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https://www.readbyqxmd.com/read/28103253/polymorphisms-in-htr2a-and-drd4-predispose-to-smoking-and-smoking-quantity
#1
Gloria Pérez-Rubio, Alejandra Ramírez-Venegas, Valeri Noé Díaz, Leonor García Gómez, Karina Elvira Fabián, Salvador García Carmona, Luis A López-Flores, Enrique Ambrocio-Ortiz, Rocío Contreras Romero, Noé Alcantar-Ayala, Raúl H Sansores, Ramcés Falfán-Valencia
BACKGROUND: Genes encoding the receptors involved in the dopaminergic and serotonergic pathways are potential candidates in the mechanisms of nicotine addiction. AIMS: To identify genetic variants in the promoter regions and exons of the DRD4 and HTR2A genes associated with tobacco smoking and the degree of nicotine addiction in Mexican mestizos. METHODS: The study included 438 non-smokers (NS) and 1,157 current smokers, ranked based on their consumption of cigarettes per day (cpd): 574 heavy smokers (HS, >20 cpd) and 583 light smokers (LS, 1-10 cpd)...
2017: PloS One
https://www.readbyqxmd.com/read/28102005/blind-prediction-of-deleterious-amino-acid-variations-with-snps-go
#2
Emidio Capriotti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
: SNPs&GO is a machine learning method for predicting the association of single amino acid variations (SAVs) to disease, considering protein functional annotation. The method is a binary classifier that implements a Support Vector Machine algorithm to discriminate between disease-related and neutral SAVs. SNPs&GO combines information from protein sequence with functional annotation encoded by Gene Ontology terms. Tested in sequence mode on more than 38,000 SAVs from the SwissVar dataset, our method reached 81% overall accuracy and an area under the receiving operating characteristic curve (AUC) of 0...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28101933/associations-of-common-variants-in-the-slc16a11-tcf7l2-and-abca1-genes-with-pediatric-onset-type-2-diabetes-and-related-glycemic-traits-in-families-a-case-control-and-case-parent-trio-study
#3
América L Miranda-Lora, Miguel Cruz, Mario Molina-Díaz, Jorge Gutiérrez, Samuel Flores-Huerta, Miguel Klünder-Klünder
BACKGROUND: There is evidence of associations of single-nucleotide polymorphisms (SNPs) with type 2 diabetes (T2D) and related glycemic traits in adults, but there is a little information about such associations in youths. OBJECTIVE: The aim of this study was to evaluate the associations of SNPs in the TCF7L2, SLC16A11, and ABCA1 genes with T2D and related glycemic traits in Mexican children and adolescents. SUBJECTS: A total of 99 families with children with T2D (n = 327) and 83 families with children without the disease (n = 212)...
January 19, 2017: Pediatric Diabetes
https://www.readbyqxmd.com/read/28101800/is-the-genetic-background-of-co-stimulatory-cd28-ctla-4-pathway-the-risk-factor-for-prostate-cancer
#4
Lidia Karabon, K Tupikowski, A Tomkiewicz, A Partyka, E Pawlak-Adamska, A Wojciechowski, A Kolodziej, J Dembowski, R Zdrojowy, I Frydecka
The impairment of immunological surveillance caused by aberrant T cell activation can lead to an inadequate anti-tumor response. Therefore, deregulation in co-stimulatory pathway might be associated with cancer susceptibility. Here we undertook a prospective study to investigate whether genetic variations in gene encoding molecule CD28 and CTLA-4 playing pivotal role in regulating adoptive immune response can influence susceptibility to prostate cancer. Single nucleotide polymorphisms (SNPs) in CTLA-4 and CD28 genes were genotyped in 301 prostate cancer (PCa) patients and 301 controls...
January 18, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28101368/polymorphisms-in-the-canine-monoamine-oxidase-a-maoa-gene-identification-and-variation-among-five-broad-dog-breed-groups
#5
James Sacco, Andrew Ruplin, Paul Skonieczny, Michael Ohman
BACKGROUND: In humans, reduced activity of the enzyme monoamine oxidase type A (MAOA) due to genetic polymorphisms within the MAOA gene leads to increased brain neurotransmitter levels associated with aggression. In order to study MAOA genetic diversity in dogs, we designed a preliminary study whose objectives were to identify novel alleles in functionally important regions of the canine MAOA gene, and to investigate whether the frequencies of these polymorphisms varied between five broad breed groups (ancient, herding, mastiff, modern European, and mountain)...
2017: Canine Genetics and Epidemiology
https://www.readbyqxmd.com/read/28101335/novel-snps-in-il-17f-and-il-17a-genes-associated-with-somatic-cell-count-in-chinese-holstein-and-inner-mongolia-sanhe-cattle
#6
Tahir Usman, Yachun Wang, Chao Liu, Yanghua He, Xiao Wang, Yichun Dong, Hongjun Wu, Airong Liu, Ying Yu
BACKGROUND: Bovine mastitis is the most common and costly disease of lactating cattle worldwide. Apart from milk somatic cell count (SCC) and somatic cell score (SCS), serum cytokines such as interleukin-17 (IL-17) and interleukin-4 (IL-4) may also be potential indicators for bovine mastitis. The present study was designed to investigate the effects of single nucleotide polymorphisms (SNPs) in bovine IL-17F and IL-17A genes on SCC, SCS and serum cytokines in Chinese Holstein and Inner-Mongolia Sanhe cattle, and to compare the mRNA expression variations of the cows with different genotypes...
2017: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/28100911/variants-on-chromosome-4q21-near-pkd2-and-siblings-are-associated-with-dental-caries
#7
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/28100790/genome-wide-analysis-in-brazilians-reveals-highly-differentiated-native-american-genome-regions
#8
Josyf C Mychaleckyj, Alexandre Havt, Uma Nayak, Relana Pinkerton, Emily Farber, Patrick Concannon, Aldo A Lima, Richard L Guerrant
Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared to the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh)...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100419/redox-dysregulation-immuno-inflammatory-alterations-and-genetic-variants-of-bdnf-and-mmp-9-in-schizophrenia-pathophysiological-and-phenotypic-implications
#9
Fahmy T Ali, Eman M Abd El-Azeem, Marwa A Hamed, Mohamed A M Ali, Nour M Abd Al-Kader, Ekrami A Hassan
BACKGROUND: Although a clear mechanism underlying the pathophysiology of schizophrenia (SZ) remains elusive, oxidative stress, inflammatory syndrome and immune activation have become an attractive hypothesis for explaining the pathophysiology of SZ. Data from prior studies on the role of matrix metalloproteinase 9 (MMP-9) and brain-derived neurotrophic factor (BDNF) single nucleotide polymorphisms (SNPs) in SZ are contradictory. We aimed to investigate whether oxidative stress, inflammatory and immune activation markers as well as MMP-9 levels may be implicated in SZ pathogenesis...
January 15, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28100189/an-snp-based-saturated-genetic-map-and-qtl-analysis-of-fruit-related-traits-in-zucchini-using-genotyping-by-sequencing
#10
Javier Montero-Pau, José Blanca, Cristina Esteras, Eva Ma Martínez-Pérez, Pedro Gómez, Antonio J Monforte, Joaquín Cañizares, Belén Picó
BACKGROUND: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100040/induced-pluripotent-stem-cell-research-in-the-era-of-precision-medicine
#11
Takashi Hamazaki, Nihal El Rouby, Natalie C Fredette, Katherine E Santostefano, Naohiro Terada
Recent advances in DNA sequencing technologies are revealing how human genetic variations associate with differential health risks, disease susceptibilities and drug responses. Such information is now expected to help evaluate individual health risks, design personalized health plans and treat patients with precision. It is still challenging, however, to understand how such genetic variations cause the phenotypic alterations in pathobiologies and treatment response. Human induced pluripotent stem cell (iPSC) technologies are emerging as a promising strategy to fill the knowledge gaps between genetic association studies and underlying molecular mechanisms...
January 18, 2017: Stem Cells
https://www.readbyqxmd.com/read/28100029/isolation-with-asymmetric-gene-flow-during-the-nonsynchronous-divergence-of-dry-forest-birds
#12
Jessica A Oswald, Isaac Overcast, William M Mauck, Michael J Andersen, Brian Tilston Smith
Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of communities often results from dynamic processes linked to numerous population histories among co-distributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28100020/independent-evolution-of-sexual-dimorphism-and-female-limited-mimicry-in-swallowtail-butterflies-papilio-dardanus-and-p-phorcas
#13
M J T N Timmermans, M J Thompson, S Collins, A P Vogler
Several species of Swallowtail butterflies (genus Papilio) are Batesian mimics that express multiple mimetic female forms, while the males are monomorphic and non-mimetic. The evolution of such sex-limited mimicry may involve sexual dimorphism arising first and mimicry subsequently. Such a stepwise scenario through a non-mimetic, sexually dimorphic stage has been proposed for two closely related sexually dimorphic species; P. phorcas, a non-mimetic species with two female forms, and P. dardanus, a female-limited polymorphic mimetic species...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28100017/subspecies-delineation-amid-phenotypic-geographic-and-genetic-discordance-in-a-songbird
#14
Jennifer Walsh, Irby J Lovette, Virginia Winder, Chris S Elphick, Brian J Olsen, W Gregory Shriver, Adrienne I Kovach
Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and saltmarsh (A...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28100011/association-mapping-of-morphological-traits-in-wild-and-captive-zebra-finches-reliable-within-but-not-between-populations
#15
Ulrich Knief, Holger Schielzeth, Niclas Backström, Georg Hemmrich-Stanisak, Michael Wittig, Andre Franke, Simon C Griffith, Hans Ellegren, Bart Kempenaers, Wolfgang Forstmeier
Identifying causal genetic variants underlying heritable phenotypic variation is a longstanding goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild-caught zebra finches...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099948/mdm4-genetic-variants-and-risk-of-gastric-cancer-in-an-eastern-chinese-population
#16
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/28099784/investigating-the-extent-of-parallelism-in-morphological-and-genomic-divergence-among-lake-trout-ecotypes-in-lake-superior
#17
Alysse Perreault-Payette, Andrew M Muir, Frederick Goetz, Charles Perrier, Eric Normandeau, Pascal Sirois, Louis Bernatchez
Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099775/the-population-genomic-signature-of-environmental-association-and-gene-flow-in-an-ecologically-divergent-tree-species-metrosideros-polymorpha-myrtaceae
#18
Ayako Izuno, Kanehiro Kitayama, Yusuke Onoda, Yuki Tsujii, Masaomi Hatakeyama, Atsushi J Nagano, Mie N Honjo, Rie Shimizu-Inatsugi, Hiroshi Kudoh, Kentaro K Shimizu, Yuji Isagi
Genome-wide markers enable us to study genetic differentiation within a species and the factors underlying it at a much higher resolution than before, which advances our understanding of adaptation in organisms. We investigated genomic divergence in Metrosideros polymorpha, a woody species that occupies a wide range of ecological habitats across the Hawaiian Islands and shows remarkable phenotypic variation. Using 1,659 single nucleotide polymorphism (SNP) markers annotated with the genome assembly, we examined the population genetic structure and demographic history of nine populations across five elevations and two ages of substrates on Mauna Loa, the island of Hawaii...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28098224/association-of-genome-wide-association-study-gwas-identified-snps-and-risk-of-breast-cancer-in-an-indian-population
#19
Rajini Nagrani, Sharayu Mhatre, Preetha Rajaraman, Nilanjan Chatterjee, Mohammad R Akbari, Paolo Boffetta, Paul Brennan, Rajendra Badwe, Sudeep Gupta, Rajesh Dikshit
To date, no studies have investigated the association of the GWAS-identified SNPs with BC risk in Indian population. We investigated the association of 30 previously reported and replicated BC susceptibility SNPs in 1,204 cases and 1,212 controls from a hospital based case-control study conducted at the Tata Memorial Hospital, Mumbai. As a measure of total susceptibility burden, the polygenic risk score (PRS) for each individual was defined by the weighted sum of genotypes from 21 independent SNPs with weights derived from previously published estimates of association odds-ratios...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096879/association-between-mitofusin-2-gene-polymorphisms-and-late-onset-alzheimer-s-disease-in-the-korean-population
#20
Young Jong Kim, Jin Kyung Park, Won Sub Kang, Su Kang Kim, Changsu Han, Hae Ri Na, Hae Jeong Park, Jong Woo Kim, Young Youl Kim, Moon Ho Park, Jong-Woo Paik
OBJECTIVE: Mitochondrial dysfunction is a prominent and early feature of Alzheimer's disease (AD). The morphologic changes observed in the AD brain could be caused by a failure of mitochondrial fusion mechanisms. The aim of this study was to investigate whether genetic polymorphisms of two genes involved in mitochondrial fusion mechanisms, optic atrophy 1 (OPA1) and mitofusin 2 (MFN2), were associated with AD in the Korean population by analyzing genotypes and allele frequencies. METHODS: One coding single nucleotide polymorphism (SNP) in the MFN2, rs1042837, and two coding SNPs in the OPA1, rs7624750 and rs9851685, were compared between 165 patients with AD (83 men and 82 women, mean age 72...
January 2017: Psychiatry Investigation
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