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Genome wide association studies

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https://www.readbyqxmd.com/read/29224151/a-guide-to-illumina-beadchip-data-analysis
#1
Michael C Wu, Pei-Fen Kuan
The Illumina Infinium BeadChips are a powerful array-based platform for genome-wide DNA methylation profiling at approximately 485,000 (450K) and 850,000 (EPIC) CpG sites across the genome. The platform is used in many large-scale population-based epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. This chapter provides an overview of the key steps in analyzing Illumina BeadChip data. We describe key preprocessing steps including data extraction and quality control as well as normalization strategies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224150/bisulphite-sequencing-of-chromatin-immunoprecipitated-dna-bischip-seq
#2
Clare Stirzaker, Jenny Z Song, Aaron L Statham, Susan J Clark
Epigenetic regulation plays a critical role in gene expression, cellular differentiation, and disease. There is a complex interplay between the different layers of epigenetic information, including DNA methylation, nucleosome positions, histone modifications, histone variants, and other important epigenetic regulators. The different modifications do not act independently of each other and their relationship plays an important role in governing the regulation of the epigenome. Of these, DNA methylation is the best-studied epigenetic modification in mammals...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224145/methyl-cpg-binding-domain-sequencing-mbd-seq
#3
Karolina A Aberg, Robin F Chan, Linying Xie, Andrey A Shabalin, Edwin J C G van den Oord
Detailed biological knowledge about the potential importance of the methylome is typically lacking for common diseases. Therefore, methylome-wide association studies (MWAS) are critical to detect disease relevant methylation sites. Methyl-CpG-binding domain sequencing (MBD-seq) offers potential advantages compared to antibody-based enrichment, but performance depends critically on using an optimal protocol. Using an optimized protocol, MBD-seq can approximate the sensitivity/specificity obtained with whole-genome bisulfite sequencing, but at a fraction of the costs and time to complete the project...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224136/a-summary-of-the-biological-processes-disease-associated-changes-and-clinical-applications-of-dna-methylation
#4
Gitte Brinch Andersen, Jörg Tost
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223971/keeping-pace-with-the-red-queen-identifying-the-genetic-basis-of-susceptibility-to-infectious-disease
#5
Ailene MacPherson, Sarah P Otto, Scott L Nuismer
Genome-wide association studies are widely used to identify "disease genes" conferring resistance/susceptibility to infectious diseases. Using a combination of mathematical models and simulations we demonstrate that genetic interactions between hosts and parasites (GxG interactions) can drastically affect the results of these association scans and hamper our ability to detect genetic variation in susceptibility. When hosts and parasites coevolve, these GxG interactions often make Genome-wide association studies unrepeatable over time or across host populations...
December 9, 2017: Genetics
https://www.readbyqxmd.com/read/29223691/genome-wide-association-analysis-of-ear-rot-resistance-caused-by-fusarium-verticillioides-in-maize
#6
Guilherme de Jong, Andrezza Kellen Alves Pamplona, Renzo Garcia Von Pinho, Marcio Balestre
The identification of causal regions associated with resistance to Fusarium verticillioides can be useful to understand resistance mechanisms and further be used in breeding programs. In this study, a genome-wide association study (GWAS) was conducted to identify candidate markers associated with resistance to the ear rot caused by the fungus F. verticillioides. A total of 242 maize inbred lines were genotyped with 23,153 DArT-seq markers. A total of 12 DArTs were associated with ear rot resistance. Some DArTs were localized close to genes with functions directly related to ear rot resistance, such as a gene responsible for the innate immune response that belongs to the class of NBS-LRR receptors...
December 6, 2017: Genomics
https://www.readbyqxmd.com/read/29222496/genome-wide-and-gene-based-association-mapping-for-rice-eating-and-cooking-characteristics-and-protein-content
#7
Xiaoqian Wang, Yunlong Pang, Jian Zhang, Zhichao Wu, Kai Chen, Jauhar Ali, Guoyou Ye, Jianlong Xu, Zhikang Li
Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221444/genome-wide-association-study-of-coronary-artery-calcified-atherosclerotic-plaque-in-african-americans-with-type-2-diabetes
#8
Jasmin Divers, Nicholette D Palmer, Carl D Langefeld, W Mark Brown, Lingyi Lu, Pamela J Hicks, S Carrie Smith, Jianzhao Xu, James G Terry, Thomas C Register, Lynne E Wagenknecht, John S Parks, Lijun Ma, Gary C Chan, Sarah G Buxbaum, Adolfo Correa, Solomon Musani, James G Wilson, Herman A Taylor, Donald W Bowden, John Jeffrey Carr, Barry I Freedman
BACKGROUND: Coronary artery calcified atherosclerotic plaque (CAC) predicts cardiovascular disease (CVD). Despite exposure to more severe conventional CVD risk factors, African Americans (AAs) are less likely to develop CAC, and when they do, have markedly lower levels than European Americans. Genetic factors likely contribute to the observed ethnic differences. To identify genes associated with CAC in AAs with type 2 diabetes (T2D), a genome-wide association study (GWAS) was performed using the Illumina 5 M chip in 691 African American-Diabetes Heart Study participants (AA-DHS), with replication in 205 Jackson Heart Study (JHS) participants with T2D...
December 8, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29220677/a-powerful-approach-to-estimating-annotation-stratified-genetic-covariance-via-gwas-summary-statistics
#9
Qiongshi Lu, Boyang Li, Derek Ou, Margret Erlendsdottir, Ryan L Powles, Tony Jiang, Yiming Hu, David Chang, Chentian Jin, Wei Dai, Qidu He, Zefeng Liu, Shubhabrata Mukherjee, Paul K Crane, Hongyu Zhao
Despite the success of large-scale genome-wide association studies (GWASs) on complex traits, our understanding of their genetic architecture is far from complete. Jointly modeling multiple traits' genetic profiles has provided insights into the shared genetic basis of many complex traits. However, large-scale inference sets a high bar for both statistical power and biological interpretability. Here we introduce a principled framework to estimate annotation-stratified genetic covariance between traits using GWAS summary statistics...
December 7, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29220643/polygenic-risk-for-alcohol-consumption-and-its-association-with-alcohol-related-phenotypes-do-stress-and-life-satisfaction-moderate-these-relationships
#10
Gabry W Mies, Karin J H Verweij, Jorien L Treur, Lannie Ligthart, Iryna O Fedko, Jouke Jan Hottenga, Gonneke Willemsen, Meike Bartels, Dorret I Boomsma, Jacqueline M Vink
BACKGROUND: Genetic and environmental factors contribute about equally to alcohol-related phenotypes in adulthood. In the present study, we examined whether more stress at home or low satisfaction with life might be associated with heavier drinking or more alcohol-related problems in individuals with a high genetic susceptibility to alcohol use. METHODS: Information on polygenic scores and drinking behavior was available in 6705 adults (65% female; 18-83 years) registered with the Netherlands Twin Register...
December 2, 2017: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/29220522/meta-analysis-of-genome-wide-association-studies-identifies-8-novel-loci-involved-in-shape-variation-of-human-head-hair
#11
Fan Liu, Yan Chen, Gu Zhu, Pirro G Hysi, Sijie Wu, Kaustubh Adhikari, Krystal Breslin, Ewelina Pospiech, Merel A Hamer, Fuduan Peng, Charanya Muralidharan, Victor Acuna-Alonzo, Samuel Canizales-Quinteros, Gabriel Bedoya, Carla Gallo, Giovanni Poletti, Francisco Rothhammer, Maria Catira Bortolini, Rolando Gonzalez-Jose, Changqing Zeng, Shuhua Xu, Li Jin, André G Uitterlinden, M Arfan Ikram, Cornelia M van Duijn, Tamar Nijsten, Susan Walsh, Wojciech Branicki, Sijia Wang, Andrés Ruiz-Linares, Timothy D Spector, Nicholas G Martin, Sarah E Medland, Manfred Kayser
Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28,964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21...
December 6, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29220501/combination-of-247-genome-wide-association-studies-reveals-high-cancer-risk-as-a-result-of-evolutionary-adaptation
#12
Konstantinos Voskarides
Analysis of GLOBOCAN-2012 data shows clearly here that cancer incidence worldwide is highly related with low average annual temperatures and extreme low temperatures. This applies for all cancers together or separately for many frequent or rare cancer types (all cancers P = 9.49 x 10-18). Supporting fact is that Inuit people, living at extreme low temperatures, have the highest cancer rates today. Hypothesizing an evolutionary explanation, 240 cancer genome-wide association studies (GWAS) and seven GWAS for cold and high-altitude adaptation were combined...
December 5, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29218913/leveraging-putative-enhancer-promoter-interactions-to-investigate-two-way-epistasis-in-type-2-diabetes-gwas
#13
Elisabetta Manduchi, Alessandra Chesi, Molly A Hall, Struan F A Grant, Jason H Moore
We utilized evidence for enhancer-promoter interactions from functional genomics data in order to build biological filters to narrow down the search space for two-way Single Nucleotide Polymorphism (SNP) interactions in Type 2 Diabetes (T2D) Genome Wide Association Studies (GWAS). This has led us to the identification of a reproducible statistically significant SNP pair associated with T2D. As more functional genomics data are being generated that can help identify potentially interacting enhancer-promoter pairs in larger collection of tissues/cells, this approach has implications for investigation of epistasis from GWAS in general...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218904/evaluation-of-predixcan-for-prioritizing-gwas-associations-and-predicting-gene-expression
#14
Binglan Li, Shefali S Verma, Yogasudha C Veturi, Anurag Verma, Yuki Bradford, David W Haas, Marylyn D Ritchie
Genome-wide association studies (GWAS) have been successful in facilitating the understanding of genetic architecture behind human diseases, but this approach faces many challenges. To identify disease-related loci with modest to weak effect size, GWAS requires very large sample sizes, which can be computational burdensome. In addition, the interpretation of discovered associations remains difficult. PrediXcan was developed to help address these issues. With built in SNP-expression models, PrediXcan is able to predict the expression of genes that are regulated by putative expression quantitative trait loci (eQTLs), and these predicted expression levels can then be used to perform gene-based association studies...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218884/how-powerful-are-summary-based-methods-for-identifying-expression-trait-associations-under-different-genetic-architectures
#15
Yogasudha Veturi, Marylyn D Ritchie
Transcriptome-wide association studies (TWAS) have recently been employed as an approach that can draw upon the advantages of genome-wide association studies (GWAS) and gene expression studies to identify genes associated with complex traits. Unlike standard GWAS, summary level data suffices for TWAS and offers improved statistical power. Two popular TWAS methods include either (a) imputing the cis genetic component of gene expression from smaller sized studies (using multi-SNP prediction or MP) into much larger effective sample sizes afforded by GWAS - TWAS-MP or (b) using summary-based Mendelian randomization - TWAS-SMR...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218375/genetic-analysis-of-multi-environmental-spring-wheat-trials-identifies-genomic-regions-for-locus-specific-trade-offs-for-grain-weight-and-grain-number
#16
Sivakumar Sukumaran, Marta Lopes, Susanne Dreisigacker, Matthew Reynolds
GWAS on multi-environment data identified genomic regions associated with trade-offs for grain weight and grain number. Grain yield (GY) can be dissected into its components thousand grain weight (TGW) and grain number (GN), but little has been achieved in assessing the trade-off between them in spring wheat. In the present study, the Wheat Association Mapping Initiative (WAMI) panel of 287 elite spring bread wheat lines was phenotyped for GY, GN, and TGW in ten environments across different wheat growing regions in Mexico, South Asia, and North Africa...
December 7, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29218031/crispr-cas-systems-in-bacteroides-fragilis-an-important-pathobiont-in-the-human-gut-microbiome
#17
Mehrdad Tajkarimi, Hannah M Wexler
Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29217827/genome-wide-association-study-of-male-sexual-orientation
#18
Alan R Sanders, Gary W Beecham, Shengru Guo, Khytam Dawood, Gerulf Rieger, Judith A Badner, Elliot S Gershon, Ritesha S Krishnappa, Alana B Kolundzija, Jubao Duan, Pablo V Gejman, J Michael Bailey, Eden R Martin
Family and twin studies suggest that genes play a role in male sexual orientation. We conducted a genome-wide association study (GWAS) of male sexual orientation on a primarily European ancestry sample of 1,077 homosexual men and 1,231 heterosexual men using Affymetrix single nucleotide polymorphism (SNP) arrays. We identified several SNPs with p < 10-5, including regions of multiple supporting SNPs on chromosomes 13 (minimum p = 7.5 × 10-7) and 14 (p = 4.7 × 10-7). The genes nearest to these peaks have functions plausibly relevant to the development of sexual orientation...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29217820/longitudinal-exome-wide-association-study-to-identify-genetic-susceptibility-loci-for-hypertension-in-a-japanese-population
#19
Yoshiki Yasukochi, Jun Sakuma, Ichiro Takeuchi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Yoshiji Yamada
Genome-wide association studies have identified various genetic variants associated with complex disorders. However, these studies have commonly been conducted in a cross-sectional manner. Therefore, we performed a longitudinal exome-wide association study (EWAS) in a Japanese cohort. We aimed to identify genetic variants that confer susceptibility to hypertension using ~244 000 single-nucleotide variants (SNVs) and physiological data from 6026 Japanese individuals who underwent annual health check-ups for several years...
December 8, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29217731/genome-wide-analysis-of-grain-yield-stability-and-environmental-interactions-in-a-multiparental-soybean-population
#20
Alencar Xavier, Diego Jarquin, Reka Howard, Vishnu Ramasubramanian, James E Specht, George L Graef, William D Beavis, Brian W Diers, Qijian Song, Perry Cregan, Randall Nelson, Rouf Mian, J G Shannon, Leah McHale, Dechun Wang, William Schapaugh, Aaron J Lorenz, Shizhong Xu, William Muir, Katy M Rainey
Genetic improvement towards optimized and stable agronomic performance of soybean genotypes is desirable for food security. Understanding how genotypes perform in different environmental conditions helps breeders develop sustainable cultivars adapted to target regions. Complex traits of importance are known to be controlled by a large number of genomic regions with small effects whose magnitude and direction are modulated by environmental factors. Knowledge of the constraints and undesirable effects resulting from genotype by environmental interactions is a key objective in improving selection procedures in soybean breeding programs...
December 7, 2017: G3: Genes—Genomes—Genetics
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