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Snp human height

Kesheng Wang, Xue Chen, Stephen C Ward, Ying Liu, Youssoufou Ouedraogo, Chun Xu, Arthur I Cederbaum, Yongke Lu
BACKGROUND/OBJECTIVES: CYP2A6 (CYP2A5 in mice) is mainly expressed in the liver. Hepatic CYP2A6 expression is increased in patients with non-alcoholic fatty liver disease (NAFLD). In mice, hepatic CYP2A5 is induced by high fat diet (HFD) feeding. Hepatic CYP2A5 is also increased in monosodium glutamate-induced obese mice. NAFLD is associated with obesity. In this study, we examined whether obesity is related to CYP2A6. SUBJECTS/METHODS: Obesity genetic association study: The SAGE is a comprehensive genome-wide association study (GWAS) with case subjects having a lifetime history of alcohol dependence and control subjects never addicted to alcohol...
February 20, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
Alexandra Shadrina, Yakov Tsepilov, Ekaterina Sokolova, Mariya Smetanina, Elena Voronina, Eugene Pakhomov, Kseniya Sevost'ianova, Andrey Shevela, Evgeny Ilyukhin, Evgeny Seliverstov, Igor Zolotukhin, Maxim Filipenko
Heredity is a well-known risk factor for varicose veins, but genetic basis of this condition remains poorly studied. Our aim was to conduct a large-scale genetic association study for primary varicose veins (PVVs) in the population of ethnic Russians. An initial scan using Illumina HumanExome-12 v1.0 BeadChip was performed for 273 patients with PVVs and 250 controls without a history of chronic venous disease and other venous disorders. After quality control and removal of monomorphic markers, 25,424 common and 48,232 rare variants were included in the analysis...
June 15, 2018: Gene
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)...
March 2018: Biochimica et Biophysica Acta
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...
December 7, 2017: American Journal of Human Genetics
Andrey Shirak, Uri Seroussi, Elisha Gootwine, Eyal Seroussi
Calculating peak-height ratios between single-nucleotide polymorphisms (SNP) alleles in sequencing chromatograms is a practical method for estimating their copy number proportions (CNPs). However, it is surprising that sequencing DNA from different directions might yield different results. We analyzed three adjacent SNPs within the ovine period circadian-clock 2 (PER2) gene that displayed such behavior. We compared Sanger and DNA-seq sequencing for this locus and applied high-resolution melt and MFOLD analyses to point to the DNA secondary structure that underlined this phenomenon...
July 2017: FEBS Open Bio
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
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
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
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
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
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
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
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...
November 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
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
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
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
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
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
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
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
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