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Genome wide association studies

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https://www.readbyqxmd.com/read/28226236/new-strategies-and-tools-in-quantitative-genetics-how-to-go-from-the-phenotype-to-the-genotype
#1
C Bazakos, M Hanemian, C Trontin, J M Jiménez-Gómez, O Loudet
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28224759/genomic-variants-at-20p11-associated-with-body-fat-mass-in-the-european-population
#2
Yu-Fang Pei, Hai-Gang Ren, Lu Liu, Xiao Li, Chen Fang, Yun Huang, Wen-Zhu Hu, Wei-Wen Kong, An-Ping Feng, Xin-Yi You, Wen Zhao, Hui Shen, Qing Tian, Yong-Hong Zhang, Hong-Wen Deng, Lei Zhang
OBJECTIVE: Body fat mass (BFM) is more homogeneous and accurate than body total mass in measuring obesity but has rarely been studied. Aiming to uncover the genetic basis of fat-induced obesity, a genome-wide association meta-analysis of BFM, after adjustment by body lean mass, was performed in the European population. METHODS: Three samples of European ancestry were included in the meta-analysis: the Framingham Heart Study (N = 6,004), the Kansas City osteoporosis study (N = 2,207), and the Omaha osteoporosis study (N = 968)...
February 22, 2017: Obesity
https://www.readbyqxmd.com/read/28224622/slc2a3-single-nucleotide-polymorphism-and-duplication-influence-cognitive-processing-and-population-specific-risk-for-attention-deficit-hyperactivity-disorder
#3
Sören Merker, Andreas Reif, Georg C Ziegler, Heike Weber, Ute Mayer, Ann-Christine Ehlis, Annette Conzelmann, Stefan Johansson, Clemens Müller-Reible, Indrajit Nanda, Thomas Haaf, Reinhard Ullmann, Marcel Romanos, Andreas J Fallgatter, Paul Pauli, Tatyana Strekalova, Charline Jansch, Alejandro Arias Vasquez, Jan Haavik, Marta Ribasés, Josep Antoni Ramos-Quiroga, Jan K Buitelaar, Barbara Franke, Klaus-Peter Lesch
BACKGROUND: Attention-deficit/hyperactivity disorder (ADHD) is a common, highly heritable neurodevelopmental disorder with profound cognitive, behavioral, and psychosocial impairments with persistence across the life cycle. Our initial genome-wide screening approach for copy number variants (CNVs) in ADHD implicated a duplication of SLC2A3, encoding glucose transporter-3 (GLUT3). GLUT3 plays a critical role in cerebral glucose metabolism, providing energy for the activity of neurons, which, in turn, moderates the excitatory-inhibitory balance impacting both brain development and activity-dependent neural plasticity...
February 22, 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
https://www.readbyqxmd.com/read/28224383/oncologist-and-organizational-factors-associated-with-variation-in-breast-cancer-multigene-testing
#4
Tracy A Lieu, G Thomas Ray, Stephanie R Prausnitz, Laurel A Habel, Stacey Alexeeff, Yan Li, Scott D Ramsey, Charles E Phelps, Neetu Chawla, Suzanne C O'Neill, Jeanne S Mandelblatt
PURPOSE: Multigene testing for breast cancer recurrence risk became available in 2007, yet many eligible patients remain untested. This study evaluated variation in testing rates, and oncologist and organizational factors associated with variation, in a setting without financial influences on testing. METHODS: We conducted a retrospective cohort study using electronic data and oncologist surveys within Kaiser Permanente Northern California, a large integrated health care system...
February 21, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28224003/darwinism-for-the-genomic-age-connecting-mutation-to-diversification
#5
Xia Hua, Lindell Bromham
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28223988/the-impact-of-genotyping-by-sequencing-pipelines-on-snp-discovery-and-identification-of-markers-associated-with-verticillium-wilt-resistance-in-autotetraploid-alfalfa-medicago-sativa-l
#6
Long-Xi Yu, Ping Zheng, Suresh Bhamidimarri, Xiang-Ping Liu, Dorie Main
Verticillium wilt (VW) of alfalfa is a soilborne disease causing severe yield loss in alfalfa. To identify molecular markers associated with VW resistance, we used an integrated framework of genome-wide association study (GWAS) with high-throughput genotyping by sequencing (GBS) to identify loci associated with VW resistance in an F1 full-sib alfalfa population. Phenotyping was performed using manual inoculation of the pathogen to cloned plants of each individual and disease severity was scored using a standard scale...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223827/common-variations-within-hace1-gene-and-neuroblastoma-susceptibility-in-a-southern-chinese-population
#7
Zhuorong Zhang, Ruizhong Zhang, Jinhong Zhu, Fenghua Wang, Tianyou Yang, Yan Zou, Jing He, Huimin Xia
Neuroblastoma is a common fatal pediatric cancer of the developing sympathetic nervous system, which accounts for ~10% of all pediatric cancer deaths. To investigate genetic risk factors related to neuroblastoma, many genome-wide association studies have been performed, and single nucleotide polymorphisms (SNPs) within HACE1 gene have been identified to associate with neuroblastoma risk. However, the association of the HACE1 SNPs with neuroblastoma needs to be validated in Southern Chinese children. We genotyped five SNPs located in the HACE1 gene (rs4336470 C>T, rs9404576 T>G, rs4079063 A>G, rs2499663 T>C, and rs2499667 A>G) in 256 Southern Chinese patients in comparison with 531 ethnically matched healthy controls...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28223688/sequence-variant-at-8q24-21-associates-with-sciatica-caused-by-lumbar-disc-herniation
#8
Gyda Bjornsdottir, Stefania Benonisdottir, Gardar Sveinbjornsson, Unnur Styrkarsdottir, Gudmar Thorleifsson, G Bragi Walters, Aron Bjornsson, Ingvar H Olafsson, Elfar Ulfarsson, Arnor Vikingsson, Ragnheidur Hansdottir, Karl O Karlsson, Thorunn Rafnar, Ingileif Jonsdottir, Michael L Frigge, Augustine Kong, Asmundur Oddsson, Gisli Masson, Olafur T Magnusson, Tomas Gudbjartsson, Hreinn Stefansson, Patrick Sulem, Daniel Gudbjartsson, Unnur Thorsteinsdottir, Thorgeir E Thorgeirsson, Kari Stefansson
Lumbar disc herniation (LDH) is common and often debilitating. Microdiscectomy of herniated lumbar discs (LDHsurg) is performed on the most severe cases to resolve the resulting sciatica. Here we perform a genome-wide association study on 4,748 LDHsurg cases and 282,590 population controls and discover 37 highly correlated markers associating with LDHsurg at 8q24.21 (between CCDC26 and GSDMC), represented by rs6651255[C] (OR=0.81; P=5.6 × 10(-12)) with a stronger effect among younger patients than older. As rs6651255[C] also associates with height, we performed a Mendelian randomization analysis using height polygenic risk scores as instruments to estimate the effect of height on LDHsurg risk, and found that the marker's association with LDHsurg is much greater than predicted by its effect on height...
February 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28222718/abnormal-epigenetic-changes-during-differentiation-of-human-skeletal-muscle-stem-cells-from-obese-subjects
#9
Cajsa Davegårdh, Christa Broholm, Alexander Perfilyev, Tora Henriksen, Sonia García-Calzón, Lone Peijs, Ninna Schiøler Hansen, Petr Volkov, Rasmus Kjøbsted, Jørgen F P Wojtaszewski, Maria Pedersen, Bente Klarlund Pedersen, Dov B Ballak, Charles A Dinarello, Bas Heinhuis, Leo A B Joosten, Emma Nilsson, Allan Vaag, Camilla Scheele, Charlotte Ling
BACKGROUND: Human skeletal muscle stem cells are important for muscle regeneration. However, the combined genome-wide DNA methylation and expression changes taking place during adult myogenesis have not been described in detail and novel myogenic factors may be discovered. Additionally, obesity is associated with low relative muscle mass and diminished metabolism. Epigenetic alterations taking place during myogenesis might contribute to these defects. METHODS: We used Infinium HumanMethylation450 BeadChip Kit (Illumina) and HumanHT-12 Expression BeadChip (Illumina) to analyze genome-wide DNA methylation and transcription before versus after differentiation of primary human myoblasts from 14 non-obese and 14 obese individuals...
February 22, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28222494/selecting-cases-and-controls-for-dna-sequencing-studies-using-family-histories-of-disease
#10
Wonji Kim, Dandi Qiao, Michael H Cho, Soo Heon Kwak, Kyong Soo Park, Edwin K Silverman, Pak Sham, Sungho Won
Recent improvements in sequencing technology have enabled the investigation of so-called missing heritability, and a large number of affected subjects have been sequenced in order to detect significant associations between human diseases and rare variants. However, the cost of genome sequencing is still high, and a statistically powerful strategy for selecting informative subjects would be useful. Therefore, in this report, we propose a new statistical method for selecting cases and controls for sequencing studies based on family history...
February 21, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28222251/prognostic-methylation-markers-for-overall-survival-in-cytogenetically-normal-patients-with-acute-myeloid-leukemia-treated-on-swog-trials
#11
Xiaoyu Qu, Megan Othus, Jerry Davison, Yu Wu, Liying Yan, Soheil Meshinchi, Fabiana Ostronoff, Elihu H Estey, Jerry P Radich, Harry P Erba, Frederick R Appelbaum, Min Fang
BACKGROUND: Aberrant DNA methylation is known to occur in patients with acute myeloid leukemia (AML), whereas methylation signatures and prognostic markers have been proposed. The objective of the current study was to evaluate all CpG sites of the genome and identify prognostic methylation markers for overall survival in patients with AML with normal karyotype (AML-NK). METHODS: AML-NK samples from 7 SWOG trials were analyzed using a novel genome-wide approach called "CHARMcox" (comprehensive high-throughput array-based relative methylation analysis combined with the Cox proportional hazards model) controlling for known clinical covariates...
February 21, 2017: Cancer
https://www.readbyqxmd.com/read/28222112/genome-wide-study-of-resistant-hypertension-identified-from-electronic-health-records
#12
Logan Dumitrescu, Marylyn D Ritchie, Joshua C Denny, Nihal M El Rouby, Caitrin W McDonough, Yuki Bradford, Andrea H Ramirez, Suzette J Bielinski, Melissa A Basford, High Seng Chai, Peggy Peissig, David Carrell, Jyotishman Pathak, Luke V Rasmussen, Xiaoming Wang, Jennifer A Pacheco, Abel N Kho, M Geoffrey Hayes, Martha Matsumoto, Maureen E Smith, Rongling Li, Rhonda M Cooper-DeHoff, Iftikhar J Kullo, Christopher G Chute, Rex L Chisholm, Gail P Jarvik, Eric B Larson, David Carey, Catherine A McCarty, Marc S Williams, Dan M Roden, Erwin Bottinger, Julie A Johnson, Mariza de Andrade, Dana C Crawford
Resistant hypertension is defined as high blood pressure that remains above treatment goals in spite of the concurrent use of three antihypertensive agents from different classes. Despite the important health consequences of resistant hypertension, few studies of resistant hypertension have been conducted. To perform a genome-wide association study for resistant hypertension, we defined and identified cases of resistant hypertension and hypertensives with treated, controlled hypertension among >47,500 adults residing in the US linked to electronic health records (EHRs) and genotyped as part of the electronic MEdical Records & GEnomics (eMERGE) Network...
2017: PloS One
https://www.readbyqxmd.com/read/28222097/a-genome-wide-association-study-identifies-a-lncrna-as-risk-factor-for-pathological-inflammatory-responses-in-leprosy
#13
Vinicius M Fava, Jeremy Manry, Aurélie Cobat, Marianna Orlova, Nguyen Van Thuc, Milton O Moraes, Carolinne Sales-Marques, Mariane M A Stefani, Ana Carla P Latini, Andrea F Belone, Vu Hong Thai, Laurent Abel, Alexandre Alcaïs, Erwin Schurr
Leprosy Type-1 Reactions (T1Rs) are pathological inflammatory responses that afflict a sub-group of leprosy patients and result in peripheral nerve damage. Here, we employed a family-based GWAS in 221 families with 229 T1R-affect offspring with stepwise replication to identify risk factors for T1R. We discovered, replicated and validated T1R-specific associations with SNPs located in chromosome region 10p21.2. Combined analysis across the three independent samples resulted in strong evidence of association of rs1875147 with T1R (p = 4...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28221366/pathway-wide-association-study-identifies-five-shared-pathways-associated-with-schizophrenia-in-three-ancestral-distinct-populations
#14
C Liu, C A Bousman, C Pantelis, E Skafidas, D Zhang, W Yue, I P Everall
Genome-wide association studies have confirmed the polygenic nature of schizophrenia and suggest that there are hundreds or thousands of alleles associated with increased liability for the disorder. However, the generalizability of any one allelic marker of liability is remarkably low and has bred the notion that schizophrenia may be better conceptualized as a pathway(s) disorder. Here, we empirically tested this notion by conducting a pathway-wide association study (PWAS) encompassing 255 experimentally validated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways among 5033 individuals diagnosed with schizophrenia and 5332 unrelated healthy controls across three distinct ethnic populations; European-American (EA), African-American (AA) and Han Chinese (CH)...
February 21, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28221285/genome-wide-methylation-analysis-of-a-large-population-sample-shows-neurological-pathways-involvement-in-chronic-widespread-musculoskeletal-pain-cwp
#15
Gregory Livshits, Ida Malkin, Maxim B Freidin, Yudong Xia, Fei Gao, Jun Wang, Timothy D Spector, Alex MacGregor, Jordana T Bell, Frances Mk Williams
Chronic widespread musculoskeletal pain (CWP), has a considerable heritable component, which remains to be explained. Epigenetic factors may contribute to and account for some of the heritability estimate. We analysed epigenome-wide methylation using MeDIPseq in whole blood DNA from 1708 monozygotic (MZ) and dizygotic (DZ) Caucasian twins having CWP prevalence of 19.9%. Longitudinally stable methylation bins (lsBINs), were established by testing repeated measurements conducted ≥3 years apart, n=292. DNA methylation variation at lsBINs was tested for association with CWP in a discovery set of 50 MZ twin pairs discordant for CWP, and in an independent dataset (n=1608 twins), and the results from the two samples were combined using Fisher's method...
February 15, 2017: Pain
https://www.readbyqxmd.com/read/28220687/environmental-factors-seven-gwas-identified-susceptibility-loci-and-risk-of-gastric-cancer-and-its-precursors-in-a-chinese-population
#16
Meng Cai, Shuyang Dai, Wanqing Chen, Changfa Xia, Lingeng Lu, Shuguang Dai, Jun Qi, Minjie Wang, Meilin Wang, Lanping Zhou, Fuhua Lei, Tingting Zuo, Hongmei Zeng, Xiaohang Zhao
Gene-environment interactions may increase gastric cancer (GC) risk. Seven susceptibility loci identified by genome-wide association studies (GWASs) suggest that genetic factors play a role in gastric carcinogenesis. Meanwhile, Helicobacter pylori (H. pylori) infection, smoking, and alcohol drinking are also important environmental factors for gastric cancer. However, studies to explore the role of gene-environment interactions in gastric carcinogenesis, and particularly the relationship between the seven susceptibility loci and their potential interactions with H...
February 21, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28220139/genome-wide-single-nucleotide-polymorphism-discovery-and-the-construction-of-a-high-density-genetic-map-for-melon-cucumis-melo-l-using-genotyping-by-sequencing
#17
Che-Wei Chang, Yu-Hua Wang, Chih-Wei Tung
Although genotyping-by-sequencing (GBS) enables the efficient and low-cost generation of large numbers of markers, the utility of resultant genotypes are limited, because they are enormously error-prone and contain high proportions of missing data. In this study, we generated single nucleotide polymorphism (SNP) markers for 109 recombinant inbred lines of melon (Cucumis melo L.) using the GBS approach and ordered them according to their physical position on the draft double haploid line DHL92 genome. Next, by investigating associations between these SNPs, we discovered that some segments on the physical map conflict with linkage relationships...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28219716/genetic-regulation-of-differentially-methylated-genes-in-visceral-adipose-tissue-of-severely-obese-men-discordant-for-the-metabolic-syndrome
#18
Frédéric Guénard, André Tchernof, Yves Deshaies, Simon Biron, Odette Lescelleur, Laurent Biertho, Simon Marceau, Louis Pérusse, Marie-Claude Vohl
A genetic influence on methylation levels has been reported and methylation quantitative trait loci (meQTL) have been identified in various tissues. The contribution of genetic and epigenetic factors in the development of the metabolic syndrome (MetS) has also been noted. To pinpoint candidate genes for testing the association of SNPs with MetS and its components, we aimed to evaluate the contribution of genetic variations to differentially methylated CpG sites in severely obese men discordant for MetS. A genome-wide differential methylation analysis was conducted in visceral adipose tissue (VAT) of 31 severely obese men discordant for MetS (16 with and 15 without MetS) and identified ∼17,800 variable CpG sites...
February 2, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28219476/genetic-parameters-and-genome-wide-associations-of-twinning-rate-in-a-local-breed-the-maremmana-cattle
#19
B Moioli, R Steri, C Marchitelli, G Catillo, L Buttazzoni
This study seeks to verify the feasibility of increasing twinning in a herd of the Italian autochtonous Maremmana breed. The data set included 1260 individuals born from 1963 to 2014, 527 males and 733 females, 402 of them calving at least once from 1983 through 2015. Breeding values for twinning were estimated by a single-trait linear animal model. However, since twinning is a dichotomous trait and the frequency of twins is far smaller than the frequency of single births, breeding values were also estimated by a single-trait animal threshold model...
February 21, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28219342/effects-of-exposure-to-streptococcus-iniae-on-microrna-expression-in-the-head-kidney-of-genetically-improved-farmed-tilapia-oreochromis-niloticus
#20
Jun Qiang, Fanyi Tao, Jie He, Lanyi Sun, Pao Xu, Wenjin Bao
BACKGROUND: Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes that are cultured widely in southern China. The role of microRNAs (miRNAs) in the regulatory response of GIFT to S. iniae infection has been underestimated and has not yet been well studied. Head kidney has an important immune function in teleost fishes. The main aim of this study was to determine the possible function of miRNAs in head kidney of S...
February 20, 2017: BMC Genomics
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