ArticleBMC proceedings2007
Normalizing a large number of quantitative traits using empirical normal quantile transformation.
Article in BMC proceedings, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed, 4 syntheses or guidelines pooled it.
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- Identification of a KCNQ1 polymorphism acting as a protective modifier against arrhythmic risk in long-QT syndrome.Circulation. Cardiovascular genetics · 2013Pooled it
- Genome-wide meta-analysis of five Asian cohorts identifies PDGFRA as a susceptibility locus for corneal astigmatism.PLoS genetics · 2011Pooled it
- Combined analysis of three genome-wide association studies on vWF and FVIII plasma levels.BMC medical genetics · 2011Pooled it
- Attenuated monocyte apoptosis, a new mechanism for osteoporosis suggested by a transcriptome-wide expression study of monocytes.PloS one · 2015Trial
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- A massive dataset of the NeuroCognitive Performance Test, a web-based cognitive assessment.Scientific data · 2022Article
- A Kinematic Data-Driven Approach to Differentiate Involuntary Choreic Movements in Individuals With Neurological Conditions.IEEE transactions on bio-medical engineering · 2022Article
- Preparation and Curation of Omics Data for Genome-Wide Association Studies.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Estrogens Regulate Placental Angiogenesis in Horses.International journal of molecular sciences · 2021Article
- Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference.Genome biology · 2020Article
- A rank-based normalization method with the fully adjusted full-stage procedure in genetic association studies.PloS one · 2020Article
- Population-based genome-wide association study of cognitive decline in older adults free of dementia: identification of a novel locus for the attention domain.Neurobiology of aging · 2019Article
- Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the UK Biobank.Science advances · 2019Article
- Genotype Imputation in Winter Wheat Using First-Generation Haplotype Map SNPs Improves Genome-Wide Association Mapping and Genomic Prediction of Traits.G3 (Bethesda, Md.) · 2019Article
- Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare.BMC genomics · 2018Article
- Are your covariates under control? How normalization can re-introduce covariate effects.European journal of human genetics : EJHG · 2018Article
- Sputum cell IL-1 receptor expression level is a marker of airway neutrophilia and airflow obstruction in asthmatic patients.The Journal of allergy and clinical immunology · 2018Article
- Developmental Changes Within the Genetic Architecture of Social Communication Behavior: A Multivariate Study of Genetic Variance in Unrelated Individuals.Biological psychiatry · 2018Article
- Partitioning Phenotypic Variance Due to Parent-of-Origin Effects Using Genomic Relatedness Matrices.Behavior genetics · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Variance-components and regression-based methods are frequently used to map quantitative trait loci. The normality of the trait values is usually assumed and violation of this assumption can have a detrimental effect on the power and type I error of such analyses. Various transformations can be used, but appropriate transformations usually require careful analysis of individual traits, which is not feasible for data sets with a large number of traits like those in Problem 1 of Genetic Analysis Workshop 15 (GAW15). A semiparametric variance-components method can estimate the transformation along with the model parameters, but existing methods are computationally intensive. In this paper, we propose the use of empirical normal quantile transformation to normalize the scaled rank of trait values using an inverse normal transformation. Despite its simplicity and potential loss of information, this transformation is shown, by extensive simulations, to have good control of power and type I error, even when compared with the semiparametric method. To investigate the impact of such a transformation on real data sets, we apply variance-components and variance-regression methods to the expression data of GAW15 and compare the results before and after transformation.
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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.