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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 …
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
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
Tutorial: a guide to performing polygenic risk score analyses.
Choi SW, Mak TS, O'Reilly PF. Choi SW, et al. Nat Protoc. 2020 Sep;15(9):2759-2772. doi: 10.1038/s41596-020-0353-1. Epub 2020 Jul 24. Nat Protoc. 2020. PMID: 32709988 Free PMC article. Review.
A polygenic score (PGS) or polygenic risk score (PRS) is an estimate of an individual's genetic liability to a trait or disease, calculated according to their genotype profile and relevant genome-wide association study (GWAS) data. ...We outline …
A polygenic score (PGS) or polygenic risk score (PRS) is an estimate of an individual's genetic liability to a trait or disease, calc …
Copy Number Variation.
Macé A, Kutalik Z, Valsesia A. Macé A, et al. Methods Mol Biol. 2018;1793:231-258. doi: 10.1007/978-1-4939-7868-7_14. Methods Mol Biol. 2018. PMID: 29876900
Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease or phenotypic traits.While the link between SNPs and disease susceptibility has been well studied, to date the …
Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its pos …
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 …
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 …
Systematic review of genome-wide association studies of abdominal aortic aneurysm.
Singh TP, Field MA, Bown MJ, Jones GT, Golledge J. Singh TP, et al. Atherosclerosis. 2021 Jun;327:39-48. doi: 10.1016/j.atherosclerosis.2021.05.001. Epub 2021 May 12. Atherosclerosis. 2021. PMID: 34038762 Review.
BACKGROUND AND AIMS: Abdominal aortic aneurysm (AAA) is an important cause of death worldwide and has an estimated heritability between 70 and 77%. Genome-wide association studies (GWAS) are an established way to discover genetic risk variants. ...RESU …
BACKGROUND AND AIMS: Abdominal aortic aneurysm (AAA) is an important cause of death worldwide and has an estimated heritability between 70 a …
Quality control for genome-wide association studies.
Gondro C, Lee SH, Lee HK, Porto-Neto LR. Gondro C, et al. Methods Mol Biol. 2013;1019:129-47. doi: 10.1007/978-1-62703-447-0_5. Methods Mol Biol. 2013. PMID: 23756889 Review.
This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide association studies. The main metrics for evaluating the quality of the genotypes are discussed followed by a worked …
This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide
Genome-Wide Association Study Identifies Risk Loci for Cluster Headache.
O'Connor E, Fourier C, Ran C, Sivakumar P, Liesecke F, Southgate L, Harder AVE, Vijfhuizen LS, Yip J, Giffin N, Silver N, Ahmed F, Hostettler IC, Davies B, Cader MZ, Simpson BS, Sullivan R, Efthymiou S, Adebimpe J, Quinn O, Campbell C, Cavalleri GL, Vikelis M, Kelderman T, Paemeleire K, Kilbride E, Grangeon L, Lagrata S, Danno D, Trembath R, Wood NW, Kockum I, Winsvold BS, Steinberg A, Sjöstrand C, Waldenlind E, Vandrovcova J, Houlden H, Matharu M, Belin AC. O'Connor E, et al. Ann Neurol. 2021 Aug;90(2):193-202. doi: 10.1002/ana.26150. Epub 2021 Jul 14. Ann Neurol. 2021. PMID: 34184781
METHODS: We carried out a genome-wide association study, where 852 UK and 591 Swedish cluster headache cases were compared with 5,614 and 1,134 controls, respectively. ...Downstream analyses implicated immunological processes in the pathogenesis
METHODS: We carried out a genome-wide association study, where 852 UK and 591 Swedish cluster headache ca
627 results