introduction to genome wide association studies

... Chr10 top200 — Chr14 top300 — (except for top100) RA Chr06 top10 Chr19 T1D Chr02 top300 top25% — — — (except for top300) Chr13 T2D Chr10 Chr21 top25% (except for top300 and top200) top100 top20 top300 ... through latent variables, to run multilocus genome-wide association studies Christine Sinoquet Abstract Background: Genome-wide association studies (GWASs) have been widely used to discover the genetic ... Chr05 top10 — Chr06 top100 — Chr01 top300 — T-Trees CAD CD One order of magnitude higher as of quantile hybrid approach (except for top100) HT Chr20 top200 top200 (except for top100 and top50)

Ngày tải lên: 25/11/2020, 15:10

... GCTA: Genome-wide complex trait analysis; GWAS: Genome-wide association study; Hip: Hippocampus; LD: Linkage disequilibrium; LMM: Linear mixed model; MEGHA: Massively expedited genome-wide heritability ... fixed with M ˆ = M0 “rand.” refers to the estimator hˆ rand with M ˆ = {1, 2, · · · , n}, “rand._SpaR” refers to the estimator refers to the oracle estimator hˆ fixed with M ˆ given by our sparse ... the ratio of the additive genetic variance to the total phenotypic variance [1] With the tremendous technological advances in genome-wide association studies (GWASs) in the last few decades, hundreds

Ngày tải lên: 25/11/2020, 12:14

... attentions in modern scientific applications For example, in genome-wide association studies (GWAS), it would be of convincing to detect an association which can be replicated in more than one study ... Replicability analysis in genome-wide association studies via Cartesian hidden Markov models Pengfei Wang and Wensheng Zhu* Abstract Background: Replicability analysis which aims to detect replicated ... Since the first publication of genome-wide association studies (GWAS) on age-related macular degeneration in 2005 [1], great progress has been made in the genetic studies of the human complex diseases

Ngày tải lên: 25/11/2020, 13:31

... Family-based designs for genome-wide association studies Nat Rev Genet 2011;12(7):465–74 Laird NM, Lange C The role of family-based designs in genome-wide association studies Stat Sci 2009;24(4):388–97 ... polymorphism (SNP) [2], the number of genome-wide association study (GWAS) has been rising exponentially [3] GWAS provides an efficient way to scan the whole genome to locate SNPs associated with the ... “milestone” events of alcoholism Earlier onset ages are indicators for higher vulnerability and have been shown to predict later progression to alcohol dependence [32] Thus, they were expected to

Ngày tải lên: 25/11/2020, 17:19

... control for multi-locus genome-wide association study Heredity 2018;120: 208–18 Page 10 of 11 25 Tamba CL, Zhang YM A fast mrMLM algorithm for multi-locus genomewide association studies bioRxiv 2018 ... et al Genome-wide association studies for pasmo resistance in flax (Linum usitatissimum L.) front Plant Sci 2019;9:1982 30 Peng Y, Liu H, Chen J, Shi T, Zhang C, Sun D, et al Genome-wide association ... the much higher number of E-M-total tagSNPs compared to the fewer Mtotal tagSNPs (Fig 4d and Table S12) Discussion To date, the GWAS approach has been widely used to investigate the genetic basis

Ngày tải lên: 28/06/2021, 20:42

... weight in soybean using multilocus genome-wide association studies Front Genet 2020;11:689 41 Li X, Zhang X, Zhu L, Bu Y, Wang X, Zhang X, et al Genome-wide association study of four yield-related ... and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica) Nat Genet 2013;45(8):957–61 27 Hwang EY, Song Q, Jia G, Specht JE, Hyten DL, Costa J, et al A genomewide ... nematode resistance revealed by genome-wide association study in soybean BMC Genomics 2015;16:593 32 Zhang J, Song Q, Cregan PB, Nelson RL, Wang X, Wu J, et al Genome-wide association study for flowering

Ngày tải lên: 30/01/2023, 20:12

... used for genome-wide association study (GWAS) for six stalk lodging resistance-related traits The heritability of all traits ranged from 0.59 to 0.72 in the association mapping panel A total of ... population size and type [20] Genome-wide association study (GWAS) is a powerful tool for analyzing the genetic basis of complex traits So far, GWAS has been used to analyze many agronomic traits ... lodging resistance, Genome-wide association study, Quantitative trait nucleotides, Candidate gene † Lifen Wu, Yunxiao Zheng, Fuchao Jiao and Ming Wang contributed equally to this work *Correspondence:

Ngày tải lên: 30/01/2023, 21:03

... Liuhong Chen1,2, Michael Vinsky1, Graham Plastow2, John Basarab5, Paul Stothard2 and Changxi Li1,2* Abstract Background: Genome wide association studies (GWAS) on residual feed intake (RFI) and ... genome sequence variants, Genome wide association studies, Feed efficiency, Beef cattle Background Improving animal meat production efficiency has become an imperative goal for the industry to ... animals for genome wide association studies (GWAS), full sequencing a large cohort of animals is not feasible at this stage due to its prohibitive costs Therefore, an alternative way is to impute

Ngày tải lên: 28/02/2023, 08:02

... Vinsky1, Graham Plastow2, John Basarab5, Paul Stothard2 and Changxi Li1,2* Abstract Background: Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants ... architecture, Imputed whole genome sequence variants, Genome wide association studies, Carcass merit traits, Beef cattle, Background Carcass merit traits are important to beef production as they ... Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits Yining Wang1,2, Feng

Ngày tải lên: 28/02/2023, 08:02

... PC: PLINK: a toolset for whole-genome association and population-based linkage analysis Am J Hum Genet 2007, 81:559–575 Page 10 of 10 42 Hardy J, Singleton A: Genome wide association studies and ... implementation of association studies for binary responses subject to misclassification Abbreviations SNP: Single nucleotide polymorphism; OR: Odds ratios; GWAS: Genome-wide association studies; PM: ... genetic association studies: lessons learned from the obesity field Int J Obes (Lond) 2012: doi:10.1038/ijo.2012.82 29 Galvan A, Ioannidis JPA, Dragani TA: Beyond genome-wide association studies:

Ngày tải lên: 27/03/2023, 03:30

... frequently in the context of genome-wide analyses across ethnicities, particularly for mood disorders This study uses genome-wide association studies of depressive symptoms in a longitudinal framework ... This study uses genome-wide association studies of depressive symptoms in a longitudinal framework and across multiple ethnicities to find common variants for depressive symptoms Ethnicity-specific ... of unique (LD R2 < 0.8) genome-wide suggestive SNPs from baseline to repeated measures for each ethnicity (EA: eight to nine; AA: four to 11; CA: one to four; HA: six to ten), with some (at least

Ngày tải lên: 27/03/2023, 05:13

... SNP-based association analyses Anderson-Darling (A-D) test for genome scanning The SNP data were further used for genome-wide scanning via A-D test to reveal the sources of resistance to NCLB The total ... molecular biology and bioinformatics tools [2] Rapid developments in genome-wide * Correspondence: yjianbing@mail.hzau.edu.cn † Equal contributors National Key Laboratory of Crop Genetic Improvement, ... lines across different environments for resistance to NCLB To identify genomic regions associated with NCLB resistance in maize, a genome-wide association analysis was conducted using 56,110 single-nucleotide

Ngày tải lên: 26/05/2020, 21:58

... efficient approach to detect regions related to the resistance to corn borers, higher resolution is needed to detect the genes involved in the defense mechanism of the plant Genome wide association ... A genome-wide association study identifies IL23R as an inflammatory bowel disease gene Science 2006;314:1461–3 38 Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D, et al A genome-wide association ... et al Genome-wide association studies for feedlot and growth traits in cattle J Anim Sci 2011;89:1684–97 42 Fan B, Onteru SK, Du Z-Q, Garrick DJ, Stalder KJ, Rothschild MF Genome-wide association

Ngày tải lên: 26/05/2020, 23:35

... interactions from genome wide studies Given a genome wide study containing thousands of markers, most existing methods either fail to report the statistically significant interactions due to the limited ... effects To handle the high dimension of genome wide data, MegaSNPHunter partitions the whole genome into multiple short subgenomes and select the relative more important SNPs from each subgenome ... interactions in genome wide association studies We evaluate MegaSNPHunter through comparative studies on simulated data and the data sets from two real studies including a genome wide study on Parkinson

Ngày tải lên: 02/11/2022, 14:27

... TDT FOR HUMAN QTL MAPPING AND GENOME-WIDE ASSOCIATION STUDY HAO YING NATIONAL UNIVERSITY OF SINGAPORE 2008 TDT FOR HUMAN QTL MAPPING AND GENOME-WIDE ASSOCIATION STUDY HAO YING (Master ... application of TDT to genomewide association study has not been tackled so far. Since the rapid improvement in SNP genotyping technology makes it possible to find the genetic contributions to common disease, ... TDT by a penalized logistic model to extend the TDT to genome-wide association study. By virtue of this model, we convert the linkage study for gene mapping to variable selection problem. A two-step

Ngày tải lên: 11/09/2015, 16:06

... onto the tomato reference genome (v2.40) – SNP p-values – Name of the locus the peak SNP belongs to (according to the tomato genome annotation v2.30) 893 31 894 Table III | Summary of trait associations ... Causse, 2012) in the last couple of years due to the release of the tomato 117 genome sequence (The Tomato Genome Consortium, 2012) and derived genomic 118 tools such as a high density SNP genotyping ... domestication of cultivated tomatoes Genetics 162(1): 365 - 379 Porcu E, Sanna S, Fuchsberger C, Fritsche LG (2013) Genotype imputation in genome-wide association studies Curr Protoc Hum Genet Chapter

Ngày tải lên: 14/12/2017, 16:03

... involved Genome-wide association studies (GWAS) are a way to directly identify new candidate genes or, more reasonably, to narrow down the chromosomal segments that carry functional factors to much ... quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development Keywords: ... North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters Roots contribute to

Ngày tải lên: 22/05/2020, 04:06

... CAD Genome wide association analysis, which is a powerful tool to identify genetic variants, is commonly employed to identify novel genetic variants currently Most genome wide association studies ... significances Study I: Genome wide scan of single nucleotide polymorphisms associated with myocardial infarction –Chapter Genome wide association analysis is a powerful tool to identify genetic ... common diseases Genome wide association studies (GWAS) have uncovered multiple variants associated with CAD or MI in Caucasians It is thus desirable to extend the method to the genetic studies of...

Ngày tải lên: 09/09/2015, 08:17

... of the Generalized Tournament Approach in Genomewide Association Studies 72 5.1 Introduction to the multiple testing for genome- wide association studies 73 5.2 The generalized tournament screening ... 1.3.1 Feature selection methods in genome- wide association studies In genome- wide association studies, a large number of statistical studies have been developed to detect genetic variants associated ... employed to develop better strategies to treat and prevent the disease Chapter1: Introduction In comparison with other approaches for mapping genetic variants, genome- wide association studies need to...

Ngày tải lên: 11/09/2015, 16:05

... to 0.76 [10] MS behaves as a prototypic complex genetic disorder, and although a single-gene etiology cannot be ruled out for a subset of pedigrees, data from recent genome- wide association studies ... receptor activity (GO:0004888) 0.0000274 Transmembrane receptor protein phosphatase activity 0.003811c Amine receptor activity Hematopoietin/interferon-class (D200-domain) cytokine receptor activity ... that failed to achieve genome- wide significance We then tested whether a significant fraction of the variance was related to contributions from additional common alleles with lower association...

Ngày tải lên: 11/08/2014, 12:21