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A tutorial on conducting genome-wide association studies: Quality control and statistical analysis.
Marees AT, de Kluiver H, Stringer S, Vorspan F, Curis E, Marie-Claire C, Derks EM. Marees AT, et al. Int J Methods Psychiatr Res. 2018 Jun;27(2):e1608. doi: 10.1002/mpr.1608. Epub 2018 Feb 27. Int J Methods Psychiatr Res. 2018. PMID: 29484742 Free PMC article.
OBJECTIVES: Genome-wide association studies (GWAS) have become increasingly popular to identify associations between single nucleotide polymorphisms (SNPs) and phenotypic traits. ...PRS does not aim to identify individual SNPs but aggregates informatio …
OBJECTIVES: Genome-wide association studies (GWAS) have become increasingly popular to identify associations bet …
Quality control procedures for genome-wide association studies.
Turner S, Armstrong LL, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, de Andrade M, Doheny KF, Haines JL, Hayes G, Jarvik G, Jiang L, Kullo IJ, Li R, Ling H, Manolio TA, Matsumoto M, McCarty CA, McDavid AN, Mirel DB, Paschall JE, Pugh EW, Rasmussen LV, Wilke RA, Zuvich RL, Ritchie MD. Turner S, et al. Curr Protoc Hum Genet. 2011 Jan;Chapter 1:Unit1.19. doi: 10.1002/0471142905.hg0119s68. Curr Protoc Hum Genet. 2011. PMID: 21234875 Free PMC article.
Genome-wide association studies (GWAS) are being conducted at an unprecedented rate in population-based cohorts and have increased our understanding of the pathophysiology of complex disease. Regardless of context, the practical utility of this informa
Genome-wide association studies (GWAS) are being conducted at an unprecedented rate in population-based cohorts
Data quality control in genetic case-control association studies.
Anderson CA, Pettersson FH, Clarke GM, Cardon LR, Morris AP, Zondervan KT. Anderson CA, et al. Nat Protoc. 2010 Sep;5(9):1564-73. doi: 10.1038/nprot.2010.116. Epub 2010 Aug 26. Nat Protoc. 2010. PMID: 21085122 Free PMC article.
This protocol details the steps for data quality assessment and control that are typically carried out during case-control association studies. ...These critical steps are paramount to the success of a case-control study and are ne …
This protocol details the steps for data quality assessment and control that are typically carried out during case-control
Statistical methods for genome-wide association studies.
Wang MH, Cordell HJ, Van Steen K. Wang MH, et al. Semin Cancer Biol. 2019 Apr;55:53-60. doi: 10.1016/j.semcancer.2018.04.008. Epub 2018 May 1. Semin Cancer Biol. 2019. PMID: 29727703 Review.
Genome-wide association studies (GWAS) detect common genetic variants associated with complex disorders. With their comprehensive coverage of common single nucleotide polymorphisms and comparatively low cost, GWAS are an attractive tool in the clinical
Genome-wide association studies (GWAS) detect common genetic variants associated with complex disorders. With th
Quality control and conduct of genome-wide association meta-analyses.
Winkler TW, Day FR, Croteau-Chonka DC, Wood AR, Locke AE, Mägi R, Ferreira T, Fall T, Graff M, Justice AE, Luan J, Gustafsson S, Randall JC, Vedantam S, Workalemahu T, Kilpeläinen TO, Scherag A, Esko T, Kutalik Z, Heid IM, Loos RJ; Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Winkler TW, et al. Nat Protoc. 2014 May;9(5):1192-212. doi: 10.1038/nprot.2014.071. Epub 2014 Apr 24. Nat Protoc. 2014. PMID: 24762786 Free PMC article.
Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This proto …
Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association
Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies.
Pavan S, Delvento C, Ricciardi L, Lotti C, Ciani E, D'Agostino N. Pavan S, et al. Front Genet. 2020 Jun 5;11:447. doi: 10.3389/fgene.2020.00447. eCollection 2020. Front Genet. 2020. PMID: 32587600 Free PMC article. Review.
High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. ...Once genotypic data have been obtained, …
High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identif …
Using PLINK for Genome-Wide Association Studies (GWAS) and data analysis.
Rentería ME, Cortes A, Medland SE. Rentería ME, et al. Methods Mol Biol. 2013;1019:193-213. doi: 10.1007/978-1-62703-447-0_8. Methods Mol Biol. 2013. PMID: 23756892
Within this chapter we introduce the basic PLINK functions for reading in data, applying quality control, and running association analyses. Three worked examples are provided to illustrate: data management and assessment of population substructure, associa
Within this chapter we introduce the basic PLINK functions for reading in data, applying quality control, and running assoc
Protocols, Methods, and Tools for Genome-Wide Association Studies (GWAS) of Dental Traits.
Agler CS, Shungin D, Ferreira Zandoná AG, Schmadeke P, Basta PV, Luo J, Cantrell J, Pahel TD Jr, Meyer BD, Shaffer JR, Schaefer AS, North KE, Divaris K. Agler CS, et al. Methods Mol Biol. 2019;1922:493-509. doi: 10.1007/978-1-4939-9012-2_38. Methods Mol Biol. 2019. PMID: 30838596 Free PMC article.
To aid in this direction, the advent and increasing affordability of high-throughput genotyping has enabled the simultaneous interrogation of millions of genetic polymorphisms for association with oral and craniofacial traits. Specifically, genome-wide ass
To aid in this direction, the advent and increasing affordability of high-throughput genotyping has enabled the simultaneous interrogation o …
SQC: secure quality control for meta-analysis of genome-wide association studies.
Huang Z, Lin H, Fellay J, Kutalik Z, Hubaux JP. Huang Z, et al. Bioinformatics. 2017 Aug 1;33(15):2273-2280. doi: 10.1093/bioinformatics/btx193. Bioinformatics. 2017. PMID: 28379351
MOTIVATION: Due to the limited power of small-scale genome-wide association studies (GWAS), researchers tend to collaborate and establish a larger consortium in order to perform large-scale GWAS. Genome-wide association meta-analys …
MOTIVATION: Due to the limited power of small-scale genome-wide association studies (GWAS), researchers tend to …
Estimating missing heritability for disease from genome-wide association studies.
Lee SH, Wray NR, Goddard ME, Visscher PM. Lee SH, et al. Am J Hum Genet. 2011 Mar 11;88(3):294-305. doi: 10.1016/j.ajhg.2011.02.002. Epub 2011 Mar 3. Am J Hum Genet. 2011. PMID: 21376301 Free PMC article.
Genome-wide association studies are designed to discover SNPs that are associated with a complex trait. ...Recently, we developed a method for quantitative traits that estimates the variation accounted for when fitting all SNPs simultaneously. Here we
Genome-wide association studies are designed to discover SNPs that are associated with a complex trait. ...Recen
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