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https://www.readbyqxmd.com/read/29792870/peripheral-complement-interactions-with-amyloid-%C3%AE-peptide-in-alzheimer-s-disease-polymorphisms-structure-and-function-of-complement-receptor-1
#1
Jenny U Johansson, William D Brubaker, Harold Javitz, Andrew W Bergen, Denise Nishita, Abhishek Trigunaite, Andrés Crane, Justine Ceballos, Diego Mastroeni, Andrea J Tenner, Marwan Sabbagh, Joseph Rogers
INTRODUCTION: Genome-wide association studies consistently show that single nucleotide polymorphisms (SNPs) in the complement receptor 1 (CR1) gene modestly but significantly alter Alzheimer's disease (AD) risk. Follow-up research has assumed that CR1 is expressed in the human brain despite a paucity of evidence for its function there. Alternatively, erythrocytes contain >80% of the body's CR1, where, in primates, it is known to bind circulating pathogens. METHODS: Multidisciplinary methods were employed...
May 21, 2018: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/29784544/classifying-alzheimer-s-disease-with-brain-imaging-and-genetic-data-using-a-neural-network-framework
#2
Kaida Ning, Bo Chen, Fengzhu Sun, Zachary Hobel, Lu Zhao, Will Matloff, Arthur W Toga
A long-standing question is how to best use brain morphometric and genetic data to distinguish Alzheimer's disease (AD) patients from cognitively normal (CN) subjects and to predict those who will progress from mild cognitive impairment (MCI) to AD. Here, we use a neural network (NN) framework on both magnetic resonance imaging-derived quantitative structural brain measures and genetic data to address this question. We tested the effectiveness of NN models in classifying and predicting AD. We further performed a novel analysis of the NN model to gain insight into the most predictive imaging and genetics features and to identify possible interactions between features that affect AD risk...
April 24, 2018: Neurobiology of Aging
https://www.readbyqxmd.com/read/29777237/dna-methylation-variant-b-vitamins-intake-and-longitudinal-change-in-body-mass-index
#3
Xiang Li, Tiange Wang, Min Zhao, Tao Huang, Dianjianyi Sun, Liyuan Han, Hoirun Nisa, Xiaoyun Shang, Yoriko Heianza, Lu Qi
BACKGROUND: Growing evidence has implicated DNA methylation (DNAm) in the regulation of body adiposity; a recent epigenome-wide association study (EWAS) identified a genetic variant determining DNAm at the SREBF1 gene that affected body mass index (BMI). OBJECTIVE: In the present study, we tested interactions between DNAm variant rs752579 and methylation metabolism-related B-vitamins (folate, vitamin B2 , vitamin B6 , and vitamin B12 ) on longitudinal change in BMI in the Women's Health Initiative Memory Study (WHIMS)...
May 17, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29773854/genome-wide-haplotype-association-analysis-of-primary-biliary-cholangitis-risk-in-japanese
#4
Cindy Im, Yadav Sapkota, Wonjong Moon, Minae Kawashima, Minoru Nakamura, Katsushi Tokunaga, Yutaka Yasui
Primary biliary cholangitis (PBC) susceptibility loci have largely been discovered through single SNP association testing. In this study, we report genic haplotype patterns associated with PBC risk genome-wide in two Japanese cohorts. Among the 74 genic PBC risk haplotype candidates we detected with a novel methodological approach in a discovery cohort of 1,937 Japanese, nearly two-thirds were replicated (49 haplotypes, Bonferroni-corrected P < 6.8 × 10-4 ) in an independent Japanese cohort (N = 949)...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29771388/gwas4d-multidimensional-analysis-of-context-specific-regulatory-variant-for-human-complex-diseases-and-traits
#5
Dandan Huang, Xianfu Yi, Shijie Zhang, Zhanye Zheng, Panwen Wang, Chenghao Xuan, Pak Chung Sham, Junwen Wang, Mulin Jun Li
Genome-wide association studies have generated over thousands of susceptibility loci for many human complex traits, and yet for most of these associations the true causal variants remain unknown. Tissue/cell type-specific prediction and prioritization of non-coding regulatory variants will facilitate the identification of causal variants and underlying pathogenic mechanisms for particular complex diseases and traits. By leveraging recent large-scale functional genomics/epigenomics data, we develop an intuitive web server, GWAS4D (http://mulinlab...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29769702/fine-mapping-of-98-obesity-loci-in-mexican-children
#6
Hsin Yen Liu, Akram Alyass, Arkan Abadi, Jesus Peralta-Romero, Fernando Suarez, Jaime Gomez-Zamudio, Astride Audirac, Esteban J Parra, Miguel Cruz, David Meyre
BACKGROUND/OBJECTIVES: Mexico has one of the highest prevalence of childhood obesity in the world. Genome-wide association studies (GWAS) for obesity have identified multiple single-nucleotide polymorphisms (SNPs) in populations of European, East Asian, and African descent. The contribution of these loci to obesity in Mexican children is unclear. We assessed the transferability of 98 obesity loci in Mexican children and fine-mapped the association signals. SUBJECTS/METHODS: The study included 405 and 390 Mexican children with normal weight and obesity...
March 12, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29766218/qtl-mapping-and-epistatic-interaction-analysis-of-field-resistance-to-sudden-death-syndrome-fusarium-virguliforme-in-soybean
#7
Ruijuan Tan, Bradley Serven, Paul J Collins, Zhongnan Zhang, Zixiang Wen, John F Boyse, Cuihua Gu, Martin I Chilvers, Brian W Diers, Dechun Wang
Two interactive quantitative trait loci (QTLs) controlled the field resistance to sudden death syndrome (SDS) in soybean. The interaction between them was confirmed. Sudden death syndrome (SDS), caused by Fusarium virguliforme, is a major disease of soybean [Glycine max (L.) Merr.] in the United States. Breeding for soybean resistance to SDS is the most cost-effective method to manage the disease. The objective of this study was to identify and characterize quantitative trait loci (QTLs) underlying field resistance to SDS in a recombinant inbred line population from the cross GD2422 × LD01-5907...
May 15, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29762780/an-intersection-network-based-on-combining-snp-co-association-and-rna-co-expression-networks-for-feed-utilization-traits-in-japanese-black-cattle
#8
D Okada, S Endo, H Matsuda, S Ogawa, Y Taniguchi, T Katsuta, T Watanabe, H Iwaisaki
Genome-wide association studies (GWAS) of quantitative traits have detected numerous genetic associations, but they encounter difficulties in pinpointing prominent candidate genes and inferring gene networks. The present study used a systems genetics approach integrating GWAS results with external RNA-expression data to detect candidate gene networks in feed utilization and growth traits of Japanese Black cattle, which are matters of concern. A SNP co-association network was derived from significant correlations between SNPs with effects estimated by GWAS across seven phenotypic traits...
May 12, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29762199/physical-activity-modifies-genetic-susceptibility-to-obesity-in-postmenopausal-women
#9
Heather M Ochs-Balcom, Leah Preus, Jing Nie, Jean Wactawski-Wende, Linda Agyemang, Marian L Neuhouser, Lesley Tinker, Cheng Zheng, Rasa Kazlauskaite, Lihong Qi, Lara E Sucheston-Campbell
OBJECTIVE: We conducted a gene-environment interaction study to evaluate whether the association of body mass index (BMI) associated meta genome-wide association study single-nucleotide polymorphisms (SNPs) (as a genetic risk score) and BMI is modified by physical activity and age. METHODS: In 8,206 women of European ancestry from the Women's Health Initiative (WHI), we used linear regression to examine main effects of the 95 SNP BMI genetic risk score (GRS) and physical activity on BMI, and evaluated whether genetic associations are modified by physical activity (two-way interaction) and age (three-way interaction)...
May 14, 2018: Menopause: the Journal of the North American Menopause Society
https://www.readbyqxmd.com/read/29760888/adaptive-phenotypic-plasticity-in-a-clonal-invader
#10
Gerlien Verhaegen, Kyle E McElroy, Laura Bankers, Maurine Neiman, Martin Haase
Organisms featuring wide trait variability and occurring in a wide range of habitats, such as the ovoviviparous New Zealand freshwater snail Potamopyrgus antipodarum , are ideal models to study adaptation. Since the mid-19th century, P. antipodarum , characterized by extremely variable shell morphology, has successfully invaded aquatic areas on four continents. Because these obligately and wholly asexual invasive populations harbor low genetic diversity compared to mixed sexual/asexual populations in the native range, we hypothesized that (1) this phenotypic variation in the invasive range might be adaptive with respect to colonization of novel habitats, and (2) that at least some of the variation might be caused by phenotypic plasticity...
May 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29760565/genome-wide-association-pathway-analysis-to-identify-candidate-single-nucleotide-polymorphisms-and-molecular-pathways-associated-with-tp53-expression-status-in-hbv-related-hepatocellular-carcinoma
#11
Xiwen Liao, Long Yu, Xiaoguang Liu, Chuangye Han, Tingdong Yu, Wei Qin, Chengkun Yang, Guangzhi Zhu, Hao Su, Tao Peng
Background: The aim of this investigation was to identify candidate single nucleotide polymorphisms (SNPs) and molecular pathways associated with tumor protein p53 (TP53) expression status in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), clarify their potential mechanisms, and generate SNP-to-gene to pathway hypothesis. Materials and methods: Identify candidate Causal SNPs and Pathways (ICSNPathway) was used to perform pathway analysis based on the results of our previous genome-wide association study of TP53 expression status in 387 HBV-related HCC patients...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/29758349/habitual-aerobic-exercise-gene-apoa5-named-rs662799-snp-and-response-of-blood-lipid-and-lipoprotein-phenotypes-among-older-chinese-adult
#12
Xiangyun Liu, Guoyuan Huang, Zhanbin Niu, Yuqin Wei, Ru Wang
BACKGROUND: The genetic component of dyslipidemia has been studied in adults but little in older population. It is remains unknown regarding influence and interaction of APOA5 gene single nucleotide polymorphism (SNP) and habitual aerobic exercise (HAE) on changes of blood lipids and lipoprotein phenotypes in older Chinese adults. METHODS: Four-hundred-twenty-three old Chinese individuals with HAE were divided into hyperlipidemia and normal groups. We genotyped polymorphic loci using matrix assisted laser desorption ionization time of flight mass spectrometry detection technology (MALDI-TOF)...
May 11, 2018: Experimental Gerontology
https://www.readbyqxmd.com/read/29755375/influence-of-crhr1-polymorphisms-and-childhood-abuse-on-suicide-attempts-in-affective-disorders-a-gxe-approach
#13
Birgit Ludwig, Klemens Kienesberger, Laura Carlberg, Patrick Swoboda, Alexandra Bernegger, Romina Koller, Qingzhong Wang, Michelle Inaner, Melanie Zotter, Nestor D Kapusta, Helmuth Haslacher, Martin Aigner, Siegfried Kasper, Alexandra Schosser
Background: Previous studies have shown that the hypothalamus-pituitary-adrenal-axis (HPA-axis) is closely involved in the development of affective disorders. Given that early life events are also linked to dysregulation of the same system, there might be an association between childhood adversities and suicidal behavior in affective disorders, moderated by HPA-axis genes. We aimed to investigate a potential association between childhood trauma and previous suicide attempts in affective disorder patients, moderated by variants of the corticotropin-releasing hormone receptor 1 (CRHR1) gene...
2018: Frontiers in Psychiatry
https://www.readbyqxmd.com/read/29752677/insight-into-the-mechanisms-and-consequences-of-recurrent-telomere-capture-associated-with-a-sub-telomeric-deletion
#14
Alexsandro Dos Santos, Francine Campagnari, Ana Cristina Victorino Krepischi, Maria de Lourdes Ribeiro Câmara, Rita de Cássia E de Arruda Brasil, Ligia Vieira, Angela M Vianna-Morgante, Paulo A Otto, Peter L Pearson, Carla Rosenberg
A complex mosaicism of the short arm of chromosome 1 detected by SNP microarray analysis is described in a patient presenting a 4-Mb 1p36 terminal deletion and associated phenotypic features. The array pattern of chromosome 1p displayed an intriguing increase in divergence of the SNP heterozygote frequency from the expected 50% from the centromere towards the 1p36 breakpoint. This suggests that various overlapping segments of UPD were derived by somatic recombination between the 1p homologues. The most likely explanation was the occurrence of a series of events initiated in either a gamete or an early embryonic cell division involving a 1pter deletion rapidly followed by multiple telomere captures, resulting in additive, stepped increases in frequency of homozygosity towards the telomere...
May 12, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29751792/discovering-novel-snps-that-are-correlated-with-patient-outcome-in-a-singaporean-cancer-patient-cohort-treated-with-gemcitabine-based-chemotherapy
#15
Vachiranee Limviphuvadh, Chee Seng Tan, Fumikazu Konishi, Piroon Jenjaroenpun, Joy Shengnan Xiang, Yuliya Kremenska, Yar Soe Mu, Nicholas Syn, Soo Chin Lee, Ross A Soo, Frank Eisenhaber, Sebastian Maurer-Stroh, Wei Peng Yong
BACKGROUND: Single Nucleotide Polymorphisms (SNPs) can influence patient outcome such as drug response and toxicity after drug intervention. The purpose of this study is to develop a systematic pathway approach to accurately and efficiently predict novel non-synonymous SNPs (nsSNPs) that could be causative to gemcitabine-based chemotherapy treatment outcome in Singaporean non-small cell lung cancer (NSCLC) patients. METHODS: Using a pathway approach that incorporates comprehensive protein-protein interaction data to systematically extend the gemcitabine pharmacologic pathway, we identified 77 related nsSNPs, common in the Singaporean population...
May 11, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29750477/apple-fruit-acidity-is-genetically-diversified-by-natural-variations-in-three-hierarchical-epistatic-genes-mdsaur37-mdpp2ch-and-mdalmtii
#16
Dongjie Jia, Fei Shen, Yi Wang, Ting Wu, Xuefeng Xu, Xinzhong Zhang, Zhenhai Han
Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, we identified four genome-wide major QTLs responsible for apple fruit acidity by MapQTL and BSA-seq analyses using two independent pedigree-based populations. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37, and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits...
May 11, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29748862/association-of-dna-methylation-in-bdnf-with-escitalopram-treatment-response-in-depressed-chinese-han-patients
#17
Peipei Wang, Cuizhen Zhang, Qinyu Lv, Chenxi Bao, Hong Sun, Guo Ma, Yiru Fang, Zhenghui Yi, Weimin Cai
PURPOSE: The neurotrophin brain-derived neurotrophic factor (BDNF) has been found to be associated with both the pathophysiology of depression and antidepressants response. Gene expression differences were partly mediated by SNP, which might be identified as a predictor of antidepressant response. In the present study, we attempt to identify whether DNA methylation, another factor known to affect gene transcription, might also predict antidepressant response. METHODS: A total of 85 depressed Chinese Han patients were followed-up 8 weeks after initiating escitalopram treatment...
May 10, 2018: European Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/29748526/association-of-single-nucleotide-polymorphisms-of-cd44-gene-with-susceptibility-to-breast-cancer-in-chinese-women
#18
Xiao Lin, Xiaojing You, Xuezhen Cao, Shenghua Pan
BACKGROUND This study aimed to evaluate the association of CD44 gene single-nucleotide polymorphisms with susceptibility to breast cancer. MATERIAL AND METHODS This case-control study included 242 breast cancer patients and 252 normal people without disease. The single-nucleotide polymorphisms of the CD44 gene in the 2 groups were genotyped by PCR-LDR method. The OR and its 95% CI was calculated by chi-square test and logistic regression analysis. The construction of haplotypes and their interaction analysis with relevant factors were carried out by SHEsis and SNPStats online...
May 11, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29745836/haplotype-analysis-of-apoe-intragenic-snps
#19
Vladimir N Babenko, Dmitry A Afonnikov, Elena V Ignatieva, Anton V Klimov, Fedor E Gusev, Evgeny I Rogaev
BACKGROUND: APOE ε4 allele is most common genetic risk factor for Alzheimer's disease (AD) and cognitive decline. However, it remains poorly understood why only some carriers of APOE ε4 develop AD and how ethnic variabilities in APOE locus contribute to AD risk. Here, to address the role of APOE haplotypes, we reassessed the diversity of APOE locus in major ethnic groups and in Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset on patients with AD, and subjects with mild cognitive impairment (MCI), and control non-demented individuals...
April 19, 2018: BMC Neuroscience
https://www.readbyqxmd.com/read/29739922/bordetella-pertussis-isolates-vary-in-their-interactions-with-human-complement-components
#20
Charlotte Brookes, Irene Freire-Martin, Breeze Cavell, Frances Alexander, Stephen Taylor, Ruby Persaud, Norman Fry, Andrew Preston, Dimitri Diavatopoulos, Andrew Gorringe
Whooping cough is a re-emerging respiratory tract infection. It has become clear that there is a need for better understanding of protective immune responses and variation between Bordetella pertussis strains to aid the development of improved vaccines. In order to survive in the host, B. pertussis has evolved mechanisms to evade complement-mediated killing, including the ability to bind complement-regulatory proteins. Here we evaluate the variation in interactions with the complement system among recently isolated strains...
May 9, 2018: Emerging Microbes & Infections
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