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Snp-snp interaction

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https://www.readbyqxmd.com/read/28081217/collective-genetic-interaction-effects-and-the-role-of-antigen-presenting-cells-in-autoimmune-diseases
#1
Hyung Jun Woo, Chenggang Yu, Jaques Reifman
Autoimmune diseases occur when immune cells fail to develop or lose their tolerance toward self and destroy body's own tissues. Both insufficient negative selection of self-reactive T cells and impaired development of regulatory T cells preventing effector cell activation are believed to contribute to autoimmunity. Genetic predispositions center around the major histocompatibility complex (MHC) class II loci involved in antigen presentation, the key determinant of CD4+ T cell activation. Recent studies suggested that variants in the MHC region also exhibit significant non-additive interaction effects...
2017: PloS One
https://www.readbyqxmd.com/read/28071057/programmed-transfer-of-sequence-information-into-molecularly-imprinted-polymer-mip-for-hexa-2-2-bithien-5-yl-dna-analog-formation-towards-single-nucleotide-polymorphism-snp-detection
#2
Katarzyna Bartold, Agnieszka Pietrzyk-Le, Tan-Phat Huynh, Zofia Iskierko, Marta I Sosnowska, Krzysztof Noworyta, Wojciech Lisowski, Francesco Maria Enrico Sannicolo, Silvia Cauteruccio, Emanuela Licandro, Francis D'Souza, Wlodzimierz Kutner
A new strategy of simple, inexpensive, rapid, and label-free single nucleotide polymorphism (SNP) detection using robust chemosensors with piezomicrogravimetric (PM), SPR, or capacitive impedimetry (CI) signal transduction is reported. Using these chemosensors, selective detection of a genetically relevant oligonucleotide under FIA conditions within 2 min is accomplished. An invulnerable to non-specific interaction molecularly imprinted polymer (MIP) with electrochemically synthesized probes of hexameric 2,2'-bithien-5-yl DNA analogs discriminating single purine-nucleobase mismatch at room temperature was used...
January 10, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28069809/the-receptor-interacting-serine-threonine-protein-kinase-1-ripk1-regulates-progranulin-levels
#3
Amanda R Mason, Lisa P Elia, Steven Finkbeiner
Progranulin (PGRN), a secreted growth factor, is a key regulator of inflammation and is genetically linked to two common and devastating neurodegenerative diseases. Haploinsufficiency mutations in GRN, the gene encoding PGRN, cause frontotemporal dementia (FTD) and a GRN SNP confers significantly increased risk for Alzheimer's disease (AD). Because cellular and animal data indicate that increasing PGRN can reverse phenotypes of both FTD and AD, modulating PGRN level has been proposed as a therapeutic strategy for both diseases...
January 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28069446/rich2-is-implicated-in-viraemic-control-of-hiv-1-in-black-south-african-individuals
#4
Maria Paximadis, Refilwe N Ngqobe, Richard E Chaisson, Neil A Martinson, Caroline T Tiemessen
An intronic single nucleotide polymorphism (SNP) in RICH2 (rs2072255; 255(i)), in complete linkage disequilibrium (LD) with an exonic SNP (rs2072254; 254(e)), has been identified in a genome wide association study to be associated with progression to AIDS in Caucasian individuals. RICH2 links tetherin to the cortical actin network and the RICH2/tetherin interaction has been shown to be important for the downstream activation of NF-κβ and the consequential promotion of proinflammatory responses. We investigated the role of these two SNPs in natural control of HIV-1 in black South Africans including healthy controls (HCs; N=102) and antiretroviral-naive HIV-1-infected controllers (HICs; N=52) and progressors (N=74)...
January 6, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28068350/genome-wide-association-mapping-and-genomic-selection-for-alfalfa-medicago-sativa-forage-quality-traits
#5
Elisa Biazzi, Nelson Nazzicari, Luciano Pecetti, E Charles Brummer, Alberto Palmonari, Aldo Tava, Paolo Annicchiarico
Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest)...
2017: PloS One
https://www.readbyqxmd.com/read/28060710/a-review-of-machine-learning-and-statistical-approaches-for-detecting-snp-interactions-in-high-dimensional-genomic-data
#6
Suneetha Uppu, Aneesh Krishna, Raj Gopalan
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature...
December 2, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28057877/previous-miscarriages-and-gli2-are-associated-with-anorectal-malformations-in-offspring
#7
Romy van de Putte, Charlotte H W Wijers, Ivo de Blaauw, Carlo L M Marcelis, Cornelius E J Sloots, Alice S Brooks, Paul M A Broens, Nel Roeleveld, Loes F M van der Zanden, Iris A L M van Rooij
STUDY QUESTION: Are anorectal malformations (ARMs) associated with previous miscarriages or single nucleotide polymorphisms (SNPs) in the Bone Morphogenetic Protein 4 (BMP4) and GLI family zinc finger 2 (GLI2) genes? SUMMARY ANSWER: The SNP rs3738880 in GLI2 and miscarriages were associated with ARM, especially in patients with multiple congenital anomalies (MCA). WHAT IS KNOWN ALREADY: ARM are one of the most common birth defects of the gastrointestinal tract...
January 5, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28057378/beneficial-effect-of-cetp-gene-polymorphism-in-combination-with-a-mediterranean-diet-influencing-lipid-metabolism-in-metabolic-syndrome-patients-cordioprev-study
#8
Antonio Garcia-Rios, Juan Francisco Alcala-Diaz, Francisco Gomez-Delgado, Javier Delgado-Lista, Carmen Marin, Ana Leon-Acuña, Antonio Camargo, Fernando Rodriguez-Cantalejo, Ruth Blanco-Rojo, Gracia Quintana-Navarro, Jose Maria Ordovas, Francisco Perez-Jimenez, Jose Lopez-Miranda, Pablo Perez-Martinez
The cholesteryl ester transfer protein (CETP) gene has been implicated in high-density lipoprotein (HDL-C) metabolism. However, little is known about the impact of this gene on metabolic syndrome (MetS) patients and its interaction with diet. Here, we evaluate whether the consumption of a Mediterranean diet, compared with a Low-fat diet, interacts with the rs3764261 SNP at the CETP locus to modify lipid metabolism in MetS patients. Plasma lipid concentrations and rs3764261 genotypes were determined in 424 MetS subjects participating in the CORDIOPREV clinical trial (NCT00924937)...
December 24, 2016: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/28056267/-association-between-eye-absent-homolog-4-gene-polymorphisms-and-occupational-noise-induced-hearing-loss
#9
Q Y Yang, X R Xu, J Jiao, Y X Zheng, L H He, S F Yu, G Z Gu, G S Chen, W H Zhou, H Wu, Y H Li, H L Zhang, Z R Zhang
Objective: To identify the association between genetic polymorphisms in the eye absent homolog 4 (EYA4) gene and noise-induced hearing loss (NIHL). Method: A nested case control study was conducted based on a cohort of noise-exposed subjects. In total, 292 cases were selected from a steel factory from 6 297 subjects during Jan 1, 2006 to Dec 12, 2015,who had an average hearing threshold of more than 40 dB(A); 584 matched control subjects for each case were designated on the basis of matched criteria including same gender, age (±5 years) and duration of exposure to noise (±2 years)...
January 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/28049826/myh9-binds-to-lncrna-gene-ptcsc2-and-regulates-foxe1-in-the-9q22-thyroid-cancer-risk-locus
#10
Yanqiang Wang, Huiling He, Wei Li, John Phay, Rulong Shen, Lianbo Yu, Baris Hancioglu, Albert de la Chapelle
A locus on chromosome 9q22 harbors a SNP (rs965513) firmly associated with risk of papillary thyroid carcinoma (PTC). The locus also comprises the forkhead box E1 (FOXE1) gene, which is implicated in thyroid development, and a long noncoding RNA (lncRNA) gene, papillary thyroid cancer susceptibility candidate 2 (PTCSC2). How these might interact is not known. Here we report that PTCSC2 binds myosin-9 (MYH9). In a bidirectional promoter shared by FOXE1 and PTCSC2, MYH9 inhibits the promoter activity in both directions...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28046022/association-of-tlr3-l412f-polymorphism-with-cytomegalovirus-infection-in-children
#11
Mirosława Studzińska, Agnieszka Jabłońska, Małgorzata Wiśniewska-Ligier, Dorota Nowakowska, Zuzanna Gaj, Zbigniew J Leśnikowski, Teresa Woźniakowska-Gęsicka, Jan Wilczyński, Edyta Paradowska
Intracellular Toll-like receptor 3 (TLR3) recognizes viral double-stranded RNA (dsRNA) and activates antiviral immune responses through the production of type I interferons (IFNs) and inflammatory cytokines. This receptor binds to dsRNA molecules produced during human cytomegalovirus (HCMV) replication. TLR7 senses viral single-stranded RNA (ssRNA) in endosomes, and it can interact with endogenous RNAs. We determined the genotype distribution of single-nucleotide polymorphisms (SNPs) within the TLR3 and TLR7 genes in children with HCMV infection and the relationship between TLR polymorphisms and viral infection...
2017: PloS One
https://www.readbyqxmd.com/read/28043560/the-importance-of-single-nucleotide-polymorphisms-in-interferon-gamma-receptor-1-gene-in-pulmonary-patients-infected-with-rapid-grower-mycobacterium
#12
Poopak Farnia, Jalaledin Ghanavi, Payam Tabasri, Shima Saif, Ali Akbar Velayati
OBJECTIVE/BACKGROUND: Interferon gamma (IFN-γ) plays a key role in protective immune response against Mycobacterial infection. IFN-γ excretes its antimycobacterial effectors mechanisms by activation of macrophages and dendritic cells via interaction with its receptor complex, that is, a ligand-binding subunit [IFN-γ receptor (IFNGR)1] and an accessory subunit (IFNGR2) on the cell surface. It has been shown that individuals with complete or partial IFNGR1 receptor deficiency are highly susceptible to infection by nontuberculous mycobacteria (NTM), Mycobacterium tuberculosis, and some Salmonella species...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28039263/variants-in-wfs1-and-other-mendelian-deafness-genes-are-associated-with-cisplatin-associated-ototoxicity
#13
Heather E Wheeler, Eric R Gamazon, Robert Frisina, Carlos Perez-Cervantes, Omar El Charif, Brandon Mapes, Sophie D Fossa, Darren Feldman, Robert Hamilton, David J Vaughn, Clair Beard, Chunkit Fung, Christian Kollmannsberger, Jeri Kim, Taisei Mushiroda, Michiaki Kubo, Shirin Ardeshir-Rouhani-Fard, Lawrence H Einhorn, Nancy Cox, M Eileen Dolan, Lois Travis
PURPOSE: Cisplatin is one of the most commonly used chemotherapy drugs worldwide and one of the most ototoxic. We sought to identify genetic variants that modulate cisplatin-associated ototoxicity (CAO). EXPERIMENTAL DESIGN: We performed a genome-wide association study (GWAS) of CAO using quantitative audiometry (4-12 kHz) in 511 testicular cancer survivors of European genetic ancestry. We performed polygenic modeling and functional analyses using a variety of publicly available databases...
December 30, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28039167/snp-interaction-pattern-identifier-sipi-an-intensive-search-for-snp-snp-interaction-patterns
#14
Hui-Yi Lin, Dung-Tsa Chen, Po-Yu Huang, Yung-Hsin Liu, Augusto Ochoa, Jovanny Zabaleta, Donald E Mercante, Zhide Fang, Thomas A Sellers, Julio M Pow-Sang, Chia-Ho Cheng, Rosalind Eeles, Doug Easton, Zsofia Kote-Jarai, Ali Amin Al Olama, Sara Benlloch, Kenneth Muir, Graham G Giles, Fredrik Wiklund, Henrik Gronberg, Christopher A Haiman, Johanna Schleutker, Børge G Nordestgaard, Ruth C Travis, Freddie Hamdy, Nora Pashayan, Kay-Tee Khaw, Janet L Stanford, William J Blot, Stephen N Thibodeau, Christiane Maier, Adam S Kibel, Cezary Cybulski, Lisa Cannon-Albright, Hermann Brenner, Radka Kaneva, Jyotsna Batra, Manuel R Teixeira, Hardev Pandha, Yong-Jie Lu, Jong Y Park
MOTIVATION: Testing SNP-SNP interactions is considered as a key for overcoming bottlenecks of genetic association studies. However, related statistical methods for testing SNP-SNP interactions are underdeveloped. RESULTS: We propose the SNP Interaction Pattern Identifier (SIPI), which tests 45 biologically meaningful interaction patterns for a binary outcome. SIPI takes non-hierarchical models, inheritance modes and mode coding direction into consideration. The simulation results show that SIPI has higher power than MDR (Multifactor Dimensionality Reduction), AA_Full, Geno_Full (full interaction model with additive or genotypic mode) and SNPassoc in detecting interactions...
December 30, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28035729/association-of-the-hnf1a-polymorphisms-and-serum-lipid-traits-the-risk-of-coronary-artery-disease-and-ischemic-stroke
#15
Yi-Jiang Zhou, Rui-Xing Yin, Shao-Cai Hong, Qian Yang, Xiao-Li Cao, Wu-Xian Chen
BACKGROUND: The hepatocyte nuclear factor-1α gene (HNF1A) single nucleotide polymorphisms (SNPs) have been associated with serum lipid traits in several previous genome-wide association studies. However, little is known about such association in the Chinese populations. The present study was to determine the association of the HNF1A rs1169288, rs2259820, rs2464196 and rs2650000 SNPs and serum lipid traits, the risk of coronary artery disease (CAD) and ischemic stroke (IS). METHODS: The genotypes of the four SNPs in 562 CAD and 521 IS patients, and 594 healthy controls were detected by the Snapshot technology platform...
December 30, 2016: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28035522/analysis-of-gene-candidate-snp-and-ancestral-origin-associated-to-obesity-and-postoperative-weight-loss-in-a-cohort-of-obese-patients-undergoing-rygb
#16
David Velázquez-Fernández, Gabriela Mercado-Celis, Jeny Flores-Morales, Diana Clavellina-Gaytán, Ramón Vidrio, Eduardo Vidrio, Maureen Mosti, Hugo Sánchez-Aguilar, Donaji Rodriguez, Pablo León, Miguel F Herrera
INTRODUCTION: Obesity is the result of a complex interaction between multiple genetic traits and psychological, behavioral, nutritional and environmental factors. OBJECTIVES: The aims of the study were (a) to comparatively evaluate the presence of 20 candidate gene single nucleotide polymorphisms (SNPs) in morbidly obese patients, (2) their association to comorbid conditions and (3) their impact on weight loss after a Roux-en-Y gastric bypass (RYGB). PATIENTS AND METHODS: Two hundred forty-nine patients were eligible for this study...
December 29, 2016: Obesity Surgery
https://www.readbyqxmd.com/read/28034305/sorl1-gene-plasma-biomarkers-and-the-risk-of-alzheimer-s-disease-for-the-han-chinese-population-in-taiwan
#17
Cheng-Ta Chou, Yi-Chu Liao, Wei-Ju Lee, Shuu-Jiun Wang, Jong-Ling Fuh
BACKGROUND: The sortilin-related receptor 1 (SORL1) gene, regulating the trafficking and recycling of amyloid precursor protein, has been related to Alzheimer's disease (AD) and mild cognitive impairment (MCI). The aim of the present study was to investigate the relationship between SORL1 polymorphisms, plasma concentrations of amyloid-beta (Aβ) isoforms, and AD and MCI susceptibility for a Han Chinese population in Taiwan. METHODS: Eight single-nucleotide polymorphisms (SNPs) in SORL1 and the apolipoprotein E gene (APOE) ε4 alleles were genotyped in 798 patients with AD, 157 patients with MCI, and 401 control subjects...
December 30, 2016: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/28031017/nitric-oxide-signaling-and-the-cross-talk-with-prostanoids-pathways-in-vascular-system
#18
Bruno R Silva, Tiago D Paula, Michele Paulo, Lusiane M Bendhack
BACKGROUND: This review provides an overview of the cellular signaling of nitric oxide (NO) and prostanoids in vascular cells and the possible cross talk between their pathways, mainly in hypertension, since the imbalance of these two systems has been attributed to development of some cardiovascular diseases. It also deals with the modulation of vasodilation induced by NO donors. NO is a well-known second messenger involved in many cellular functions. CONCLUSION: In the vascular system, the NO produced by endothelial NO-synthase (eNOS) or released by NO donors acts in vascular smooth muscle cells, the binding of NO to Fe2+-heme of soluble guanylyl-cyclase (sGC) activates sGC and the production of cyclic guanosine-3-5-monophosphate (cGMP)...
December 28, 2016: Medicinal Chemistry
https://www.readbyqxmd.com/read/28029742/functional-interaction-of-erap2-and-hla-b27-activates-the-unfolded-protein-response
#19
Zhenbo Zhang, Francesco Ciccia, Fanxing Zeng, Giuliana Guggino, Kirby Yee, Hasan Abdullah, Mark S Silverberg, Riccardo Alessandro, Giovanni Triolo, Nigil Haroon
OBJECTIVES: The basic mechanisms underlying ankylosing spondylitis (AS) pathogenesis remain unresolved. We previously reported an association of the single nucleotide polymorphisms (SNP) rs2549782 in Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) with AS. It is known that patients homozygous for the G allele (GG) of another ERAP2 SNP rs2248374 have no ERAP2 expression (ERAP2-null). We utilized this information to study the impact of ERAP2 deficiency on HLA-B27 expression in AS patients...
December 28, 2016: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28029312/impact-of-a-panel-of-88-single-nucleotide-polymorphisms-on-the-risk-of-breast-cancer-in-high-risk-women-results-from-two-randomized-tamoxifen-prevention-trials
#20
Jack Cuzick, Adam R Brentnall, Corrinne Segal, Helen Byers, Caroline Reuter, Simone Detre, Elena Lopez-Knowles, Ivana Sestak, Anthony Howell, Trevor J Powles, William G Newman, Mitchell Dowsett
Purpose At least 94 common single nucleotide polymorphisms (SNPs) are associated with breast cancer. The extent to which an SNP panel can refine risk in women who receive preventive therapy has not been directly assessed previously. Materials and Methods A risk score on the basis of 88 SNPs (SNP88) was investigated in a nested case-control study of women enrolled in the International Breast Intervention Study (IBIS-I) or the Royal Marsden study. A total of 359 women who developed cancer were matched to 636 controls by age, trial, follow-up time, and treatment arm...
December 28, 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
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