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Snp interaction

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https://www.readbyqxmd.com/read/28100911/variants-on-chromosome-4q21-near-pkd2-and-siblings-are-associated-with-dental-caries
#1
Scott Eckert, Eleanor Feingold, Margaret Cooper, Michael M Vanyukov, Brion S Maher, Rebecca L Slayton, Marcia C Willing, Steven E Reis, Daniel W McNeil, Richard J Crout, Robert J Weyant, Steven M Levy, Alexandre R Vieira, Mary L Marazita, John R Shaffer
A recent genome-wide association study (GWAS) for dental caries nominated the chromosomal region 4q21 near ABCG2, PKD2 and the SIBLING (small integrin-binding ligand N-linked glycoprotein) gene family. In this investigation, we followed up and fine-mapped this region using a tag-SNP (single-nucleotide polymorphism) approach in 13 age- and race-stratified samples from 6 independent studies (N=4089). Participants were assessed for dental caries via intraoral examination and 49 tag-SNPs were genotyped capturing much of the variation in the 4q21 locus...
January 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28099948/mdm4-genetic-variants-and-risk-of-gastric-cancer-in-an-eastern-chinese-population
#2
Meng-Yun Wang, Ming Jia, Jing He, Fei Zhou, Li-Xin Qiu, Meng-Hong Sun, Ya-Jun Yang, Jiu-Cun Wang, Li Jin, Ya-Nong Wang, Qing-Yi Wei
MDM4 is a p53-interacting protein and plays an important role in carcinogenesis. In this study of 1,077 gastric cancer (GCa) cases and 1,173 matched cancer-free controls, we investigated associations between three tagging single nucleotide polymorphisms (SNPs) (rs11801299 G>A, rs1380576 C>G and rs10900598 G>T) in MDM4 and gastric cancer risk in an Eastern Chinese Population. In logistic regression analysis, a significantly decreased GCa risk was associated with the rs1380576 GG variant genotype (adjusted odds ratio [OR] =0...
January 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28094323/gene-set-based-association-analyses-for-the-wssv-resistance-of-pacific-white-shrimp-litopenaeus-vannamei
#3
Yang Yu, Jingwen Liu, Fuhua Li, Xiaojun Zhang, Chengsong Zhang, Jianhai Xiang
White Spot Syndrome Virus (WSSV) is regarded as a virus with the strongest pathogenicity to shrimp. For the threshold trait such as disease resistance, marker assisted selection (MAS) was considered to be a more effective approach. In the present study, association analyses of single nucleotide polymorphisms (SNPs) located in a set of immune related genes were conducted to identify markers associated with WSSV resistance. SNPs were detected by bioinformatics analysis on RNA sequencing data generated by Illimina sequencing platform and Roche 454 sequencing technology...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090039/interaction-between-the-rgs6-gene-and-psychosocial-stress-on-obesity-related-traits
#4
Hyun-Jin Kim, Jin-Young Min, Kyoung-Bok Min
Obesity is a major risk factor for chronic diseases and arises from the interactions between environmental factors and multiple genes. Psychosocial stress may affect the risk for obesity, modifying food intake and choice. A recent study suggested regulator of G-protein signaling 6 (RGS6) as a novel candidate gene for obesity in terms of reward-related feeding under stress. In this study, we tried to verify the unidentified connection between RGS6 and human obesity with psychosocial stress in a Korean population...
January 13, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/28089900/the-rs4238326-polymorphism-in-aldh1a2-gene-potentially-associated-with-non-post-traumatic-knee-osteoarthritis-susceptibility-a-two-stage-population-based-study
#5
Minjie Chu, Xiaoyue Zhu, Chunli Wang, Jiesheng Rong, Yidan Wang, Shengyu Wang, Baifen Xing, Yuchun Tao, Xun Zhuang, Liying Jiang
OBJECTIVE: A recent genome-wide association study reported significant associations of genetic variants within the ALDH1A2 gene with osteoarthritis (OA) of the hand in European populations. However, these findings have not been well generalized to other joints, or to other populations. METHODS: We performed a two-stage population-based case-control study including 196 non-post traumatic knee OA cases and 442 controls in the first stage and independent 143 non-post traumatic knee OA cases and 238 controls in the second stage in a Chinese population by genotyping 8 tagging polymorphisms in ALDH1A2...
January 12, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28081217/collective-genetic-interaction-effects-and-the-role-of-antigen-presenting-cells-in-autoimmune-diseases
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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 17, 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
#16
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
#17
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
#18
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
#19
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
#20
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
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