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https://www.readbyqxmd.com/read/28454565/combined-gwas-and-guilt-by-association-based-prioritization-analysis-identifies-functional-candidate-genes-for-body-size-in-sheep
#1
Antonios Kominakis, Ariadne L Hager-Theodorides, Evangelos Zoidis, Aggeliki Saridaki, George Antonakos, George Tsiamis
BACKGROUND: Body size in sheep is an important indicator of productivity, growth and health as well as of environmental adaptation. It is a composite quantitative trait that has been studied with high-throughput genomic methods, i.e. genome-wide association studies (GWAS) in various mammalian species. Several genomic markers have been associated with body size traits and genes have been identified as causative candidates in humans, dog and cattle. A limited number of related GWAS have been performed in various sheep breeds and have identified genomic regions and candidate genes that partly account for body size variability...
April 28, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28441456/genome-wide-association-study-of-facial-morphology-reveals-novel-associations-with-frem1-and-park2
#2
Myoung Keun Lee, John R Shaffer, Elizabeth J Leslie, Ekaterina Orlova, Jenna C Carlson, Eleanor Feingold, Mary L Marazita, Seth M Weinberg
Several studies have now shown evidence of association between common genetic variants and quantitative facial traits in humans. The reported associations generally involve simple univariate measures and likely represent only a small fraction of the genetic loci influencing facial morphology. In this study, we applied factor analysis to a set of 276 facial linear distances derived from 3D facial surface images of 2187 unrelated individuals of European ancestry. We retained 23 facial factors, which we then tested for genetic associations using a genome-wide panel of 10,677,593 single nucleotide polymorphisms (SNPs)...
2017: PloS One
https://www.readbyqxmd.com/read/28401901/missing-heritability-is-the-gap-closing-an-analysis-of-32-complex-traits-in-the-lifelines-cohort-study
#3
Ilja M Nolte, Peter J van der Most, Behrooz Z Alizadeh, Paul Iw de Bakker, H Marike Boezen, Marcel Bruinenberg, Lude Franke, Pim van der Harst, Gerjan Navis, Dirkje S Postma, Marianne G Rots, Ronald P Stolk, Morris A Swertz, Bruce Hr Wolffenbuttel, Cisca Wijmenga, Harold Snieder
Despite the recent explosive rise in number of genetic markers for complex disease traits identified in genome-wide association studies, there is still a large gap between the known heritability of these traits and the part explained by these markers. To gauge whether this 'heritability gap' is closing, we first identified genome-wide significant SNPs from the literature and performed replication analyses for 32 highly relevant traits from five broad disease areas in 13 436 subjects of the Lifelines Cohort...
June 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28388634/phenome-wide-heritability-analysis-of-the-uk-biobank
#4
Tian Ge, Chia-Yen Chen, Benjamin M Neale, Mert R Sabuncu, Jordan W Smoller
Heritability estimation provides important information about the relative contribution of genetic and environmental factors to phenotypic variation, and provides an upper bound for the utility of genetic risk prediction models. Recent technological and statistical advances have enabled the estimation of additive heritability attributable to common genetic variants (SNP heritability) across a broad phenotypic spectrum. Here, we present a computationally and memory efficient heritability estimation method that can handle large sample sizes, and report the SNP heritability for 551 complex traits derived from the interim data release (152,736 subjects) of the large-scale, population-based UK Biobank, comprising both quantitative phenotypes and disease codes...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28251396/polymorphisms-in-ptk2-are-associated-with-skeletal-muscle-specific-force-an-independent-replication-study
#5
Georgina K Stebbings, A G Williams, C I Morse, S H Day
PURPOSE: The aim of the study was to investigate two single nucleotide polymorphisms (SNP) in PTK2 for associations with human muscle strength phenotypes in healthy men. METHODS: Measurement of maximal isometric voluntary knee extension (MVCKE) torque, net MVCKE torque and vastus lateralis (VL) specific force, using established techniques, was completed on 120 Caucasian men (age = 20.6 ± 2.3 year; height = 1.79 ± 0.06 m; mass = 75.0 ± 10...
April 2017: European Journal of Applied Physiology
https://www.readbyqxmd.com/read/27896743/analysis-of-quantitative-trait-loci
#6
David L Duffy
Although the term quantitative trait locus (QTL) strictly refers merely to a genetic variant that causes changes in a quantitative phenotype such as height, QTL analysis more usually describes techniques used to study oligogenic or polygenic traits where each identified locus contributes a relatively small amount to the genetic determination of the trait, which may be categorical in nature. Originally, too, it would be clear that it covered segregation and genetic linkage analysis, but now genetic association analysis in a genome-wide SNP or sequencing experiment would be the commonest application...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27436263/detection-of-gene-environment-interaction-in-pedigree-data-using-genome-wide-genotypes
#7
Michel G Nivard, Christel M Middeldorp, Gitta Lubke, Jouke-Jan Hottenga, Abdel Abdellaoui, Dorret I Boomsma, Conor V Dolan
Heritability may be estimated using phenotypic data collected in relatives or in distantly related individuals using genome-wide single nucleotide polymorphism (SNP) data. We combined these approaches by re-parameterizing the model proposed by Zaitlen et al and extended this model to include moderation of (total and SNP-based) genetic and environmental variance components by a measured moderator. By means of data simulation, we demonstrated that the type 1 error rates of the proposed test are correct and parameter estimates are accurate...
December 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27338933/population-variation-of-lin28b-in-the-mediterranean-novel-markers-for-microgeographic-discrimination
#8
Miguel M Álvarez-Álvarez, Robert Carreras-Torres, Daniela Zanetti, Esteban Vegas, Pedro Moral
OBJECTIVES: The aim of this study is to determine whether the LIN28B gene is differentially distributed in the Mediterranean region through the analysis of the allele distribution of three single nucleotide polymorphisms (SNPs), namely rs7759938, rs314277, and rs221639, in 24 populations. These SNPs have been recently related to the age at menarche, pubertal height growth, peripubertal body mass index, levels of prenatal testosterone exposure, and cancer survival. METHODS: A total of 1,197 DNA samples were genotyped...
June 24, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/26890892/early-developmental-gene-enhancers-affect-subcortical-volumes-in-the-adult-human-brain
#9
Martin Becker, Tulio Guadalupe, Barbara Franke, Derrek P Hibar, Miguel E Renteria, Jason L Stein, Paul M Thompson, Clyde Francks, Sonja C Vernes, Simon E Fisher
Genome-wide association screens aim to identify common genetic variants contributing to the phenotypic variability of complex traits, such as human height or brain morphology. The identified genetic variants are mostly within noncoding genomic regions and the biology of the genotype-phenotype association typically remains unclear. In this article, we propose a complementary targeted strategy to reveal the genetic underpinnings of variability in subcortical brain volumes, by specifically selecting genomic loci that are experimentally validated forebrain enhancers, active in early embryonic development...
May 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/26691201/an-ultra-high-density-map-as-a-community-resource-for-discerning-the-genetic-basis-of-quantitative-traits-in-maize
#10
Hongjun Liu, Yongchao Niu, Pedro J Gonzalez-Portilla, Huangkai Zhou, Liya Wang, Tao Zuo, Cheng Qin, Shuaishuai Tai, Constantin Jansen, Yaou Shen, Haijian Lin, Michael Lee, Doreen Ware, Zhiming Zhang, Thomas Lübberstedt, Guangtang Pan
BACKGROUND: To safeguard the food supply for the growing human population, it is important to understand and exploit the genetic basis of quantitative traits. Next-generation sequencing technology performs advantageously and effectively in genetic mapping and genome analysis of diverse genetic resources. Hence, we combined re-sequencing technology and a bin map strategy to construct an ultra-high-density bin map with thousands of bin markers to precisely map a quantitative trait locus...
2015: BMC Genomics
https://www.readbyqxmd.com/read/26689153/good-response-to-long-term-therapy-with-growth-hormone-in-a-patient-with-9p-trisomy-syndrome-a-case-report-and-review-of-the-literature
#11
REVIEW
Ana Pinheiro Machado Canton, Mirian Yumie Nishi, Tatiane Katsue Furuya, Rosimeire Aparecida Roela, Alexander Augusto Lima Jorge
The 9p trisomy syndrome is a rare condition, clinically characterized by a wide range of dysmorphic features, intellectual disability, and, in most patients, by short stature. Recombinant human growth hormone (rhGH) therapy is still controversial in syndromic disorders, the reason for which it is not currently indicated. Here we report a 7-year-old boy with 9p trisomy syndrome and marked short stature. Results of routine laboratory assessments were normal. IGF1 and IGFBP3 levels were both in the normal range (-1...
April 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/26400282/relationship-between-vitamin-d-receptor-vdr-polymorphisms-and-the-efficacy-of-recombinant-human-growth-hormone-rhgh-treatment-in-children-with-idiopathic-short-stature
#12
W Wang, X P Luo, L X Cai, Z R Cui, X Y Luo, R K Luo
Polymorphisms in the vitamin D receptor (VDR) gene are associated with idiopathic short stature (ISS) in several countries. This study aimed to identify a possible correlation between polymorphisms in the VDR promoter in Chinese children with ISS and the efficacy of the recombinant human growth hormone (rhGH) treatment. Pre-pubertal children with ISS and healthy age- and gender-matched children (N = 95 each) were enrolled in this study. Two single nucleotide polymorphisms (SNPs) in the VDR promoter (rs11568820 at the Cdx-2-binding site upstream of exon 1e and rs4516035 at -1012 upstream of exon 1a) were typed...
September 8, 2015: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/26323059/genetic-variance-estimation-with-imputed-variants-finds-negligible-missing-heritability-for-human-height-and-body-mass-index
#13
Jian Yang, Andrew Bakshi, Zhihong Zhu, Gibran Hemani, Anna A E Vinkhuyzen, Sang Hong Lee, Matthew R Robinson, John R B Perry, Ilja M Nolte, Jana V van Vliet-Ostaptchouk, Harold Snieder, Tonu Esko, Lili Milani, Reedik Mägi, Andres Metspalu, Anders Hamsten, Patrik K E Magnusson, Nancy L Pedersen, Erik Ingelsson, Nicole Soranzo, Matthew C Keller, Naomi R Wray, Michael E Goddard, Peter M Visscher
We propose a method (GREML-LDMS) to estimate heritability for human complex traits in unrelated individuals using whole-genome sequencing data. We demonstrate using simulations based on whole-genome sequencing data that ∼97% and ∼68% of variation at common and rare variants, respectively, can be captured by imputation. Using the GREML-LDMS method, we estimate from 44,126 unrelated individuals that all ∼17 million imputed variants explain 56% (standard error (s.e.) = 2.3%) of variance for height and 27% (s...
October 2015: Nature Genetics
https://www.readbyqxmd.com/read/26272623/genome-wide-association-study-of-body-weight-in-australian-merino-sheep-reveals-an-orthologous-region-on-oar6-to-human-and-bovine-genomic-regions-affecting-height-and-weight
#14
Hawlader A Al-Mamun, Paul Kwan, Samuel A Clark, Mohammad H Ferdosi, Ross Tellam, Cedric Gondro
BACKGROUND: Body weight (BW) is an important trait for meat production in sheep. Although over the past few years, numerous quantitative trait loci (QTL) have been detected for production traits in cattle, few QTL studies have been reported for sheep, with even fewer on meat production traits. Our objective was to perform a genome-wide association study (GWAS) with the medium-density Illumina Ovine SNP50 BeadChip to identify genomic regions and corresponding haplotypes associated with BW in Australian Merino sheep...
2015: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/26266778/-progress-in-genetic-research-of-human-height
#15
REVIEW
Kaixu Chen, Weilan Wang, Fuchun Zhang, Xiufen Zheng
It is well known that both environmental and genetic factors contribute to adult height variation in general population. However, heritability studies have shown that the variation in height is more affected by genetic factors. Height is a typical polygenic trait which has been studied by traditional linkage analysis and association analysis to identify common DNA sequence variation associated with height, but progress has been slow. More recently, with the development of genotyping and DNA sequencing technologies, tremendous achievements have been made in genetic research of human height...
August 2015: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/26125186/methodological-considerations-in-estimation-of-phenotype-heritability-using-genome-wide-snp-data-illustrated-by-an-analysis-of-the-heritability-of-height-in-a-large-sample-of-african-ancestry-adults
#16
Fang Chen, Jing He, Jianqi Zhang, Gary K Chen, Venetta Thomas, Christine B Ambrosone, Elisa V Bandera, Sonja I Berndt, Leslie Bernstein, William J Blot, Qiuyin Cai, John Carpten, Graham Casey, Stephen J Chanock, Iona Cheng, Lisa Chu, Sandra L Deming, W Ryan Driver, Phyllis Goodman, Richard B Hayes, Anselm J M Hennis, Ann W Hsing, Jennifer J Hu, Sue A Ingles, Esther M John, Rick A Kittles, Suzanne Kolb, M Cristina Leske, Robert C Millikan, Kristine R Monroe, Adam Murphy, Barbara Nemesure, Christine Neslund-Dudas, Sarah Nyante, Elaine A Ostrander, Michael F Press, Jorge L Rodriguez-Gil, Ben A Rybicki, Fredrick Schumacher, Janet L Stanford, Lisa B Signorello, Sara S Strom, Victoria Stevens, David Van Den Berg, Zhaoming Wang, John S Witte, Suh-Yuh Wu, Yuko Yamamura, Wei Zheng, Regina G Ziegler, Alexander H Stram, Laurence N Kolonel, Loïc Le Marchand, Brian E Henderson, Christopher A Haiman, Daniel O Stram
Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44...
2015: PloS One
https://www.readbyqxmd.com/read/26017218/spag17-deficiency-results-in-skeletal-malformations-and-bone-abnormalities
#17
Maria Eugenia Teves, Gobalakrishnan Sundaresan, David J Cohen, Sharon L Hyzy, Illya Kajan, Melissa Maczis, Zhibing Zhang, Richard M Costanzo, Jamal Zweit, Zvi Schwartz, Barbara D Boyan, Jerome F Strauss
Height is the result of many growth and development processes. Most of the genes associated with height are known to play a role in skeletal development. Single-nucleotide polymorphisms in the SPAG17 gene have been associated with human height. However, it is not clear how this gene influences linear growth. Here we show that a targeted mutation in Spag17 leads to skeletal malformations. Hind limb length in mutants was significantly shorter than in wild-type mice. Studies revealed differences in maturation of femur and tibia suggesting alterations in limb patterning...
2015: PloS One
https://www.readbyqxmd.com/read/25799442/sensitive-detection-of-chromatin-altering-polymorphisms-reveals-autoimmune-disease-mechanisms
#18
Ricardo Cruz-Herrera del Rosario, Jeremie Poschmann, Sigrid Laure Rouam, Eileen Png, Chiea Chuen Khor, Martin Lloyd Hibberd, Shyam Prabhakar
Most disease associations detected by genome-wide association studies (GWAS) lie outside coding genes, but very few have been mapped to causal regulatory variants. Here, we present a method for detecting regulatory quantitative trait loci (QTLs) that does not require genotyping or whole-genome sequencing. The method combines deep, long-read chromatin immunoprecipitation-sequencing (ChIP-seq) with a statistical test that simultaneously scores peak height correlation and allelic imbalance: the genotype-independent signal correlation and imbalance (G-SCI) test...
May 2015: Nature Methods
https://www.readbyqxmd.com/read/25765547/a-systems-genetics-study-of-swine-illustrates-mechanisms-underlying-human-phenotypic-traits
#19
Jun Zhu, Congying Chen, Bin Yang, Yuanmei Guo, Huashui Ai, Jun Ren, Zhiyu Peng, Zhidong Tu, Xia Yang, Qingying Meng, Stephen Friend, Lusheng Huang
BACKGROUND: The pig, which shares greater similarities with human than with mouse, is important for agriculture and for studying human diseases. However, similarities in the genetic architecture and molecular regulations underlying phenotypic variations in humans and swine have not been systematically assessed. RESULTS: We systematically surveyed ~500 F2 pigs genetically and phenotypically. By comparing candidates for anemia traits identified in swine genome-wide SNP association and human genome-wide association studies (GWAS), we showed that both sets of candidates are related to the biological process "cellular lipid metabolism" in liver...
2015: BMC Genomics
https://www.readbyqxmd.com/read/25712083/intelligence-shared-genetic-basis-between-mendelian-disorders-and-a-polygenic-trait
#20
Sanja Franić, Maria M Groen-Blokhuis, Conor V Dolan, Mathijs V Kattenberg, René Pool, Xiangjun Xiao, Paul A Scheet, Erik A Ehli, Gareth E Davies, Sophie van der Sluis, Abdel Abdellaoui, Narelle K Hansell, Nicholas G Martin, James J Hudziak, Catherina E M van Beijsterveldt, Suzanne C Swagerman, Hilleke E Hulshoff Pol, Eco J C de Geus, Meike Bartels, H Hilger Ropers, Jouke-Jan Hottenga, Dorret I Boomsma
Multiple inquiries into the genetic etiology of human traits indicated an overlap between genes underlying monogenic disorders (eg, skeletal growth defects) and those affecting continuous variability of related quantitative traits (eg, height). Extending the idea of a shared genetic basis between a Mendelian disorder and a classic polygenic trait, we performed an association study to examine the effect of 43 genes implicated in autosomal recessive cognitive disorders on intelligence in an unselected Dutch population (N=1316)...
October 2015: European Journal of Human Genetics: EJHG
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