ArticleGenetic epidemiology2009
Genome-wide association studies: quality control and population-based measures.
Article in Genetic epidemiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 4 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- A systematic review of analytical methods used in genetic association analysis of the X-chromosome.Briefings in bioinformatics · 2022Pooled it
- Common genetic variation in obesity, lipid transfer genes and risk of Metabolic Syndrome: Results from IDEFICS/I.Family study and meta-analysis.Scientific reports · 2020Pooled it
- No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis.Scientific reports · 2016Pooled it
- A genome-wide association study identifies LIPA as a susceptibility gene for coronary artery disease.Circulation. Cardiovascular genetics · 2011Pooled it
- A robust test for X-chromosome genetic association accounting for X-chromosome inactivation and imprinting.Genetics research · 2020Article
- Gene Influence in the Effectiveness of Plant Sterols Treatment in Children: Pilot Interventional Study.Nutrients · 2019Article
- X chromosome genetic data in a Spanish children cohort, dataset description and analysis pipeline.Scientific data · 2019Article
- X-chromosome association study reveals genetic susceptibility loci of nasopharyngeal carcinoma.Biology of sex differences · 2019Article
- Genomic Influence in the Prevention of Cardiovascular Diseases with a Sterol-Based Treatment.Diseases (Basel, Switzerland) · 2018Article
- Genome-Enabled Prediction of Breeding Values for Feedlot Average Daily Weight Gain in Nelore Cattle.G3 (Bethesda, Md.) · 2017Article
- Article
- Comparison of pre-processing methods for multiplex bead-based immunoassays.BMC genomics · 2016Article
- Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity.eLife · 2016Article
- Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases.PloS one · 2014Article
- Risk estimation and risk prediction using machine-learning methods.Human genetics · 2012Review
- Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep.BMC genetics · 2012Article
- Association tests for X-chromosomal markers--a comparison of different test statistics.Human heredity · 2011Article
- Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic evidence for folate-pathway abnormalities.PLoS genetics · 2010Article
- Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2.Nature genetics · 2010Article
- Modulation of plasma triglycerides concentration by sterol-based treatment in children carrying different genes.Annals of pediatric cardiologyArticle
Corrections and comments
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Authors and funding
1 author.
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Abstract
Genome-wide association studies, using hundreds of thousands of single-nucleotide polymorphism (SNP) markers, have become a standard approach for identifying disease susceptibility genes. The change in the technology poses substantial computational and statistical challenges that have been addressed in the quality control, imputation, and population-based measure groups of the Genetic Analysis Workshop 16. The computational challenges pertain to efficient memory management and computational speed of the statistical procedures, and we discuss an approach for efficient SNP storage. Accuracy and computational speed is relevant for genotype calling, and the results from a comparison of three calling algorithms are discussed. The first statistical challenge is related to statistical quality control, and we discuss two novel quality control procedures. These low-level analyses have an effect on subsequent preparatory steps for high-level analyses, e.g., the quality of genotype imputation approaches. After the conduct of a genome-wide association study with successful replication and/or validation, measures of diagnostic accuracy, including the area under the curve, are investigated. The area under the curve can be constructed from summary data in some situations. Finally, we discuss how the population-attributable risk of a genetic variant that is only measured in a reference data set can be determined.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.