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Quantitative trait loci

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https://www.readbyqxmd.com/read/28335076/fine-mapping-of-chromosome-5p15-33-identifies-novel-lung-cancer-susceptibility-loci-in-han-chinese
#1
Jing Dong, Yang Cheng, Meng Zhu, Yang Wen, Cheng Wang, Yuzhuo Wang, Liguo Geng, Wei Shen, Jia Liu, Zhihua Li, Jiahui Zhang, Hongxia Ma, Juncheng Dai, Guangfu Jin, Zhibin Hu, Hongbing Shen
Genome-wide association studies in European and Asian populations have consistently identified chromosome 5p15.33 as a lung cancer susceptibility region. To investigate further the genetic architecture of common variants in this region, we conducted a two-stage fine-mapping analysis discovered by targeted resequencing of 200 cases and 300 controls individually, and validated in multiethnic lung cancer GWASs with 12,843 cases and 12,639 controls. Two independent variants were identified in approximate conditional analysis with GCTA and consistently validated in lung cancer GWASs in both Asian and European populations...
March 23, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28334830/predicting-the-impact-of-non-coding-variants-on-dna-methylation
#2
Haoyang Zeng, David K Gifford
DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variation. We introduce CpGenie, a sequence-based framework that learns a regulatory code of DNA methylation using a deep convolutional neural network and uses this network to predict the impact of sequence variation on proximal CpG site DNA methylation...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334234/breast-cancer-risk-associated-variants-at-6q25-1-influence-risk-of-hepatocellular-carcinoma-in-a-chinese-population
#3
Jiaoyuan Li, Ying Wang, Ying Zhu, Yajie Gong, Yang Yang, Jianbo Tian, Yi Zhang, Danyi Zou, Xiating Peng, Juntao Ke, Jing Gong, Rong Zhong, Jiang Chang
The gender disparity observed in the incidence of hepatocellular carcinoma (HCC) suggests an important role of estrogens in HCC pathogenesis. In this study, we conducted a case-control study to investigate whether breast cancer risk-associated single nucleotide polymorphisms (SNPs) located at estrogens loci identified by genome-wide association studies (GWASs) also predispose to HCC in a Chinese population. Three candidate SNPs at 6q25.1 were genotyped in 2,025 HCC cases and 2,032 healthy controls. Differential expression analyses and expression quantitative trait loci (eQTL) analyses were conducted to further explore the role of significant SNPs and genes they reside in...
March 3, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28334222/qrank-a-novel-quantile-regression-tool-for-eqtl-discovery
#4
Xiaoyu Song, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza, Ying Wei
Motivation: Over the past decade, there has been a remarkable improvement in our understanding of the role of genetic variation in complex human diseases, especially via genome-wide association studies. However, the underlying molecular mechanisms are still poorly characterized, impending the development of therapeutic interventions. Identifying genetic variants that influence the expression level of a gene, i.e. expression quantitative trait loci (eQTLs), can help us understand how genetic variants influence traits at the molecular level...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28330615/differential-aging-analysis-in-human-cerebral-cortex-identifies-variants-in-tmem106b-and-grn-that-regulate-aging-phenotypes
#5
Herve Rhinn, Asa Abeliovich
Human age-associated traits, such as cognitive decline, can be highly variable across the population, with some individuals exhibiting traits that are not expected at a given chronological age. Here we present differential aging (Δ-aging), an unbiased method that quantifies individual variability in age-associated phenotypes within a tissue of interest, and apply this approach to the analysis of existing transcriptome-wide cerebral cortex gene expression data from several cohorts totaling 1,904 autopsied human brain samples...
March 15, 2017: Cell Systems
https://www.readbyqxmd.com/read/28327519/identification-of-quantitative-trait-loci-conditioning-the-main-biomass-yield-components-and-resistance-to-melampsora-spp-in-salix-viminalis-%C3%A3-salix-schwerinii-hybrids
#6
Paweł Sulima, Jerzy A Przyborowski, Anna Kuszewska, Dariusz Załuski, Małgorzata Jędryczka, Witold Irzykowski
The biomass of Salix viminalis is the most highly valued source of green energy, followed by S. schwerinii, S. dasyclados and other species. Significant variability in productivity and leaf rust resistance are noted both within and among willow species, which creates new opportunities for improving willow yield parameters through selection of desirable recombinants supported with molecular markers. The aim of this study was to identify quantitative trait loci (QTLs) linked with biomass yield-related traits and the resistance/susceptibility of Salix mapping population to leaf rust...
March 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28325924/genome-wide-association-analysis-identifies-loci-governing-mercury-accumulation-in-maize
#7
Zhan Zhao, Zhongjun Fu, Yanan Lin, Hao Chen, Kun Liu, Xiaolong Xing, Zonghua Liu, Weihua Li, Jihua Tang
Owing to the rapid development of urbanisation and industrialisation, heavy metal pollution has become a widespread environmental problem. Maize planted on mercury (Hg)-polluted soil can absorb and accumulate Hg in its edible parts, posing a potential threat to human health. To understand the genetic mechanism of Hg accumulation in maize, we performed a genome-wide association study using a mixed linear model on an association population consisting of 230 maize inbred lines with abundant genetic variation. The order of relative Hg concentrations in different maize tissues was as follows: leaves > bracts > stems > axes > kernels...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28321907/systematical-analyses-of-variants-in%C3%A2-dnase-i-hypersensitive-sites-identified-two-novel-hepatocellular-carcinoma-susceptibility-loci-among-chinese-population
#8
Tao Jiang, Fangzhi Du, Na Qin, Qun Lu, Juncheng Dai, Hongbing Shen, Zhibin Hu
BACKGROUND AND AIM: Although several variants located at coding and non-coding regions were evaluated by previous studies, the evidence for associations between variants located in DNase I-hypersensitive sites (DHSs) and hepatocellular carcinoma (HCC) risk was still limited. Recent advances using ENCODE data indicated that genetic variants in DHSs played an important role in carcinogenesis. Therefore, systematically investigate the associations between regulatory variants in DHSs and HCC risk should be put on the agenda...
March 20, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28320757/additional-candidate-genes-for-human-atherosclerotic-disease-identified-through-annotation-based-on-chromatin-organization
#9
Saskia Haitjema, Claartje A Meddens, Sander W van der Laan, Daniel Kofink, Magdalena Harakalova, Vinicius Tragante, Hassan Foroughi Asl, Jessica van Setten, Maarten M Brandt, Joshua C Bis, Christopher O'Donnell, Caroline Cheng, Imo E Hoefer, Johannes Waltenberger, Erik Biessen, J Wouter Jukema, Pieter A F M Doevendans, Edward E S Nieuwenhuis, Jeanette Erdmann, Johan L M Björkegren, Gerard Pasterkamp, Folkert W Asselbergs, Hester M den Ruijter, Michal Mokry
BACKGROUND: As genome-wide association efforts, such as CARDIoGRAM and METASTROKE, are ongoing to reveal susceptibility loci for their underlying disease-atherosclerotic disease-identification of candidate genes explaining the associations of these loci has proven the main challenge. Many disease susceptibility loci colocalize with DNA regulatory elements, which influence gene expression through chromatin interactions. Therefore, the target genes of these regulatory elements can be considered candidate genes...
April 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28317323/a-functional-snp-regulated-by-mir-196a-3p-in-the-3-utr-of-fgf2-is-associated-with-bone-mineral-density-in-the-chinese-population
#10
Dong-Li Zhu, Yan Guo, Yan Zhang, Shan-Shan Dong, Wen Xu, Ruo-Han Hao, Xiao-Feng Chen, Han Yan, Shui-Yun Yang, Tie-Lin Yang
Previous studies have identified FGF2 as a susceptibility gene for osteoporosis in Caucasians. Evaluating the genetic associations in different ethnicities is necessary. Moreover, elucidating the functional mechanism for the susceptibility loci is important to offer new targets for therapeutic studies. Here, we genotyped ten SNPs in FGF2 and tested for associations with bone mineral density (BMD) in a discovery sample of 1300 Chinese subjects. Nominally significant results were subjected to replication in another sample of 1039 Chinese subjects...
March 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28315831/evaluating-methods-of-updating-training-data-in-long-term-genomewide-selection
#11
Jeffrey L Neyhart, Tyler Tiede, Aaron J Lorenz, Kevin P Smith
Genomewide selection is hailed for its ability to facilitate greater genetic gains per unit time. Over breeding cycles, the requisite linkage disequilibrium (LD) between quantitative trait loci (QTL) and markers is expected to change as a result of recombination, selection, and drift, leading to a decay in prediction accuracy. Previous research has identified the need to update the training population using data that may capture new LD generated over breeding cycles, however optimal methods of updating have not been explored...
March 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28302177/cepip-context-dependent-epigenomic-weighting-for-prioritization-of-regulatory-variants-and-disease-associated-genes
#12
Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S Liu, Junwen Wang
It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitative trait loci (eQTLs) in a wide range of human tissues/cell types, we identify critical chromatin features that predict variant regulatory potential. We present cepip, a joint likelihood framework, for estimating a variant's regulatory probability in a context-dependent manner. Our method exhibits significant GWAS signal enrichment and is superior to existing cell type-specific methods...
March 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28301713/population-structure-and-genetic-basis-of-the-agronomic-traits-of-upland-cotton-in-china-revealed-by-a-genome-wide-association-study-using-high-density-snps
#13
Cong Huang, Xinhui Nie, Chao Shen, Chunyuan You, Wu Li, Wenxia Zhao, Xianlong Zhang, Zhongxu Lin
Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton producing and consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nation-wide population containing 503 G. hirsutum accessions was collected for a genome-wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping...
March 16, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28299864/robust-inference-of-genetic-architecture-in-mapping-studies
#14
Jon Slate
The genetic architecture of a trait usually refers to the number and magnitude of loci that explain phenotypic variation. A description of genetic architecture can help us to understand how genetic variation is maintained, how traits have evolved and how phenotypes might respond to selection. However, linkage mapping and association studies can suffer from problems of bias, especially when conducted in natural populations where the opportunity to perform studies with very large sample sizes can be limited. In this issue of Molecular Ecology, Li and colleagues perform an association study of brain traits in ninespine sticklebacks Pungitius pungitius...
March 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28295376/both-maternally-and-paternally-imprinted-genes-regulate-seed-development-in-rice
#15
Jingya Yuan, Sushu Chen, Wu Jiao, Longfei Wang, Limei Wang, Wenxue Ye, Jie Lu, Delin Hong, Siliang You, Zhukuan Cheng, Dong-Lei Yang, Z Jeffrey Chen
Genetic imprinting refers to the unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms, including mammals and flowering plants. Although many imprinted genes have been identified in plants, the functions of these imprinted genes have remained largely uninvestigated. We report genome-wide analysis of gene expression, DNA methylation and small RNAs in the rice endosperm and functional tests of five imprinted genes during seed development using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated gene9 (CRISPR/Cas9) gene editing technology...
March 13, 2017: New Phytologist
https://www.readbyqxmd.com/read/28293708/inverse-gene-for-gene-interactions-contribute-additively-to-tan-spot-susceptibility-in-wheat
#16
Zhaohui Liu, Jason D Zurn, Gayan Kariyawasam, Justin D Faris, Gongjun Shi, Jana Hansen, Jack B Rasmussen, Maricelis Acevedo
Tan spot susceptibility is conferred by multiple interactions of necrotrophic effector and host sensitivity genes. Tan spot of wheat, caused by Pyrenophora tritici-repentis, is an important disease in almost all wheat-growing areas of the world. The disease system is known to involve at least three fungal-produced necrotrophic effectors (NEs) that interact with the corresponding host sensitivity (S) genes in an inverse gene-for-gene manner to induce disease. However, it is unknown if the effects of these NE-S gene interactions contribute additively to the development of tan spot...
March 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28289802/genetic-dissection-of-the-maize-zea-mays-l-mamp-response
#17
Xinye Zhang, Oswaldo Valdés-López, Consuelo Arellano, Gary Stacey, Peter Balint-Kurti
Loci associated with variation in maize responses to two microbe-associated molecular patterns (MAMPs) were identified. MAMP responses were correlated. No relationship between MAMP responses and quantitative disease resistance was identified. Microbe-associated molecular patterns (MAMPs) are highly conserved molecules commonly found in microbes which can be recognized by plant pattern recognition receptors. Recognition triggers a suite of responses including production of reactive oxygen species (ROS) and nitric oxide (NO) and expression changes of defense-related genes...
March 13, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28289475/combined-genome-wide-linkage-and-targeted-association-analysis-of-head-circumference-in-autism-spectrum-disorder-families
#18
M Woodbury-Smith, D A Bilder, J Morgan, L Jerominski, T Darlington, T Dyer, A D Paterson, H Coon
BACKGROUND: It has long been recognized that there is an association between enlarged head circumference (HC) and autism spectrum disorder (ASD), but the genetics of HC in ASD is not well understood. In order to investigate the genetic underpinning of HC in ASD, we undertook a genome-wide linkage study of HC followed by linkage signal targeted association among a sample of 67 extended pedigrees with ASD. METHODS: HC measurements on members of 67 multiplex ASD extended pedigrees were used as a quantitative trait in a genome-wide linkage analysis...
2017: Journal of Neurodevelopmental Disorders
https://www.readbyqxmd.com/read/28289284/the-schizophrenia-risk-gene-znf804a-clinical-associations-biological-mechanisms-and-neuronal-functions
#19
REVIEW
H Chang, X Xiao, M Li
ZNF804A (zinc-finger protein 804A) has been recognized as a schizophrenia risk gene across multiple world populations. Its intronic single-nucleotide polymorphism (SNP) rs1344706 is among one of the strongest susceptibility variants that have achieved genome-wide significance in genome-wide association studies (GWAS) for schizophrenia and has been widely and intensively studied. To elucidate the biological mechanisms underlying the genetic risk conferred by rs1344706, we retrospectively analyzed the progresses in brain gene expression quantitative trait loci (eQTL) analyses, ZNF804A-induced pathway alterations in neural cells and changes in synaptic phenotypes associated with ZNF804A expression...
March 14, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28287462/snp-discovery-using-a-pangenome-has-the-single-reference-approach-become-obsolete
#20
REVIEW
Bhavna Hurgobin, David Edwards
Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species; it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation...
March 11, 2017: Biology
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