ArticleGenetic epidemiology2010
A simple and fast two-locus quality control test to detect false positives due to batch effects in 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 10 papers.
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Who cites it
10 citing papers in PubMed.
- Elevated risk of invasive group A streptococcal disease and host genetic variation in the human leucocyte antigen locus.Genes and immunity · 2020Article
- Local Joint Testing Improves Power and Identifies Hidden Heritability in Association Studies.Genetics · 2016Article
- Shared genetics underlying epidemiological association between endometriosis and ovarian cancer.Human molecular genetics · 2015Article
- Most common 'sporadic' cancers have a significant germline genetic component.Human molecular genetics · 2014Article
- Gradient Boosting as a SNP Filter: an Evaluation Using Simulated and Hair Morphology Data.Journal of data mining in genomics & proteomics · 2013Article
- Estimation and partitioning of polygenic variation captured by common SNPs for Alzheimer's disease, multiple sclerosis and endometriosis.Human molecular genetics · 2013Article
- GWIS--model-free, fast and exhaustive search for epistatic interactions in case-control GWAS.BMC genomics · 2013Article
- Estimating the genetic variance of major depressive disorder due to all single nucleotide polymorphisms.Biological psychiatry · 2012Article
- Impact of diagnostic misclassification on estimation of genetic correlations using genome-wide genotypes.European journal of human genetics : EJHG · 2012Article
- Estimating missing heritability for disease from genome-wide association studies.American journal of human genetics · 2011Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The impact of erroneous genotypes having passed standard quality control (QC) can be severe in genome-wide association studies, genotype imputation, and estimation of heritability and prediction of genetic risk based on single nucleotide polymorphisms (SNP). To detect such genotyping errors, a simple two-locus QC method, based on the difference in test statistic of association between single SNPs and pairs of SNPs, was developed and applied. The proposed approach could detect many problematic SNPs with statistical significance even when standard single SNP QC analyses fail to detect them in real data. Depending on the data set used, the number of erroneous SNPs that were not filtered out by standard single SNP QC but detected by the proposed approach varied from a few hundred to thousands. Using simulated data, it was shown that the proposed method was powerful and performed better than other tested existing methods. The power of the proposed approach to detect erroneous genotypes was ∼80% for a 3% error rate per SNP. This novel QC approach is easy to implement and computationally efficient, and can lead to a better quality of genotypes for subsequent genotype-phenotype investigations.
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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.