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Snp human height

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...
June 24, 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
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
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
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
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
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
Swetlana Berger, Paulino Pérez-Rodríguez, Yogasudha Veturi, Henner Simianer, Gustavo de los Campos
Genome-wide association studies (GWAS) have detected large numbers of variants associated with complex human traits and diseases. However, the proportion of variance explained by GWAS-significant single nucleotide polymorphisms has been usually small. This brought interest in the use of whole-genome regression (WGR) methods. However, there has been limited research on the factors that affect prediction accuracy (PA) of WGRs when applied to human data of distantly related individuals. Here, we examine, using real human genotypes and simulated phenotypes, how trait complexity, marker-quantitative trait loci (QTL) linkage disequilibrium (LD), and the model used affect the performance of WGRs...
March 2015: Annals of Human Genetics
Joseph D Buxbaum, Nadia Bolshakova, Jessica M Brownfeld, Richard Jl Anney, Patrick Bender, Raphael Bernier, Edwin H Cook, Hilary Coon, Michael Cuccaro, Christine M Freitag, Joachim Hallmayer, Daniel Geschwind, Sabine M Klauck, John I Nurnberger, Guiomar Oliveira, Dalila Pinto, Fritz Poustka, Stephen W Scherer, Andy Shih, James S Sutcliffe, Peter Szatmari, Astrid M Vicente, Veronica Vieland, Louise Gallagher
BACKGROUND: There is an urgent need for expanding and enhancing autism spectrum disorder (ASD) samples, in order to better understand causes of ASD. METHODS: In a unique public-private partnership, 13 sites with extensive experience in both the assessment and diagnosis of ASD embarked on an ambitious, 2-year program to collect samples for genetic and phenotypic research and begin analyses on these samples. The program was called The Autism Simplex Collection (TASC)...
2014: Molecular Autism
Pieter Stijnen, Krizia Tuand, Tibor V Varga, Paul W Franks, Bert Aertgeerts, John W M Creemers
Congenital deficiency of the proprotein convertase subtilisine/kexin type 1 gene (PCSK1), which encodes proprotein convertase 1/3, causes a severe multihormonal disorder marked by early-onset obesity. The single nucleotide polymorphisms (SNPs) rs6232 and rs6234-rs6235 in PCSK1 have been associated with obesity. However, case-control studies carried out in populations of different ethnicities have only partly replicated this association. Moreover, these SNPs have only weakly been associated with body mass index (weight (kg)/height (m)(2)) at a genome-wide level of significance...
December 1, 2014: American Journal of Epidemiology
R Toro, J-B Poline, G Huguet, E Loth, V Frouin, T Banaschewski, G J Barker, A Bokde, C Büchel, F M Carvalho, P Conrod, M Fauth-Bühler, H Flor, J Gallinat, H Garavan, P Gowland, A Heinz, B Ittermann, C Lawrence, H Lemaître, K Mann, F Nees, T Paus, Z Pausova, M Rietschel, T Robbins, M N Smolka, A Ströhle, G Schumann, T Bourgeron
Human brain anatomy is strikingly diverse and highly inheritable: genetic factors may explain up to 80% of its variability. Prior studies have tried to detect genetic variants with a large effect on neuroanatomical diversity, but those currently identified account for <5% of the variance. Here, based on our analyses of neuroimaging and whole-genome genotyping data from 1765 subjects, we show that up to 54% of this heritability is captured by large numbers of single-nucleotide polymorphisms of small-effect spread throughout the genome, especially within genes and close regulatory regions...
August 2015: Molecular Psychiatry
Kehua Wu, Eric R Gamazon, Hae Kyung Im, Paul Geeleher, Steven R White, Julian Solway, George L Clemmer, Scott T Weiss, Kelan G Tantisira, Nancy J Cox, Mark J Ratain, R Stephanie Huang
RATIONALE: Most genomic studies of lung function have used phenotypic data derived from a single time-point (e.g., presence/absence of disease) without considering the dynamic progression of a chronic disease. OBJECTIVES: To characterize lung function change over time in subjects with asthma and identify genetic contributors to a longitudinal phenotype. METHODS: We present a method that models longitudinal FEV1 data, collected from 1,041 children with asthma who participated in the Childhood Asthma Management Program...
September 15, 2014: American Journal of Respiratory and Critical Care Medicine
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