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https://www.readbyqxmd.com/read/29315403/joint-associations-of-a-polygenic-risk-score-and-environmental-risk-factors-for-breast-cancer-in-the-breast-cancer-association-consortium
#1
Anja Rudolph, Minsun Song, Mark N Brook, Roger L Milne, Nasim Mavaddat, Kyriaki Michailidou, Manjeet K Bolla, Qin Wang, Joe Dennis, Amber N Wilcox, John L Hopper, Melissa C Southey, Renske Keeman, Peter A Fasching, Matthias W Beckmann, Manuela Gago-Dominguez, Jose E Castelao, Pascal Guénel, Thérèse Truong, Stig E Bojesen, Henrik Flyger, Hermann Brenner, Volker Arndt, Hiltrud Brauch, Thomas Brüning, Arto Mannermaa, Veli-Matti Kosma, Diether Lambrechts, Machteld Keupers, Fergus J Couch, Celine Vachon, Graham G Giles, Robert J MacInnis, Jonine Figueroa, Louise Brinton, Kamila Czene, Judith S Brand, Marike Gabrielson, Keith Humphreys, Angela Cox, Simon S Cross, Alison M Dunning, Nick Orr, Anthony Swerdlow, Per Hall, Paul D P Pharoah, Marjanka K Schmidt, Douglas F Easton, Nilanjan Chatterjee, Jenny Chang-Claude, Montserrat García-Closas
Background: Polygenic risk scores (PRS) for breast cancer can be used to stratify the population into groups at substantially different levels of risk. Combining PRS and environmental risk factors will improve risk prediction; however, integrating PRS into risk prediction models requires evaluation of their joint association with known environmental risk factors. Methods: Analyses were based on data from 20 studies; datasets analysed ranged from 3453 to 23 104 invasive breast cancer cases and similar numbers of controls, depending on the analysed environmental risk factor...
January 5, 2018: International Journal of Epidemiology
https://www.readbyqxmd.com/read/29304028/high-density-single-nucleotide-polymorphism-snp-mapping-and-quantitative-trait-loci-qtl-analysis-in-a-biparental-spring-triticale-population-localized-major-and-minor-effect-fusarium-head-blight-resistance-and-associated-traits-qtl
#2
Raman Dhariwal, George Fedak, Yves Dion, Curtis Pozniak, André Laroche, François Eudes, Harpinder Singh Randhawa
Triticale (xTriticosecale Wittmack) is an important feed crop which suffers severe yield, grade and end-use quality losses due to Fusarium head blight (FHB). Development of resistant triticale cultivars is hindered by lack of effective genetic resistance sources. To dissect FHB resistance, a doubled haploid spring triticale population produced from the cross TMP16315/AC Ultima using a microspore culture method, was phenotyped for FHB incidence, severity, visual rating index (VRI), deoxynivalenol (DON) and some associated traits (ergot, grain protein content, test weight, yield, plant height and lodging) followed by single nucleotide polymorphism (SNP) genotyping...
January 5, 2018: Genes
https://www.readbyqxmd.com/read/29250097/genetic-parameters-and-the-impact-of-off-types-for-theobroma-cacao-l-in-a-breeding-program-in-brazil
#3
Ashley DuVal, Salvador A Gezan, Guiliana Mustiga, Conrad Stack, Jean-Philippe Marelli, José Chaparro, Donald Livingstone, Stefan Royaert, Juan C Motamayor
Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29237553/the-snp-rs4252548-r112h-which-is-associated-with-reduced-human-height-compromises-the-stability-of-il-11
#4
Juliane Lokau, Sascha Göttert, Philipp Arnold, Stefan Düsterhöft, David Massa López, Joachim Grötzinger, Christoph Garbers
Height is a complex human phenotype that is influenced by variations in a high number of genes. Recently, a single nucleotide polymorphism (SNP) within IL11 (rs4252548) has been described to be associated with height in adults of European ancestry. This coding SNP leads to the exchange of Arg-112 to His-112 within the cytokine Interleukin-11 (IL-11), which has a well-established role in osteoclast development and bone turnover. The functional consequences of the R112H mutation are unknown so far. In this study, we show by molecular replacement that Arg-112 does not participate in binding of IL-11 to its receptors IL-11R and glycoprotein 130 (gp130)...
December 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29220676/penetrance-of-polygenic-obesity-susceptibility-loci-across-the-body-mass-index-distribution
#5
Arkan Abadi, Akram Alyass, Sebastien Robiou du Pont, Ben Bolker, Pardeep Singh, Viswanathan Mohan, Rafael Diaz, James C Engert, Salim Yusuf, Hertzel C Gerstein, Sonia S Anand, David Meyre
A growing number of single-nucleotide polymorphisms (SNPs) have been associated with body mass index (BMI) and obesity, but whether the effects of these obesity-susceptibility loci are uniform across the BMI distribution remains unclear. We studied the effects of 37 BMI-associated SNPs in 75,230 adults of European ancestry across BMI percentiles by using conditional quantile regression (CQR) and meta-regression (MR) models. The effects of nine SNPs (24%)-rs1421085 (FTO; p = 8.69 × 10-15), rs6235 (PCSK1; p = 7...
December 7, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29198721/a-selection-operator-for-summary-association-statistics-reveals-allelic-heterogeneity-of-complex-traits
#6
Zheng Ning, Youngjo Lee, Peter K Joshi, James F Wilson, Yudi Pawitan, Xia Shen
In recent years, as a secondary analysis in genome-wide association studies (GWASs), conditional and joint multiple-SNP analysis (GCTA-COJO) has been successful in allowing the discovery of additional association signals within detected loci. This suggests that many loci mapped in GWASs harbor more than a single causal variant. In order to interpret the underlying mechanism regulating a complex trait of interest in each discovered locus, researchers must assess the magnitude of allelic heterogeneity within the locus...
November 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29198016/advantages-and-limitations-of-multiple-trait-genomic-prediction-for-fusarium-head-blight-severity-in-hybrid-wheat-triticum-aestivum-l
#7
Albert W Schulthess, Yusheng Zhao, C Friedrich H Longin, Jochen C Reif
Predictabilities for wheat hybrids less related to the estimation set were improved by shifting from single- to multiple-trait genomic prediction of Fusarium head blight severity. Breeding for improved Fusarium head blight resistance (FHBr) of wheat is a very laborious and expensive task. FHBr complexity is mainly due to its highly polygenic nature and because FHB severity (FHBs) is greatly influenced by the environment. Associated traits plant height and heading date may provide additional information related to FHBr, but this is ignored in single-trait genomic prediction (STGP)...
December 2, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29181734/pleiotropy-of-cardiometabolic-syndrome-with-obesity-related-anthropometric-traits-determined-using-empirically-derived-kinships-from-the-busselton-health-study
#8
Gemma Cadby, Phillip E Melton, Nina S McCarthy, Marcio Almeida, Sarah Williams-Blangero, Joanne E Curran, John L VandeBerg, Jennie Hui, John Beilby, A W Musk, Alan L James, Joseph Hung, John Blangero, Eric K Moses
Over two billion adults are overweight or obese and therefore at an increased risk of cardiometabolic syndrome (CMS). Obesity-related anthropometric traits genetically correlated with CMS may provide insight into CMS aetiology. The aim of this study was to utilise an empirically derived genetic relatedness matrix to calculate heritabilities and genetic correlations between CMS and anthropometric traits to determine whether they share genetic risk factors (pleiotropy). We used genome-wide single nucleotide polymorphism (SNP) data on 4671 Busselton Health Study participants...
November 27, 2017: Human Genetics
https://www.readbyqxmd.com/read/29176820/genome-wide-association-study-for-grain-yield-and-related-traits-in-elite-wheat-varieties-and-advanced-lines-using-snp-markers
#9
Sheng-Xing Wang, Yu-Lei Zhu, De-Xin Zhang, Hui Shao, Peng Liu, Jian-Bang Hu, Heng Zhang, Hai-Ping Zhang, Cheng Chang, Jie Lu, Xian-Chun Xia, Gen-Lou Sun, Chuan-Xi Ma
Genetic improvement of grain yield is always an important objective in wheat breeding. Here, a genome-wide association study was conducted to parse the complex genetic composition of yield-related traits of 105 elite wheat varieties (lines) using the Wheat 90K Illumina iSelect SNP array. Nine yield-related traits, including maximum number of shoots per square meter (MSN), effective number of spikes per square meter (ESN), percentage of effective spike (PES), number of kernels per spike (KPS), thousand-kernel weight (TKW), the ratio of kernel length/kernel width (RLW), leaf-area index (LAI), plant height (PH), and grain yield (GY), were evaluated across four environments...
2017: PloS One
https://www.readbyqxmd.com/read/29168265/two-stage-identification-of-snp-effects-on-dynamic-poplar-growth
#10
Jingyuan Liu, Meixia Ye, Sheng Zhu, Libo Jiang, Mengmeng Sang, Jingwen Gan, Qian Wang, Minren Huang, Rongling Wu
This project proposes an approach to identifying significant single nucleotide polymorphism (SNP) effects, both additive and dominant, on the dynamic growth of poplar in diameter and height. The annual changes in yearly phenotypes based on regular observation periods are considered to represent multiple responses. A total of 156, 362 candidate SNPs are studied, and the phenotypes of 64 poplar trees are recorded. To address this ultrahigh dimension ality issue, this paper adopts the two-stage approach. First, the conventional GWAS and the distance correlation sure independence screening (DC-SIS) methods(Li, Zhong and Zhu, 2012) are combined to reduce the model dimensions at the sample size; second, a grouped penalized regression is applied to further refine the model and choose the final sparse SNPs...
November 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29166878/the-andromeda-prospective-cohort-study-predictive-value-of-combined-criteria-to-tailor-breast-cancer-screening-and-new-opportunities-from-circulating-markers-study-protocol
#11
Livia Giordano, Federica Gallo, Elisabetta Petracci, Giovanna Chiorino, Nereo Segnan
BACKGROUND: In recent years growing interest has been posed on alternative ways to screen women for breast cancer involving different imaging techniques or adjusting screening interval by breast cancer risk estimates. A new research area is studying circulating microRNAs as molecular biomarkers potentially useful for non invasive early detection together with the analysis of single-nucleotide polymorphisms (SNPs). The Andromeda study is a prospective cohort study on women attending breast cancer screening in a northern Italian area...
November 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29147571/a-surprising-treatment-response-in-a-patient-with-rare-isolated-growth-hormone-deficiency-type-ib
#12
Jordan Yardain Amar, Kimberly Borden, Elizabeth Watson, Talin Arslanian
Isolated Growth Hormone Deficiency (IGHD) is a rare cause of short stature, treated with the standard regimen of subcutaneous synthetic growth hormone (GH). Patients typically achieve a maximum height velocity in the first year of treatment, which then tapers shortly after treatment is stopped. We report a case of a 9-year-old male who presented with short stature (<3rd percentile for age and race). Basal hormone levels showed undetectable serum IGF1. Skeletal wrist age was consistent with chronologic age...
2017: Endocrinology, Diabetes & Metabolism Case Reports
https://www.readbyqxmd.com/read/29143708/genome-wide-association-study-for-growth-traits-in-nelore-cattle
#13
A P N Terakado, R B Costa, G M F de Camargo, N Irano, T Bresolin, L Takada, C V D Carvalho, H N Oliveira, R Carvalheiro, F Baldi, L G de Albuquerque
The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) with birth weight, weight gain from birth to weaning and from weaning to yearling, yearling height and cow weight in Nelore cattle. Data from 5064 animals participating in the DeltaGen and PAINT breeding programs were used. The animals were genotyped with a panel of 777 962 SNPs (Illumina BovineHD BeadChip) and 412 993 SNPs remained after quality control analysis of the genomic data. A genome-wide association study was performed using a single-step methodology...
November 16, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29143671/gwas-of-agronomic-traits-in-soybean-collection-included-in-breeding-pool-in-kazakhstan
#14
Alibek Zatybekov, Saule Abugalieva, Svetlana Didorenko, Yelena Gerasimova, Ivan Sidorik, Shynar Anuarbek, Yerlan Turuspekov
BACKGROUND: In recent years soybean is becoming one of the most important oilseed crops in Kazakhstan. Only within the last ten years (2006-2016), the area under soybean is expanded from 45 thousand hectares (ha) in 2006 to 120 thousand ha in 2016. The general trend of soybean expansion is from south-eastern to eastern and northern regions of the country, where average temperatures are lower and growing seasons are shorter. These new soybean growing territories were poorly examined in terms of general effects on productivity level among the diverse sample of soybean accessions...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143610/development-of-f1-hybrid-population-and-the-high-density-linkage-map-for-european-aspen-populus-tremula-l-using-radseq-technology
#15
Anatoly V Zhigunov, Pavel S Ulianich, Marina V Lebedeva, Peter L Chang, Sergey V Nuzhdin, Elena K Potokina
BACKGROUND: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. RESULTS: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143598/gwas-for-plant-growth-stages-and-yield-components-in-spring-wheat-triticum-aestivum-l-harvested-in-three-regions-of-kazakhstan
#16
Yerlan Turuspekov, Aida Baibulatova, Kanat Yermekbayev, Laura Tokhetova, Vladimir Chudinov, Grigoriy Sereda, Martin Ganal, Simon Griffiths, Saule Abugalieva
BACKGROUND: Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29129827/genetic-predisposition-clinical-risk-factor-burden-and-lifetime-risk-of-atrial-fibrillation
#17
Lu-Chen Weng, Sarah R Preis, Olivia L Hulme, Martin G Larson, Seung Hoan Choi, Biqi Wang, Ludovic Trinquart, David D McManus, Laila Staerk, Honghuang Lin, Kathryn L Lunetta, Patrick T Ellinor, Emelia J Benjamin, Steven A Lubitz
Background -The long-term probability of developing atrial fibrillation (AF) considering genetic predisposition and clinical risk factor burden is unknown. Methods -We estimated lifetime risk of AF in individuals from the community-based Framingham Heart Study. Polygenic risk for AF was derived using a score of approximately 1,000 AF-associated single nucleotide polymorphisms. Clinical risk factor burden was calculated for each individual using a validated risk score for incident AF comprised of height, weight, systolic and diastolic blood pressure, current smoking status, antihypertensive medication use, diabetes, history of myocardial infarction, and history of heart failure...
November 12, 2017: Circulation
https://www.readbyqxmd.com/read/29121402/incorporating-functional-genomic-information-to-enhance-polygenic-signal-and-identify-variants-involved-in-gene-by-environment-interaction-for-young-adult-alcohol-problems
#18
Jessica E Salvatore, Jeanne E Savage, Peter Barr, Aaron R Wolen, Fazil Aliev, Eero Vuoksimaa, Antti Latvala, Lea Pulkkinen, Richard J Rose, Jaakko Kaprio, Danielle M Dick
BACKGROUND: Characterizing aggregate genetic risk for alcohol misuse and identifying variants involved in gene-by-environment interaction (G×E) effects has so far been a major challenge. We hypothesized that functional genomic information could be used to enhance detection of polygenic signal underlying alcohol misuse, and to prioritize identification of single nucleotide polymorphisms (SNPs) most likely to exhibit G×E effects. METHODS: We examined these questions in the young adult FinnTwin12 sample (n=1170)...
November 9, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29113935/predicting-age-by-mining-electronic-medical-records-with-deep-learning-characterizes-differences-between-chronological-and-physiological-age
#19
Zichen Wang, Li Li, Benjamin S Glicksberg, Ariel Israel, Joel T Dudley, Avi Ma'ayan
Determining the discrepancy between chronological and physiological age of patients is central to preventative and personalized care. Electronic medical records (EMR) provide rich information about the patient physiological state, but it is unclear whether such information can be predictive of chronological age. Here we present a deep learning model that uses vital signs and lab tests contained within the EMR of Mount Sinai Health System (MSHS) to predict chronological age. The model is trained on 377,686 EMR from patients of ages 18-85 years old...
December 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29094466/joint-effects-of-prothrombotic-genotypes-and-body-height-on-the-risk-of-venous-thromboembolism-the-troms%C3%A3-study
#20
Lars D Horvei, Sigrid K Braekkan, Erin N Smith, Terry Solomon, Kristian Hindberg, Kelly A Frazer, Frits R Rosendaal, John-Bjarne Hansen
BACKGROUND: Studies have reported synergistic effects of prothrombotic single nucleotide polymorphisms (SNPs) and obesity on the risk of venous thromboembolism (VTE). Tall stature is associated with increased VTE risk, but the joint effect of prothrombotic genotypes and tall stature on VTE risk is unknown. AIMS: To investigate the joint effects of prothrombotic genotypes and tall stature on the risk of VTE. METHODS: Cases with incident VTE (n=676) and a randomly selected age-weighted subcohort (n=1842) were sampled from the Tromsø study (cohort follow-up: 1994-2012)...
November 2, 2017: Journal of Thrombosis and Haemostasis: JTH
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