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https://www.readbyqxmd.com/read/27931206/survivalgwas_power-a-user-friendly-tool-for-power-calculations-in-pharmacogenetic-studies-with-time-to-event-outcomes
#1
Hamzah Syed, Andrea L Jorgensen, Andrew P Morris
BACKGROUND: Power calculators are currently available for the design of genetic association studies of binary phenotypes and quantitative traits, but not for "time to event" outcomes, which are of particular relevance in pharmacogenetics. With the rapid emergence of pharmacogenetic association studies of single nucleotide polymorphisms (SNPs), and the complexity of clinical outcomes they consider, there is a need for software to perform power calculations of time to event data over a range of design scenarios and analytical methodologies...
December 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27929054/in-silico-identification-of-snp-diversity-in-cultivated-and-wild-tomato-species-insight-from-molecular-simulations
#2
Archana Bhardwaj, Yogeshwar Vikram Dhar, Mehar Hasan Asif, Sumit K Bag
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27926527/meqtl-analysis-of-childhood-obesity-links-epigenetics-with-a-risk-snp-rs17782313-near-mc4r-from-meta-analysis
#3
Yuping Tang, Bo Jin, Lingling Zhou, Weifeng Lu
Earlier GWAS has identified that rs17782313 near MC4R was associated with obesity. However, subsequent studies showed conflicting results, especially among childhood. Besides, the mechanisms underlying the association between rs17782313 and childhood obesity remain largely unexplored, and genetic and epigenetic may interact and together affect the development of childhood obesity. We conducted a comprehensive meta-analysis to assess the association between rs17782313 and childhood obesity. MeQTL and eQTL analysis was applied to explore the effect of rs17782313 on DNA methylation and MC4R expression...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27925593/a-review-of-machine-learning-and-statistical-approaches-for-detecting-snp-interactions-in-high-dimensional-genomic-data
#4
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/27923663/pharmacogenetics-of-lithium-effects-on-glomerular-function-in-bipolar-disorder-patients-under-chronic-lithium-treatment-a-pilot-study
#5
Evangelia Eirini Tsermpini, Yanfei Zhang, Paola Niola, Caterina Chillotti, Raffaella Ardau, Alberto Bocchetta, George P Patrinos, Maria Del Zompo, Giovanni Severino, Ming Ta Michael Lee, Alessio Squassina
Bipolar disorder (BD) is a psychiatric disease characterized by alternating episodes of mania and depression. Lithium (Li) represents the mainstay treatment for BD, although a significant proportion of patients show insufficient or no response. Li is also associated with potentially severe side effects, including renal effects. Several studies reported that Li may induce reduction of glomerular filtration rate (GFR) in patients under long-term treatment. The biological systems and the genetic factors involved in susceptibility to Li-induced renal-side effects have been scarcely explored...
December 3, 2016: Neuroscience Letters
https://www.readbyqxmd.com/read/27920664/investigation-of-snp-rs2060546-immediately-upstream-to-ntn4-in-a-danish-gilles-de-la-tourette-syndrome-cohort
#6
Shanmukha S Padmanabhuni, Rayan Houssari, Ann-Louise Esserlind, Jes Olesen, Thomas M Werge, Thomas F Hansen, Birgitte Bertelsen, Fotis Tsetsos, Peristera Paschou, Zeynep Tümer
Gilles de la Tourette syndrome (GTS) is a neuropsychiatric disorder characterized by multiple motor and vocal tics. GTS is a complex disorder, with environmental factors and several genes involved. Although variations within a few genes such as AADAC, NRXN1, SLITRK1, HDC, and IMMP2L have been tentatively associated with GTS (in a small number of patients), the causative genes underlying GTS pathophysiology remain unknown. In a previous genome-wide association study (GWAS) a single nucleotide polymorphism (SNP, rs2060546) near the Netrin-4 (NTN4 - MIM 610401) gene was shown to be associated with GTS [odds ratio (OR) = 1...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27920536/evaluation-of-potential-novel-variations-and-their-interactions-related-to-bipolar-disorders-analysis-of-genome-wide-association-study-data
#7
Cengizhan Acikel, Yesim Aydin Son, Cemil Celik, Husamettin Gul
BACKGROUND: Multifactor dimensionality reduction (MDR) is a nonparametric approach that can be used to detect relevant interactions between single-nucleotide polymorphisms (SNPs). The aim of this study was to build the best genomic model based on SNP associations and to identify candidate polymorphisms that are the underlying molecular basis of the bipolar disorders. METHODS: This study was performed on Whole-Genome Association Study of Bipolar Disorder (dbGaP [database of Genotypes and Phenotypes] study accession number: phs000017...
2016: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/27919301/the-integration-of-epigenetics-and-genetics-in-nutrition-research-for-cvd-risk-factors
#8
Yiyi Ma, Jose M Ordovas
There is increasing evidence documenting gene-by-environment (G × E) interactions for CVD related traits. However, the underlying mechanisms are still unclear. DNA methylation may represent one of such potential mechanisms. The objective of this review paper is to summarise the current evidence supporting the interplay among DNA methylation, genetic variants, and environmental factors, specifically (1) the association between SNP and DNA methylation; (2) the role that DNA methylation plays in G × E interactions...
December 6, 2016: Proceedings of the Nutrition Society
https://www.readbyqxmd.com/read/27917368/sex-steroid-hormone-single-nucleotide-polymorphisms-pesticide-use-and-the-risk-of-prostate-cancer-a-nested-case-control-study-within-the-agricultural-health-study
#9
Carol H Christensen, Kathryn Hughes Barry, Gabriella Andreotti, Michael C R Alavanja, Michael B Cook, Scott P Kelly, Laurie A Burdett, Meredith Yeager, Laura E Beane Freeman, Sonja I Berndt, Stella Koutros
Experimental and epidemiologic investigations suggest that certain pesticides may alter sex steroid hormone synthesis, metabolism or regulation, and the risk of hormone-related cancers. Here, we evaluated whether single-nucleotide polymorphisms (SNPs) involved in hormone homeostasis alter the effect of pesticide exposure on prostate cancer risk. We evaluated pesticide-SNP interactions between 39 pesticides and SNPs with respect to prostate cancer among 776 cases and 1,444 controls nested in the Agricultural Health Study cohort...
2016: Frontiers in Oncology
https://www.readbyqxmd.com/read/27909914/association-of-snp-variants-of-mhc-class-ii-drb-gene-with-thermo-physiological-traits-in-tropical-goats
#10
Abdulmojeed Yakubu, Adebowale E Salako, Marcos De Donato, Sunday O Peters, Michael I Takeet, Mathew Wheto, Moses Okpeku, Ikhide G Imumorin
Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats...
December 1, 2016: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/27901618/genome-wide-interaction-analysis-of-air-pollution-exposure-and-childhood-asthma-with-functional-follow-up
#11
Anna Gref, Simon Kebede Merid, Olena Gruzieva, Stéphane Ballereau, Allan Becker, Tom Bellander, Anna Bergström, Yohan Bossé, Matteo Bottai, Moira Chan-Yeung, Elaine Fuertes, Despo Ierodiakonou, Ruiwei Jiang, Stéphane Joly, Meaghan Jones, Michael S Kobor, Michal Korek, Anita L Kozyrskyj, Ashish Kumar, Nathanaël Lemonnier, Elaina MacIntyre, Camille Ménard, David Nickle, Ma'en Obeidat, Johann Pellet, Marie Standl, Annika Sääf, Cilla Söderhäll, Carla Mt Tiesler, Maarten van den Berge, Judith M Vonk, Hita Vora, Cheng-Jian Xu, Josep M Antó, Charles Auffray, Michael Brauer, Jean Bousquet, Bert Brunekreef, W James Gauderman, Joachim Heinrich, Juha Kere, Gerard H Koppelman, Dirkje Postma, Christopher Carlsten, Göran Pershagen, Erik Melén
RATIONALE: The evidence supporting an association between traffic-related air pollution exposure and incident childhood asthma is inconsistent, and may depend on genetic factors. OBJECTIVES: To identify gene-environment interaction effects on childhood asthma using genome-wide single nucleotide polymorphism (SNP) data and air pollution exposure. Identified loci were further analyzed at epigenetic and transcriptomic levels. METHODS: We used land use regression models to estimate individual air pollution exposure (represented by outdoor NO2 levels) at the birth address and performed a genome-wide interaction study for doctor's diagnosis of asthma up to 8 years in three European birth cohorts (n=1,534) with look-up for interaction in two separate North American cohorts, CHS and CAPPS/SAGE (n=1,602 and 186 subjects, respectively)...
November 30, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27900402/effects-of-ugt1a9-genetic-polymorphisms-on-monohydroxylated-derivative-of-oxcarbazepine-concentrations-and-oxcarbazepine-monotherapeutic-efficacy-in-chinese-patients-with-epilepsy
#12
Yao Lu, Youxin Fang, Xunyi Wu, Chunlai Ma, Yue Wang, Lan Xu
AIM: The human UDP-glucuronosyltransferase which is genetically polymorphic catalyzes glucuronidations of various drugs. The interactions among UGT1A4, UGT1A6, UGT1A9, and UGT2B15 genetic polymorphisms, monohydroxylated derivative (MHD) of oxcarbazepine (OXC) plasma concentrations, and OXC monotherapeutic efficacy were explored in 124 Chinese patients with epilepsy receiving OXC monotherapy. METHOD: MHD is the major active metabolite of OXC, and its plasma concentration was measured using high-performance liquid chromatography when patients reached their maintenance dose of OXC...
November 29, 2016: European Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/27899942/adiponectin-receptor-1-and-small-ubiquitin-like-modifier-4-polymorphisms-are-associated-with-risk-of-coronary-artery-disease-without-diabetes
#13
Hong Li, Ze Yang, Lian-Mei Pu, Xiang Li, Yang Ruan, Fan Yang, Shuai Meng, Duo Yang, Wei Yao, Hao Fu, Feng Zhang, Ze-Ning Jin
BACKGROUND: The genes encoding adiponectin receptor 1 (ADIPOR1) and small ubiquitin-like modifier 4 (SUMO4) have been linked to anti-atherogenic effects, but little is known about whether polymorphisms in the two genes, acting separately or interacting, affect risk of coronary artery disease (CAD) without diabetes. METHODS: We genotyped 200 CAD patients without diabetes and 200 controls without CAD or diabetes at three single-nucleotide polymorphisms (SNPs) in ADIPOR1 and one SNP in SUMO4, which were chosen based on previous studies...
September 2016: Journal of Geriatric Cardiology: JGC
https://www.readbyqxmd.com/read/27899667/rice-snp-seek-database-update-new-snps-indels-and-queries
#14
Locedie Mansueto, Roven Rommel Fuentes, Frances Nikki Borja, Jeffery Detras, Juan Miguel Abriol-Santos, Dmytro Chebotarov, Millicent Sanciangco, Kevin Palis, Dario Copetti, Alexandre Poliakov, Inna Dubchak, Victor Solovyev, Rod A Wing, Ruaraidh Sackville Hamilton, Ramil Mauleon, Kenneth L McNally, Nickolai Alexandrov
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898923/growth-and-development-symposium-adenosine-monophosphate-activated-protein-kinase-and-mitochondria-in-rendement-napole-pig-growth
#15
T L Scheffler, D E Gerrard
The Rendement Napole mutation (RN-), which is well known to influence pork quality, also has a profound impact on metabolic characteristics of muscle. Pigs with RN- possess a SNP in the γ3 subunit of adenosine monophosphate (AMP)-activated protein kinase (AMPK); AMPK, a key energy sensor in skeletal muscle, modulates energy producing and energy consuming pathways to maintain cellular homeostasis. Importantly, AMPK regulates not only acute response to energy stress but also facilitates long-term adaptation via changes in gene and protein expression...
September 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898838/assessment-of-cultivar-distinctness-in-alfalfa-a-comparison-of-genotyping-by-sequencing-simple-sequence-repeat-marker-and-morphophysiological-observations
#16
Paolo Annicchiarico, Nelson Nazzicari, Acharya Ananta, Maria Carelli, Yanling Wei, E Charles Brummer
Cultivar registration agencies typically require morphophysiological trait-based distinctness of candidate cultivars. This requirement is difficult to achieve for cultivars of major perennial forages because of their genetic structure and ever-increasing number of registered material, leading to possible rejection of agronomically valuable cultivars. This study aimed to explore the value of molecular markers applied to replicated bulked plants (three bulks of 100 independent plants each per cultivar) to assess alfalfa ( L...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898823/genome-wide-association-studies-of-grain-yield-components-in-diverse-sorghum-germplasm
#17
Richard E Boyles, Elizabeth A Cooper, Matthew T Myers, Zachary Brenton, Bradley L Rauh, Geoffrey P Morris, Stephen Kresovich
Grain yield and its primary determinants, grain number and weight, are important traits in cereal crops that have been well studied; however, the genetic basis of and interactions between these traits remain poorly understood. Characterization of grain yield per primary panicle (YPP), grain number per primary panicle (GNP), and 1000-grain weight (TGW) in sorghum [ (L.) Moench], a hardy C cereal with a genome size of ∼730 Mb, was implemented in a diversity panel containing 390 accessions. These accessions were genotyped to obtain 268,830 single-nucleotide polymorphisms (SNPs)...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898808/candidate-gene-sequence-analyses-toward-identifying-type-resistance-to
#18
N R Redekar, E M Clevinger, M A Laskar, R M Biyashev, T Ashfield, R V Jensen, S C Jeong, S A Tolin, M A Saghai Maroof
is one of three genetic loci conferring strain-specific resistance to (SMV). The locus has been mapped to a 154-kb region on chromosome 14, containing a cluster of five nucleotide-binding leucine-rich repeat (NB-LRR) resistance genes. High sequence similarity between the candidate genes challenges fine mapping of the locus. Among the five, Glyma14g38533 showed the highest transcript abundance in 1 to 3 h of SMV-G7 inoculation. Comparative sequence analyses were conducted with the five candidate NB-LRR genes from susceptible (-type) soybean [ (L...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27897266/evaluation-of-association-of-common-variants-in-htr1a-and-htr5a-with-schizophrenia-and-executive-function
#19
Fanglin Guan, Huali Lin, Gang Chen, Lu Li, Teng Chen, Xinshe Liu, Jiuqiang Han, Tao Li
The 5-HT1A receptor (HTR1A) and the 5-HT5A receptor (HTR5A) are key 5-HT receptors with distinct inhibitory functions. Studies have been conducted to investigate the association of a few HTR1A polymorphisms with schizophrenia, producing conflicting results, and the relationship between HTR5A and schizophrenia has not yet been well investigated. We aimed to examine the association of HTR1A and HTR5A with schizophrenia and executive function. The study included a discovery stage with 1,115 patients and 2,289 controls and a replication stage with 2,128 patients and 3,865 controls...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896278/lack-of-association-between-slc30a8-variants-and-type-2-diabetes-in-mexican-american-families
#20
Hemant Kulkarni, Manju Mamtani, Juan Manuel Peralta, Vincent Diego, Thomas D Dyer, Harald Goring, Laura Almasy, Michael C Mahaney, Sarah Williams-Blangero, Ravindranath Duggirala, Joanne E Curran, John Blangero
SLC30A8 encodes zinc transporter 8 which is involved in packaging and release of insulin. Evidence for the association of SLC30A8 variants with type 2 diabetes (T2D) is inconclusive. We interrogated single nucleotide polymorphisms (SNPs) around SLC30A8 for association with T2D in high-risk, pedigreed individuals from extended Mexican American families. This study of 118 SNPs within 50 kb of the SLC30A8 locus tested the association with eight T2D-related traits at four levels: (i) each SNP using measured genotype approach (MGA); (ii) interaction of SNPs with age and sex; (iii) combinations of SNPs using Bayesian Quantitative Trait Nucleotide (BQTN) analyses; and (iv) entire gene locus using the gene burden test...
2016: Journal of Diabetes Research
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