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Snp-snp interaction

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https://www.readbyqxmd.com/read/28346566/gene-gene-interaction-between-pparg-and-apoe-gene-on-late-onset-alzheimer-s-disease-a-case-control-study-in-chinese-han-population
#1
S Wang, L Guan, D Luo, J Liu, H Lin, X Li, X Liu
AIMS: The aim was to investigate the impact of PPARG and APOE gene single nucleotide polymorphisms (SNPs) and additional gene- gene interaction on late-onset Alzheimer's disease (LOAD) risk based on Chinese Han population. METHODS: A total of 928 participants (466 males, 462 females), with a mean age of 81.3 ± 16.4 years old, were included in the study, including 460 LOAD patients and 468 normal controls participants. Logistic regression was performed to investigate association between SNP and LOAD risk and generalized multifactor dimensionality reduction (GMDR) was used to analysis the gene-gene interaction...
2017: Journal of Nutrition, Health & Aging
https://www.readbyqxmd.com/read/28345816/germline-variation-in-the-3-untranslated-region-of-the-pou2af1-gene-is-associated-with-susceptibility-to-lymphoma
#2
Kan Zhai, Jiang Chang, Jinlong Hu, Chen Wu, Dongxin Lin
Genetic variations in certain genes may alter the susceptibility to lymphoma. We searched electronic databases and selected candidate single-nucleotide polymorphisms (SNPs) located within 3'-untranslated regions (3'-UTRs) that might affect miRNA-binding ability in the 50 most dysregulated genes in lymphoma for further study. We found that rs1042752-located in the 3'-UTR of POU2AF1, which plays a vital role in lymphomagenesis-was significantly associated with lymphoma risk in a case-control study with 793 patients and 939 controls...
March 27, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28345493/genetic-risk-scores-sex-and-dietary-factors-interact-to-alter-serum-uric-acid-trajectory-among-african-american-urban-adults
#3
May A Beydoun, Jose-Atilio Canas, Marie T Fanelli-Kuczmarski, Salman M Tajuddin, Michele K Evans, Alan B Zonderman
Serum uric acid (SUA), a causative agent for gout among others, is affected by both genetic and dietary factors, perhaps differentially by sex. We evaluated cross-sectional (SUAbase) and longitudinal (SUArate) associations of SUA with a genetic risk score (GRS), diet and sex. We then tested the interactive effect of GRS, diet and sex on SUA. Longitudinal data on 766 African-American urban adults participating in the Healthy Aging in Neighborhood of Diversity across the Lifespan study were used. In all, three GRS for SUA were created from known SUA-associated SNP (GRSbase (n 12 SNP), GRSrate (n 3 SNP) and GRStotal (n 15 SNP))...
March 27, 2017: British Journal of Nutrition
https://www.readbyqxmd.com/read/28345264/blood-transcriptomes-and-de-novo-identification-of-candidate-loci-for-mating-success-in-lekking-great-snipe-gallinago-media
#4
Jacob Höglund, Biao Wang, Stein Are Saether, Mozes Pil Kyu Blom, Peder Fiske, Peter Halvarsson, Gavin J Horsburgh, Terry Burke, John Atle Kålås, Robert Ekblom
We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called Single Nucleotide Polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking...
March 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28344560/nitric-oxide-has-a-concentration-dependent-effect-on-the-cell-cycle-acting-via-ein2-in-arabidopsis-thaliana-cultured-cells
#5
Galina V Novikova, Luis A J Mur, Alexander V Nosov, Artem A Fomenkov, Kirill S Mironov, Anna S Mamaeva, Evgeny S Shilov, Victor Y Rakitin, Michael A Hall
Ethylene is known to influence the cell cycle (CC) via poorly characterized roles whilst nitric oxide (NO) has well-established roles in the animal CC but analogous role(s) have not been reported for plants. As NO and ethylene signaling events often interact we examined their role in CC in cultured cells derived from Arabidopsis thaliana wild-type (Col-0) plants and from ethylene-insensitive mutant ein2-1 plants. Both NO and ethylene were produced mainly during the first 5 days of the sub-cultivation period corresponding to the period of active cell division...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28343162/mesothelin-promoter-variants-are-associated-with-increased-soluble-mesothelin-related-peptide-levels-in-asbestos-exposed-individuals
#6
Chiara De Santi, Perla Pucci, Alessandra Bonotti, Ombretta Melaiu, Monica Cipollini, Roberto Silvestri, Veronika Vymetalkova, Elisa Barone, Elisa Paolicchi, Alda Corrado, Irene Lepori, Irene Dell'Anno, Lucia Pellè, Pavel Vodicka, Luciano Mutti, Rudy Foddis, Alfonso Cristaudo, Federica Gemignani, Stefano Landi
BACKGROUND: Soluble mesothelin-related peptide (SMRP) is a promising diagnostic biomarker for malignant pleural mesothelioma (MPM), but various confounders hinder its usefulness in surveillance programmes. We previously showed that a single nucleotide polymorphism (SNP) within the 3'untranslated region (3'UTR) of the mesothelin (MSLN) gene could affect the levels of SMRP. OBJECTIVES: To focus on SNPs located within MSLN promoter as possible critical genetic variables in determining SMRP levels...
March 25, 2017: Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/28334077/a-powerful-and-efficient-two-stage-method-for-detecting-gene-to-gene-interactions-in-gwas
#7
Jakub Pecanka, Marianne A Jonker, Zoltan Bochdanovits, Aad W Van Der Vaart
For over a decade functional gene-to-gene interaction (epistasis) has been suspected to be a determinant in the "missing heritability" of complex traits. However, searching for epistasis on the genome-wide scale has been challenging due to the prohibitively large number of tests which result in a serious loss of statistical power as well as computational challenges. In this article, we propose a two-stage method applicable to existing case-control data sets, which aims to lessen both of these problems by pre-assessing whether a candidate pair of genetic loci is involved in epistasis before it is actually tested for interaction with respect to a complex phenotype...
February 6, 2017: Biostatistics
https://www.readbyqxmd.com/read/28327142/exome-sequencing-identified-rare-variants-in-genes-hspg2-and-atp2b4-in-a-family-segregating-developmental-dysplasia-of-the-hip
#8
Sulman Basit, Alia M Albalawi, Essa Alharby, Khalid I Khoshhal
BACKGROUND: Developmental dysplasia of the hip (DDH) is a common pathological condition of the musculoskeletal system in infants which results in a congenital and developmental malformation of the hip joint. DDH is a spectrum of pathologies affecting the infant hip ranging from asymptomatic subtle radiographic signs through mild instability to frank dislocations with acetabular dysplasia. A Saudi family with three affected individuals with DDH was identified and genetic analysis was performed to detect the possible genetic defect(s) underlying DDH in the affected members of the family...
March 21, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28322508/the-influence-of-ampk-subunit-alpha-2-prkaa2-genetic-polymorphisms-with-susceptibility-with-type-2-diabetes-mellitus-and-diabetic-nephropathy-in-chinese-population
#9
Qingchu Li, Cuilin Li, Haoyun Li, Liu Zeng, Zhiqiang Kang, Yu Mao, Xinyue Tang, Panpan Zheng, Li He, Fang Luo, Zhi Li
BACKGROUND: It has been well recognized that the AMP-activated protein kinase (AMPK) is a key factor influencing the development of type 2 diabetes mellitus (T2DM). The single-nucleotide polymorphism (SNP) rs2746342 in AMPK α2 subunit gene (PRKAA2) has been found to be associated with the susceptibility to T2DM in the Chinese Han population recently. This study further investigates the association of PRKAA2 genotypes with the susceptibility to T2DM and its complication disease, diabetic nephropathy...
March 21, 2017: Journal of Diabetes
https://www.readbyqxmd.com/read/28321238/association-of-non-synonymous-variants-in-wipf3-and-lipa-genes-with-abdominal-aortic-aneurysm-an-autopsy-study
#10
Yuko Maeda, Noriko Sato, Makiko Naka-Mieno, Seijiro Mori, Tomio Arai, Masashi Tanaka, Masaaki Muramatsu, Motoji Sawabe
BACKGROUND: Abdominal aortic aneurysm (AAA) is a multifactorial disease with strong genetic components. Various genetic loci have been associated with clinical AAA, but few studies have investigated pathological AAA, an intermediate phenotype of the disease. METHODS: We examined 2263 consecutive autopsies of older Japanese subjects from a study on geriatric diseases in Japanese individuals (The JG-SNP study). The presence of AAA was determined with a pathological diagnosis during autopsy...
December 2016: Journal of Geriatric Cardiology: JGC
https://www.readbyqxmd.com/read/28319867/phototherapeutic-spectrum-expansion-through-synergistic-effect-of-mesoporous-silica-trio-nanohybrids-against-antibiotic-resistant-gram-negative-bacterium
#11
Yaswanth Kuthati, Ranjith Kumar Kankala, Prabhakar Busa, Shi-Xiang Lin, Jin-Pei Deng, Chung-Yuan Mou, Chia-Hung Lee
The extensive impact of antibiotic resistance has led to the exploration of new anti-bacterial modalities. We designed copper impregnated mesoporous silica nanoparticles (Cu-MSN) with immobilizing silver nanoparticles (SNPs) to apply photodynamic inactivation (PDI) of antibiotic-resistant E. coli. SNPs were decorated over the Cu-MSN surfaces by coordination of silver ions on diamine-functionalized Cu-MSN and further reduced to silver nanoparticles with formalin. We demonstrate that silver is capable of sensitizing the gram-negative bacteria E...
March 7, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28318885/genetic-association-of-the-functional-cdhr3-genotype-with-early-onset-adult-asthma-in-japanese-populations
#12
Jun Kanazawa, Hironori Masuko, Yohei Yatagai, Tohru Sakamoto, Hideyasu Yamada, Yoshiko Kaneko, Haruna Kitazawa, Hiroaki Iijima, Takashi Naito, Takefumi Saito, Emiko Noguchi, Satoshi Konno, Masaharu Nishimura, Tomomitsu Hirota, Mayumi Tamari, Nobuyuki Hizawa
BACKGROUND: Recent studies have demonstrated that a coding SNP (rs6967330, Cys529→Tyr) in cadherin-related family member 3 (CDHR3), which was previously associated with wheezing illness and hospitalizations in infancy, could support efficient human rhinovirus C (RV-C) entry and replication. Here, we sought to examine the genetic contribution of this variant to the development of adult asthma. METHODS: We performed a candidate gene case-control association study of 2 independent Japanese populations (a total of 3366 adults)...
March 16, 2017: Allergology International: Official Journal of the Japanese Society of Allergology
https://www.readbyqxmd.com/read/28302551/role-of-structural-bioinformatics-in-drug-discovery-by-computational-snp-analysis-a-proposed-protocol-for-analyzing-variation-at-the-protein-level
#13
REVIEW
David K Brown, Özlem Tastan Bishop
With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps toward an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as genome-wide association studies and candidate gene association studies. However, these statistical methods do not provide an understanding of the functional effects of variation...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28301549/a-comprehensive-survey-of-genetic-variation-in-20-691-subjects-from-four-large-cohorts
#14
Sara Lindström, Stephanie Loomis, Constance Turman, Hongyan Huang, Jinyan Huang, Hugues Aschard, Andrew T Chan, Hyon Choi, Marilyn Cornelis, Gary Curhan, Immaculata De Vivo, A Heather Eliassen, Charles Fuchs, Michael Gaziano, Susan E Hankinson, Frank Hu, Majken Jensen, Jae H Kang, Christopher Kabrhel, Liming Liang, Louis R Pasquale, Eric Rimm, Meir J Stampfer, Rulla M Tamimi, Shelley S Tworoger, Janey L Wiggs, David J Hunter, Peter Kraft
The Nurses' Health Study (NHS), Nurses' Health Study II (NHSII), Health Professionals Follow Up Study (HPFS) and the Physicians Health Study (PHS) have collected detailed longitudinal data on multiple exposures and traits for approximately 310,000 study participants over the last 35 years. Over 160,000 study participants across the cohorts have donated a DNA sample and to date, 20,691 subjects have been genotyped as part of genome-wide association studies (GWAS) of twelve primary outcomes. However, these studies utilized six different GWAS arrays making it difficult to conduct analyses of secondary phenotypes or share controls across studies...
2017: PloS One
https://www.readbyqxmd.com/read/28299468/gw-sem-a-statistical-package-to-conduct-genome-wide-structural-equation-modeling
#15
Brad Verhulst, Hermine H Maes, Michael C Neale
Improving the accuracy of phenotyping through the use of advanced psychometric tools will increase the power to find significant associations with genetic variants and expand the range of possible hypotheses that can be tested on a genome-wide scale. Multivariate methods, such as structural equation modeling (SEM), are valuable in the phenotypic analysis of psychiatric and substance use phenotypes, but these methods have not been integrated into standard genome-wide association analyses because fitting a SEM at each single nucleotide polymorphism (SNP) along the genome was hitherto considered to be too computationally demanding...
March 15, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/28298201/the-patterns-of-genomic-variances-and-covariances-across-genome-for-milk-production-traits-between-chinese-and-nordic-holstein-populations
#16
Xiujin Li, Mogens Sandø Lund, Luc Janss, Chonglong Wang, Xiangdong Ding, Qin Zhang, Guosheng Su
BACKGROUND: With the development of SNP chips, SNP information provides an efficient approach to further disentangle different patterns of genomic variances and covariances across the genome for traits of interest. Due to the interaction between genotype and environment as well as possible differences in genetic background, it is reasonable to treat the performances of a biological trait in different populations as different but genetic correlated traits. In the present study, we performed an investigation on the patterns of region-specific genomic variances, covariances and correlations between Chinese and Nordic Holstein populations for three milk production traits...
March 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28295819/variants-in-bak1-spry4-and-gab2-are-associated-with-pediatric-germ-cell-tumors-a-report-from-the-children-s-oncology-group
#17
Erin L Marcotte, Nathan Pankratz, James F Amatruda, A Lindsay Frazier, Mark Krailo, Stella Davies, Jacqueline R Starr, C Lau Ching, Michelle Roesler, Erica Langer, Caroline Hallstrom, Anthony J Hooten, Jenny N Poynter
Germ cell tumors (GCT) are a rare form of childhood cancer that originate from the primordial germ cell. Recent genome-wide association studies (GWAS) have identified susceptibility alleles for adult testicular GCT (TGCT). We test whether these SNPs are associated with GCT in pediatric and adolescent populations. This case-parent triad study includes individuals with GCT diagnosed between ages 0-19. We evaluated 26 SNPs from GWAS of adult TGCT and estimated main effects for pediatric GCT within complete trios (N=366) using the transmission disequilibrium test...
March 13, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28294375/identification-of-the-interaction-between-bta-mir-370-and-olr1-gene-in-bovine-adipocyte
#18
H F Li, S H Wang, Y Guo, H B Zhao, X Y Li, X Wang
It has been shown that the oxidized low density lipoprotein receptor 1 (OLR1) gene plays an important role in the degradation of oxidized low density lipoprotein. Previous studies found a SNP in the 3'-untranslated region (3'-UTR) of the OLR1 gene associated with milk production traits in different dairy cattle populations and with loin eye area and marbling depth in beef cattle. MicroRNAs can regulate gene expression by binding the 3'-UTR of target genes to degrade or to repress the translation of target genes...
March 10, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28294290/genetic-obesity-risk-and-attenuation-effect-of-physical-fitness-in-mexican-mestizo-population-a-case-control-study
#19
Paula Costa-Urrutia, Carolina Abud, Valentina Franco-Trecu, Valentina Colistro, Martha Eunice Rodríguez-Arellano, Joel Vázquez-Pérez, Julio Granados, Marilia Seelaender
We analyzed commonly reported European and Asian obesity-related gene variants in a Mexican-Mestizo population through each single nucleotide polymorphism (SNP) and a genetic risk score (GRS) based on 23 selected SNPs. Study subjects were physically active Mexican-Mestizo adults (n  =  608) with body mass index (BMI) values from 18 to 55 kg/m(2) . For each SNP and for the GRS, logistic models were performed to test for simple SNP associations with BMI, fat mass percentage (FMP), waist circumference (WC), and the interaction with VO2max and muscular endurance (ME)...
March 15, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28293931/investigation-of-the-possible-role-of-the-hippo-yap1-pathway-in-asthma-and-allergy
#20
Lili E Fodor, András Gézsi, Ldikó Ungvári, Agnes F Semsei, Zsófia Gál, Adrienne Nagy, Gabriella Gálffy, Lilla Tamási, András Kiss, Péter Antal, Csaba Szalai
PURPOSE: Several lines of evidence indicate that the Hippo/Yes-associated protein 1 (YAP1) pathways might play a role in the pathogenesis of asthma. To investigate the possible role of the Hippo/YAP1 pathway in the pathogenesis of asthma or its phenotypes. METHODS: The levels of gene expressions of the members of the Hippo/YAP1 were compared. The presence of the proteins of the YAP1 and FRMD6 were analyzed with Western blot in induced sputum of 18 asthmatic subjects and 10 control subjects...
May 2017: Allergy, Asthma & Immunology Research
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