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https://www.readbyqxmd.com/read/28195643/clinical-and-genetic-predictors-of-weight-gain-in-patients-diagnosed-with-breast-cancer
#1
Maureen Sadim, Yanfei Xu, Katharina Selig, Julie Paulus, Regina Uthe, Surbhi Agarwl, Iram Dubin, Panagiota Oikonomopoulou, Lesya Zaichenko, Silvia Aki McCandlish, Linda Van Horn, Christos Mantzoros, Donna Pauler Ankerst, Virginia G Kaklamani
BACKGROUND: Postdiagnosis weight gain in patients with breast cancer has been associated with increased cancer recurrence and mortality. This study was designed to identify risk factors for weight gain and create a predictive model to identify a high-risk population for targeted interventions. METHODS: The weight of 393 patients with breast cancer from the Northwestern Robert H. Lurie Cancer Center was measured over a 2-year period from diagnosis, with body mass index (BMI) change over 18 months as the primary endpoint...
February 14, 2017: Cancer
https://www.readbyqxmd.com/read/28194004/genetic-contributions-to-self-reported-tiredness
#2
V Deary, S P Hagenaars, S E Harris, W D Hill, G Davies, D C M Liewald, A M McIntosh, C R Gale, I J Deary
Self-reported tiredness and low energy, often called fatigue, are associated with poorer physical and mental health. Twin studies have indicated that this has a heritability between 6 and 50%. In the UK Biobank sample (N=108 976), we carried out a genome-wide association study (GWAS) of responses to the question, 'Over the last two weeks, how often have you felt tired or had little energy?' Univariate GCTA-GREML found that the proportion of variance explained by all common single-nucleotide polymorphisms for this tiredness question was 8...
February 14, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28161533/prevalence-determinants-and-clinical-correlates-of-vitamin-d-deficiency-in-patients-with-chronic-obstructive-pulmonary-disease-in-london-uk
#3
David A Jolliffe, Wai Yee James, Richard L Hooper, Neil C Barnes, Claire L Greiller, Kamrul Islam, Angshu Bhowmik, Peter M Timms, Raj K Rajakulasingam, Aklak B Choudhury, David E Simcock, Elina Hyppönen, Robert T Walton, Christopher J Corrigan, Christopher J Griffiths, Adrian R Martineau
Vitamin D deficiency is common in patients with chronic obstructive pulmonary disease (COPD), yet a comprehensive analysis of environmental and genetic determinants of serum 25-hydroxyvitamin D (25[OH]D) concentration in patients with this condition is lacking. We conducted a multi-centre cross-sectional study in 278 COPD patients aged 41-92 years in London, UK. Details of potential environmental determinants of vitamin D status and COPD symptom control and severity were collected by questionnaire, and blood samples were taken for analysis of serum 25(OH)D concentration and DNA extraction...
February 1, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28158253/qtls-associated-with-agronomic-traits-in-the-attila-%C3%A3-cdc-go-spring-wheat-population-evaluated-under-conventional-management
#4
Jun Zou, Kassa Semagn, Muhammad Iqbal, Hua Chen, Mohammad Asif, Amidou N'Diaye, Alireza Navabi, Enid Perez-Lara, Curtis Pozniak, Rong-Cai Yang, Harpinder Randhawa, Dean Spaner
Recently, we investigated the effect of the wheat 90K single nucleotide polymorphic (SNP) array and three gene-specific (Ppd-D1, Vrn-A1 and Rht-B1) markers on quantitative trait loci (QTL) detection in a recombinant inbred lines (RILs) population derived from a cross between two spring wheat (Triticum aestivum L.) cultivars, 'Attila' and 'CDC Go', and evaluated for eight agronomic traits at three environments under organic management. The objectives of the present study were to investigate the effect of conventional management on QTL detection in the same mapping population using the same set of markers as the organic management and compare the results with organic management...
2017: PloS One
https://www.readbyqxmd.com/read/28152092/a-genome-wide-association-study-for-agronomic-traits-in-soybean-using-snp-markers-and-snp-based-haplotype-analysis
#5
Rodrigo Iván Contreras-Soto, Freddy Mora, Marco Antônio Rott de Oliveira, Wilson Higashi, Carlos Alberto Scapim, Ivan Schuster
Mapping quantitative trait loci through the use of linkage disequilibrium (LD) in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max). The haplotype-based genome-wide association study (GWAS) has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW), plant height (PH) and seed yield (SY) in a soybean association mapping panel using single nucleotide polymorphism (SNP) markers and haplotype information...
2017: PloS One
https://www.readbyqxmd.com/read/28117334/a-systematic-snp-selection-approach-to-identify-mechanisms-underlying-disease-aetiology-linking-height-to-post-menopausal-breast-and-colorectal-cancer-risk
#6
Rachel J J Elands, Colinda C J M Simons, Mona Riemenschneider, Aaron Isaacs, Leo J Schouten, Bas A Verhage, Kristel Van Steen, Roger W L Godschalk, Piet A van den Brandt, Monika Stoll, Matty P Weijenberg
Data from GWAS suggest that SNPs associated with complex diseases or traits tend to co-segregate in regions of low recombination, harbouring functionally linked gene clusters. This phenomenon allows for selecting a limited number of SNPs from GWAS repositories for large-scale studies investigating shared mechanisms between diseases. For example, we were interested in shared mechanisms between adult-attained height and post-menopausal breast cancer (BC) and colorectal cancer (CRC) risk, because height is a risk factor for these cancers, though likely not a causal factor...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28095416/meta-gwas-accuracy-and-power-metagap-calculator-shows-that-hiding-heritability-is-partially-due-to-imperfect-genetic-correlations-across-studies
#7
Ronald de Vlaming, Aysu Okbay, Cornelius A Rietveld, Magnus Johannesson, Patrik K E Magnusson, André G Uitterlinden, Frank J A van Rooij, Albert Hofman, Patrick J F Groenen, A Roy Thurik, Philipp D Koellinger
Large-scale genome-wide association results are typically obtained from a fixed-effects meta-analysis of GWAS summary statistics from multiple studies spanning different regions and/or time periods. This approach averages the estimated effects of genetic variants across studies. In case genetic effects are heterogeneous across studies, the statistical power of a GWAS and the predictive accuracy of polygenic scores are attenuated, contributing to the so-called 'missing heritability'. Here, we describe the online Meta-GWAS Accuracy and Power (MetaGAP) calculator (available at www...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28056267/-association-between-eye-absent-homolog-4-gene-polymorphisms-and-occupational-noise-induced-hearing-loss
#8
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/28056266/-association-between-variations-in-protocadherin-15-gene-and-occupational-noise-induced-hearing-loss
#9
X R Xu, Q Y Yang, 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: The aim of this study was to investigate whether genetic variability in the protocadherin 15 (PCDH15) gene may correspond with increased susceptibility to noise-induced hearing loss (NIHL) in a Chinese population. Methods: A nested case-control study was performed that followed a cohort of 7 445 noise-exposed workers in a steel factory of Henan province in China from January 1, 2006 to December 31, 2015. In this study, 394 cases who had an average hearing threshold of more than 40 dB (A) in high frequency were defined as the case group, and 721 controls who had an average hearing threshold of less than 35 dB (A) in high frequency and less than 25 dB (A) in speech frequency were defined as the control group...
January 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/28055148/genome-wide-association-study-for-13-agronomic-traits-reveals-distribution-of-superior-alleles-in-bread-wheat-from-the-yellow-and-huai-valley-of-china
#10
Congwei Sun, Fuyan Zhang, Xuefang Yan, Xiangfen Zhang, Zhongdong Dong, Dangqun Cui, Feng Chen
Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here we revealed new allelic variation distribution for 13 yield-related traits in series of genome-wide association studies (GWAS) using the Wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over three years. After filtering SNP datasets, GWAS using 20,689 high-quality SNPs associated 1,769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions...
January 5, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28028632/the-rs3736228-polymorphism-in-the-lrp5-gene-is-associated-with-calcaneal-ultrasound-parameter-but-not-with-body-composition-in-a-cohort-of-young-caucasian-adults
#11
María Correa-Rodríguez, Jacqueline Schmidt-RioValle, Blanca Rueda-Medina
The aim of the present study was to investigate the possible influence of low-density lipoprotein receptor-related protein 5 (LRP5) and sclerostin (SOST) genes as genetic factors contributing to calcaneal quantitative ultrasound (QUS) and body composition variables in a population of young Caucasian adults. The study population comprised a total of 575 individuals (mean age 20.41years; SD 2.36) whose bone mass was assessed through QUS to determine broadband ultrasound attenuation (BUA, dB/MHz). Body composition measurements were performed using a body composition analyser...
December 27, 2016: Journal of Bone and Mineral Metabolism
https://www.readbyqxmd.com/read/28008729/parental-and-child-genetic-contributions-to-obesity-traits-in-early-life-based-on-83-loci-validated-in-adults-the-family-study
#12
A Li, S Robiou-du-Pont, S S Anand, K M Morrison, S D McDonald, S A Atkinson, K K Teo, D Meyre
BACKGROUND: The genetic influence on child obesity has not been fully elucidated. OBJECTIVE: This study investigated the parental and child contributions of 83 adult body mass index (BMI)-associated single-nucleotide polymorphisms (SNPs) to obesity-related traits in children from birth to 5 years old. METHODS: A total of 1402 individuals were genotyped for 83 SNPs. An unweighted genetic risk score (GRS) was generated by the sum of BMI-increasing alleles...
December 23, 2016: Pediatric Obesity
https://www.readbyqxmd.com/read/27997600/exploring-identity-by-descent-segments-and-putative-functions-using-different-foundation-parents-in-maize
#13
Xun Wu, Yongxiang Li, Junjie Fu, Xin Li, Chunhui Li, Dengfeng Zhang, Yunsu Shi, Yanchun Song, Yu Li, Tianyu Wang
Maize foundation parents (FPs) play no-alternative roles in hybrid breeding because they were widely used in the development of new lines and hybrids. The combination of different identity-by-descent (IBD) segments and genes could account for the formation patterns of different FPs, and knowledge of these IBD regions would provide an extensive foundation for the development of new candidate FP lines in future maize breeding. In this paper, a panel of 304 elite lines derived from FPs, i.e., B73, 207, Mo17, and Huangzaosi (HZS), was collected and analyzed using 43,252 single nucleotide polymorphism (SNP) markers...
2016: PloS One
https://www.readbyqxmd.com/read/27994193/association-and-expression-analyses-of-the-ucp2-and-ucp3-gene-polymorphisms-with-body-measurement-and-meat-quality-traits-in-qinchuan-cattle
#14
Yaning Wang, Wucai Yang, Linsheng Gui, Hongbao Wang, Linsen Zan
The uncoupling proteins (UCPs) belong to the mitochondrial inner membrane anion carrier superfamily and play an important role in energy homeostasis. Genetic studies have demonstrated that Ucp2 and Ucp3 gene variants are involved in obesity and metabolic syndrome. The aim of this study was to identify associations between polymorphisms of Ucp2 and Ucp3 genes and economically-important traits in Qinchuan cattle. In the present study, one single-nucleotide polymorphism (SNP) in the 5'UTR region (SNP1:g.C-754G) of the Ucp2 gene was identified by direct sequencing of 441 Qinchuan cattle...
December 2016: Journal of Genetics
https://www.readbyqxmd.com/read/27928975/assessing-causality-in-associations-between-cannabis-use-and-schizophrenia-risk-a-two-sample-mendelian-randomization-study
#15
S H Gage, H J Jones, S Burgess, J Bowden, G Davey Smith, S Zammit, M R Munafò
BACKGROUND: Observational associations between cannabis and schizophrenia are well documented, but ascertaining causation is more challenging. We used Mendelian randomization (MR), utilizing publicly available data as a method for ascertaining causation from observational data. METHOD: We performed bi-directional two-sample MR using summary-level genome-wide data from the International Cannabis Consortium (ICC) and the Psychiatric Genomics Consortium (PGC2). Single nucleotide polymorphisms (SNPs) associated with cannabis initiation (p < 10-5) and schizophrenia (p < 5 × 10-8) were combined using an inverse-variance-weighted fixed-effects approach...
December 8, 2016: Psychological Medicine
https://www.readbyqxmd.com/read/27924921/birth-weight-and-risk-of-ischemic-heart-disease-a-mendelian-randomization-study
#16
Shiu Lun Au Yeung, Shi Lin Lin, Albert Martin Li, C Mary Schooling
Low birth weight is a risk factor for cardiovascular disease. However, the association could be confounded by many factors. We used Mendelian randomization to clarify the role of birth weight in ischemic heart disease (IHD) and lipids. We used all 7 single nucleotide polymorphisms (SNPs) independently contributing to birth weight at genome wide significance (p < 5 × 10(-8)) in separate sample instrumental variable analysis to estimate the effect of birth weight on IHD using the CARDIoGRAMplusC4D 1000 Genomes based GWAS case (n = 60,801)-control (n = 123,504) study and on lipids using GLGC (n = 188,577)...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27918628/phenotypic-and-genome-wide-association-analysis-of-spike-ethylene-in-diverse-wheat-genotypes-under-heat-stress
#17
Ravi Valluru, Matthew P Reynolds, William J Davies, Sivakumar Sukumaran
The gaseous phytohormone ethylene plays an important role in spike development in wheat (Triticum aestivum). However, the genotypic variation and the genomic regions governing spike ethylene (SET) production in wheat under long-term heat stress remain unexplored. We investigated genotypic variation in the production of SET and its relationship with spike dry weight (SDW) in 130 diverse wheat elite lines and landraces under heat-stressed field conditions. We employed an Illumina iSelect 90K single nucleotide polymorphism (SNP) genotyping array to identify the genetic loci for SET and SDW through a genome-wide association study (GWAS) in a subset of the Wheat Association Mapping Initiative (WAMI) panel...
April 2017: New Phytologist
https://www.readbyqxmd.com/read/27912109/characterization-and-fine-mapping-of-a-novel-premature-leaf-senescence-mutant-yellow-leaf-and-dwarf-1-in-rice
#18
Luchang Deng, Peng Qin, Zhi Liu, Geling Wang, Weilan Chen, Jianhua Tong, Langtao Xiao, Bin Tu, Yuantao Sun, Wei Yan, Hang He, Jun Tan, Xuewei Chen, Yuping Wang, Shigui Li, Bingtian Ma
Leaves are the main organs in which photosynthates are produced. Leaf senescence facilitates the translocation of photosynthates and nutrients from source to sink, which is important for plant development and especially for crop yield. However, the molecular mechanism of leaf senescence is unknown. Here, we identified a mutant, yellow leaf and dwarf 1 (yld1), which exhibited decreased plant height and premature leaf senescence. Nitroblue tetrazolium and diamiobenzidine staining analyses revealed that the concentrations of reactive oxygen species were higher in yld1 leaves than in wild type leaves...
November 22, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27902795/genome-wide-association-study-identifies-candidate-loci-underlying-agronomic-traits-in-a-middle-american-diversity-panel-of-common-bean
#19
Samira Mafi Moghaddam, Sujan Mamidi, Juan M Osorno, Rian Lee, Mark Brick, James Kelly, Phillip Miklas, Carlos Urrea, Qijian Song, Perry Cregan, Jane Grimwood, Jeremy Schmutz, Phillip E McClean
Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27898815/germplasm-architecture-revealed-through-chromosomal-effects-for-quantitative-traits-in-maize
#20
Rex Bernardo, Addie M Thompson
Germplasm architecture refers to how favorable alleles for a given trait are distributed across the genome in a germplasm collection. Our objective was to assess germplasm architecture for quantitative traits among US maize ( L.) inbreds. A total of 271 inbreds were genotyped at 28,626 single nucleotide polymorphism (SNP) loci and phenotyped for anthesis date, plant height, starch and protein concentration, and resistance to northern corn leaf blight (NCLB, caused by ). Chromosomal effects were calculated as the sum of the trait effects of SNP alleles carried on a specific chromosome by an inbred...
July 2016: Plant Genome
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