ArticleGenetic epidemiology2010
Quality control and quality assurance in genotypic data for genome-wide association studies.
Article in Genetic epidemiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 310 papers, 19 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
310 citing papers in PubMed, 19 syntheses or guidelines pooled it.
- Variants in CALD1, ESRP1, and RBFOX1 are associated with orofacial cleft risk.PLoS genetics · 2025Pooled it
- Skeletons in the closet? Using a bibliometric lens to visualise phytochemical and pharmacological activities linked toFrontiers in plant science · 2024Pooled it
- Lowering of Circulating Sclerostin May Increase Risk of Atherosclerosis and Its Risk Factors: Evidence From a Genome-Wide Association Meta-Analysis Followed by Mendelian Randomization.Arthritis & rheumatology (Hoboken, N.J.) · 2023Pooled it
- Multi-ancestry genome-wide analysis identifies shared genetic effects and common genetic variants for self-reported sleep duration.Human molecular genetics · 2023Pooled it
- Genome-Wide Gene-Set Analysis Identifies Molecular Mechanisms Associated with ALS.International journal of molecular sciences · 2023Pooled it
- A stop-gain variant inHGG advances · 2023Pooled it
- Identification of shared genetic architecture between non-alcoholic fatty liver disease and type 2 diabetes: A genome-wide analysis.Frontiers in endocrinology · 2023Pooled it
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Large trans-ethnic meta-analysis identifies AKR1C4 as a novel gene associated with age at menarche.Human reproduction (Oxford, England) · 2021Pooled it
- Pooled it
- Sex-Specific Genetic Associations for Barrett's Esophagus and Esophageal Adenocarcinoma.Gastroenterology · 2020Pooled it
- Genome-wide association study of cognitive function in diverse Hispanics/Latinos: results from the Hispanic Community Health Study/Study of Latinos.Translational psychiatry · 2020Pooled it
- Genome-wide association reveals contribution of MRAS to painful temporomandibular disorder in males.Pain · 2019Pooled it
- Discovery of common and rare genetic risk variants for colorectal cancer.Nature genetics · 2019Pooled it
- GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle.Scientific reports · 2018Pooled it
- Genome-wide meta-analyses identifies novel taxane-induced peripheral neuropathy-associated loci.Pharmacogenetics and genomics · 2018Pooled it
- GWAS Identifies New Loci for Painful Temporomandibular Disorder: Hispanic Community Health Study/Study of Latinos.Journal of dental research · 2017Pooled it
- Meta-Analysis of Genome-Wide Association Studies with Correlated Individuals: Application to the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).Genetic epidemiology · 2016Pooled it
- Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology.PLoS genetics · 2016Pooled it
- The influence of genetic susceptibility and calcium plus vitamin D supplementation on fracture risk.The American journal of clinical nutrition · 2017Trial
250 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
26 authors.
Funding
Abstract
Genome-wide scans of nucleotide variation in human subjects are providing an increasing number of replicated associations with complex disease traits. Most of the variants detected have small effects and, collectively, they account for a small fraction of the total genetic variance. Very large sample sizes are required to identify and validate findings. In this situation, even small sources of systematic or random error can cause spurious results or obscure real effects. The need for careful attention to data quality has been appreciated for some time in this field, and a number of strategies for quality control and quality assurance (QC/QA) have been developed. Here we extend these methods and describe a system of QC/QA for genotypic data in genome-wide association studies (GWAS). This system includes some new approaches that (1) combine analysis of allelic probe intensities and called genotypes to distinguish gender misidentification from sex chromosome aberrations, (2) detect autosomal chromosome aberrations that may affect genotype calling accuracy, (3) infer DNA sample quality from relatedness and allelic intensities, (4) use duplicate concordance to infer SNP quality, (5) detect genotyping artifacts from dependence of Hardy-Weinberg equilibrium test P-values on allelic frequency, and (6) demonstrate sensitivity of principal components analysis to SNP selection. The methods are illustrated with examples from the "Gene Environment Association Studies" (GENEVA) program. The results suggest several recommendations for QC/QA in the design and execution of GWAS.
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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.