20, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/29165669/clinvar-improving-access-to-variant-interpretations-and-supporting-evidence
#5
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth R Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang, Karen Karapetyan, Kenneth Katz, Chunlei Liu, Zenith Maddipatla, Adriana Malheiro, Kurt McDaniel, Michael Ovetsky, George Riley, George Zhou, J Bradley Holmes, Brandi L Kattman, Donna R Maglott
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165633/genetic-variation-at-ifnl4-influences-extrahepatic-interferon-stimulated-gene-expression-in-chronic-hcv-patients
#6
Brad R Rosenberg, Catherine A Freije, Naoko Imanaka, Spencer T Chen, Jennifer L Eitson, Rachel Caron, Skyler A Uhl, Marija Zeremski, Andrew Talal, Ira M Jacobson, Charles M Rice, John W Schoggins
Polymorphisms at IFNL4 strongly influence spontaneous resolution and interferon therapeutic response in hepatitis C virus (HCV) infection. In chronic HCV, unfavorable alleles are associated with elevated interferon stimulated gene (ISG) expression in the liver, but extrahepatic effects are less well characterized. We used RNA-Seq to examine whether IFNL4 genetic variation (rs368234815) modulates ISG expression in peripheral blood mononuclear cells (PBMC) during chronic HCV. ISG expression was elevated in unstimulated PBMC homozygous for the unfavorable ΔG IFNL4 variant; expression following IFNα stimulation was comparable across genotypes...
November 20, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29165333/pressure-for-pattern-specific-intertypic-recombination-between-sabin-polioviruses-evolutionary-implications
#7
Ekaterina Korotkova, Majid Laassri, Tatiana Zagorodnyaya, Svetlana Petrovskaya, Elvira Rodionova, Elena Cherkasova, Anatoly Gmyl, Olga E Ivanova, Tatyana P Eremeeva, Galina Y Lipskaya, Vadim I Agol, Konstantin Chumakov
Complete genomic sequences of a non-redundant set of 70 recombinants between three serotypes of attenuated Sabin polioviruses as well as location (based on partial sequencing) of crossover sites of 28 additional recombinants were determined and compared with the previously published data. It is demonstrated that the genomes of Sabin viruses contain distinct strain-specific segments that are eliminated by recombination. The presumed low fitness of these segments could be linked to mutations acquired upon derivation of the vaccine strains and/or may have been present in wild-type parents of Sabin viruses...
November 22, 2017: Viruses
https://www.readbyqxmd.com/read/29165231/sequence-optimized-real-time-reverse-transcription-polymerase-chain-reaction-assay-for-detection-of-crimean-congo-hemorrhagic-fever-virus
#8
Jeffrey W Koehler, Korey L Delp, Adrienne T Hall, Scott P Olschner, Brian J Kearney, Aura R Garrison, Louis A Altamura, Cynthia A Rossi, Timothy D Minogue
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus of the genus Nairovirus within the family Bunyaviridae. Infection can result in general myalgia, fever, and headache with some patients developing hemorrhagic fever with mortality rates ranging from 5% to 30%. CCHFV has a wide geographic range that includes Africa, Asia, the Middle East, and Europe with nucleotide sequence variation approaching 20% across the three negative-sense RNA genome segments. While phylogenetic clustering generally aligns with geographic origin of individual strains, distribution can be wide due to tick/CCHFV dispersion via migrating birds...
November 20, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29165176/the-different-roles-of-innate-immune-receptors-in-inflammation-and-carcinogenesis-between-races
#9
Natsu Yamaguchi, Yoshimi Suzuki, M H Mahbub, Hidekazu Takahashi, Ryosuke Hase, Yasutaka Ishimaru, Hiroshi Sunagawa, Rie Watanabe, Yoshinobu Eishi, Tsuyoshi Tanabe
Innate immune factors exert widespread effects on cytokine secretion, cell survival, autophagy, and apoptosis. Nucleotide-binding and oligomerization domain-like receptors (NLRs) are members of the innate immune system in the cytosol that sense pathogens, endogenous danger molecules such as uric acid, and pollutants. Nucleotide-binding oligomerization domain-containing protein 1 and 2 (NOD1 and NOD2) are components of NLR family, and ligands of these factors are γ-D-glutamyl-meso-diaminopimelic acid (iE-DAP) and muramyl dipeptide (MDP), respectively...
October 11, 2017: Environmental Health and Preventive Medicine
https://www.readbyqxmd.com/read/29165161/rare-variants-of-rnf213-and-moyamoya-non-moyamoya-intracranial-artery-stenosis-occlusion-disease-risk-a-meta-analysis-and-systematic-review
#10
Xin Liao, Jing Deng, Wenjie Dai, Tong Zhang, Junxia Yan
BACKGROUND: The p.R4810K and other rare variants of ring finger protein 213 gene (RNF213) were illustrated as susceptibility variants for moyamoya (MMD) and non-moyamoya intracranial artery stenosis/occlusion disease (ICASO) recently. However, the effect sizes of p.R4810K were in great discrepancy even in studies of the same ethnic population and firm conclusions of other rare variants have been elusive given the small sample sizes and lack of replication. Thus, we performed this study to quantitatively evaluate whether or to what extent the rare variants of RNF213 contribute to MMD and ICASO in different populations...
November 2, 2017: Environmental Health and Preventive Medicine
https://www.readbyqxmd.com/read/29165136/genetic-analysis-of-rnf213-p-r4810k-variant-in-non-moyamoya-intracranial-artery-stenosis-occlusion-disease-in-a-chinese-population
#11
Tong Zhang, Congrong Guo, Xin Liao, Jian Xia, XiaoXiao Wang, Jing Deng, Junxia Yan
OBJECTIVES: RNF213 p.R4810K was identified as a susceptibility variant for moyamoya disease in Asia and non-moyamoya intracranial artery stenosis/occlusion disease in Japan and Korea recently. The occurrence of this variant was evaluated in patients with non-moyamoya intracranial artery stenosis/occlusion disease in China. METHODS: Two study populations were used in this study. One was recruited from the Second Hospital of Hebei Medical University from April 2015 to May 2016...
April 24, 2017: Environmental Health and Preventive Medicine
https://www.readbyqxmd.com/read/29165086/association-between-ltf-polymorphism-and-risk-of-hiv-1-transmission-among-zambian-seropositive-mothers
#12
Luisa Zupin, Vania Polesello, Ludovica Segat, Anselmo Jiro Kamada, Louise Kuhn, Sergio Crovella
BACKGROUND: Lactoferrin is a member of the innate immune system acting in the first line of defence against pathogens, and it is known for its antibacterial, antifungal and antiviral activity, including HIV-1. Two polymorphisms, T29A and R47K, in the exon 1 region of the LTF gene (encoding for the lactoferrin protein) were previously described as able to influence the lactoferrin antimicrobial function. OBJECTIVES: LTF T29A and R47K genetic variants were analysed in a Zambian population to unravel if these polymorphisms could play a role in HIV-1 mother-to-child HIV-1 transmission...
November 19, 2017: Current HIV Research
https://www.readbyqxmd.com/read/29164999/collagen-type-i-a2-gene-polymorphisms-and-susceptibility-to-intracranial-aneurysms-a-meta-analysis-of-genetic-association-studies
#13
Alexandros G Brotis, Anastasia Tasiou, Theofanis Giannis, Athanasios Paschalis, Kostas N Fountas
BACKGROUND: The development, evolution and rupture of intracranial aneurysms is in part related to genetic factors. The role Collagen type I a2 genetic polymorphisms has not been clarified yet. MATERIAL AND METHODS: A meta-analysis was realized by means of a genotype model-fitting processes (allele contrast, recessive, dominant, additive, and co-dominant), and a model-free approach using the generalized odds ratio (ORG). The latter was assessed in association to the degree of dominance (h-index)...
November 22, 2017: International Journal of Neuroscience
https://www.readbyqxmd.com/read/29164717/antibiotics-reduce-genetic-diversity-of-core-species-in-the-honeybee-gut-microbiome
#14
Kasie Raymann, Louis-Marie Bobay, Nancy A Moran
The gut microbiome plays a key role in animal health, and perturbing it can have detrimental effects. One major source of perturbation to microbiomes, in humans and human-associated animals, is exposure to antibiotics. Most studies of how antibiotics affect the microbiome have used amplicon sequencing of highly conserved 16S rRNA sequences, as in a recent study showing that antibiotic treatment severely alters the species-level composition of the honeybee gut microbiome. But because the standard 16S rRNA-based methods cannot resolve closely related strains, strain-level changes could not be evaluated...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29164635/influence-of-genetic-variants-of-idh1-idh2-tet2-and-dnmt3a-on-cytarabine-cytotoxicity-in-different-populations
#15
Y Wang, J K Lamba
WHAT IS KNOWN AND OBJECTIVE: Cytarabine (ara-C) is the mainstay of treatment for acute myeloid leukaemia. Resistance and toxicity are common reasons for its treatment failure. Genetic variants of susceptibility genes may be involved in resistance and toxicity to ara-C. This study is aimed to explore the association between influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in European and/or African populations. METHODS: HapMap cell lines derived from European descent (CEU) and African descent (YRI) were exposed to ara-C at different concentrations (1, 5, 40 and 80 μmol/L)...
November 21, 2017: Journal of Clinical Pharmacy and Therapeutics
https://www.readbyqxmd.com/read/29164477/genetic-variants-within-molecular-targets-of-antipsychotic-treatment-effects-on-treatment-response-schizophrenia-risk-and-psychopathological-features
#16
Marco Calabrò, Stefano Porcelli, Concetta Crisafulli, Sheng-Min Wang, Soo-Jung Lee, Changsu Han, Ashwin A Patkar, Prakash S Masand, Diego Albani, Ilaria Raimondi, Gianluigi Forloni, Sofia Bin, Carlotta Cristalli, Vilma Mantovani, Chi-Un Pae, Alessandro Serretti
Schizophrenia (SCZ) is a common and severe mental disorder. Genetic factors likely play a role in its pathophysiology as well as in treatment response. In the present study, we investigated the effects of several single nucleotide polymorphisms (SNPs) within 9 genes involved with antipsychotic (AP) mechanisms of action. Two independent samples were recruited. The Korean sample included 176 subjects diagnosed with SCZ and 326 healthy controls, while the Italian sample included 83 subjects and 194 controls. AP response as measured by the positive and negative syndrome scale (PANSS) was the primary outcome, while the secondary outcome was the SCZ risk...
November 21, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/29164277/high-prevalence-of-dengue-antibodies-and-the-arginine-variant-of-the-fc%C3%AE-riia-polymorphism-in-asymptomatic-individuals-in-a-population-of-minas-gerais-state-southeast-brazil
#17
Anna Carolina Toledo da Cunha Pereira, Tatiane Ribeiro de Siqueira, Andressa Anunciação de Oliveira Prado, Camila Almeida Veiga da Silva, Thaís de Fátima Silva Moraes, Alan Alex Aleixo, José Carlos de Magalhaes, Gabriel Augusto Pires de Souza, Betânia Paiva Drumond, Gustavo Portela Ferreira, Breno de Mello Silva, Cintia Lopes de Brito Magalhães, Luciana Lara Santos, Jaqueline Maria Siqueira Ferreira, Luiz Cosme Cotta Malaquias, Luiz Felipe Leomil Coelho
Dengue is the most prevalent arthropod-borne viral illness in humans worldwide. Single-nucleotide polymorphisms (SNPs) in genes involved in the immune response, such as dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN), IgG Fc receptor II-A (FcγRIIa), vitamin D receptor (VDR), and tumor necrosis factor alpha (TNF-α), were previously reported to be associated with susceptibility to dengue disease in different human populations. Therefore, due to the relevant association of host immune and genetic status with disease susceptibility/severity of dengue, this work aims to verify the frequency of anti-dengue virus antibodies and some dengue-associated risk SNPs in a population in Minas Gerais State, Southeast Brazil...
November 21, 2017: Immunogenetics
https://www.readbyqxmd.com/read/29164072/a-new-strain-collection-for-improved-expression-of-outer-membrane-proteins
#18
Ina Meuskens, Marcin Michalik, Nandini Chauhan, Dirk Linke, Jack C Leo
Almost all integral membrane proteins found in the outer membranes of Gram-negative bacteria belong to the transmembrane β-barrel family. These proteins are not only important for nutrient uptake and homeostasis, but are also involved in such processes as adhesion, protein secretion, biofilm formation, and virulence. As surface exposed molecules, outer membrane β-barrel proteins are also potential drug and vaccine targets. High production levels of heterologously expressed proteins are desirable for biochemical and especially structural studies, but over-expression and subsequent purification of membrane proteins, including outer membrane proteins, can be challenging...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29163652/phylogenic-analysis-of-serotype-asia1-foot-and-mouth-disease-virus-from-sulaimani-iraq-using-vp1-protein-heterogeneity-with-vaccine-strain-as1-shamir-89
#19
M O Baba Sheikh, P M A Rashid, A S Marouf, Z H Raheem, S C Janga
Foot-and-mouth disease virus (FMDV) serotypes O, A and Asia1 are responsible for a significant number of disease outbreaks in Iraq. The current study can be considered as the first molecular characterization of serotype Asia1 in Iraq. The present investigation reports the detection of serotype FMDV Asia1 from local farms in Sulaimani districts in 2012 and 2014 outbreaks. Phylogenetic analysis of the complete VP1 gene has shown that FMDV Asia1 field isolates were under genetic novel variant Sindh-08 (group VII) including PAK/iso/11 and TUR/13 strains...
2017: Iranian journal of veterinary research
https://www.readbyqxmd.com/read/29163640/a-review-of-pathway-based-analysis-tools-that-visualize-genetic-variants
#20
REVIEW
Elisa Cirillo, Laurence D Parnell, Chris T Evelo
Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological processes in which the affected genes and proteins are involved. Such analyses support an interactive evaluation of the possible effects of variations on function, regulation or interaction of gene products...
2017: Frontiers in Genetics
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