ArticleGenetics2005
Ranks of genuine associations in whole-genome scans.
Article in Genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 3 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
41 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Pooled it
- Allelic heterogeneity in genetic association meta-analysis: an application to DTNBP1 and schizophrenia.Human heredity · 2010Pooled it
- Meta-analysis of two genome-wide association studies of bipolar disorder reveals important points of agreement.Molecular psychiatry · 2008Pooled it
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- TreeMap: a structured approach to fine mapping of eQTL variants.Bioinformatics (Oxford, England) · 2021Article
- From genome-wide associations to candidate causal variants by statistical fine-mapping.Nature reviews. Genetics · 2018Review
- Informing Prevention and Intervention Policy Using Genetic Studies of Resistance.Prevention science : the official journal of the Society for Prevention Research · 2018Article
- Critical Issues in the Inclusion of Genetic and Epigenetic Information in Prevention and Intervention Trials.Prevention science : the official journal of the Society for Prevention Research · 2018Article
- Multivariate association between single-nucleotide polymorphisms in Alzgene linkage regions and structural changes in the brain: discovery, refinement and validation.Statistical applications in genetics and molecular biology · 2017Article
- Convergent evidence for the molecular basis of musical traits.Scientific reports · 2016Review
- Polygenic Scores in Epidemiology: Risk Prediction, Etiology, and Clinical Utility.Current epidemiology reports · 2015Article
- A novel method, the Variant Impact On Linkage Effect Test (VIOLET), leads to improved identification of causal variants in linkage regions.European journal of human genetics : EJHG · 2014Article
- Diverse convergent evidence in the genetic analysis of complex disease: coordinating omic, informatic, and experimental evidence to better identify and validate risk factors.BioData mining · 2014Article
- Genotype to phenotype maps: multiple input abiotic signals combine to produce growth effects via attenuating signaling interactions in maize.G3 (Bethesda, Md.) · 2013Article
- The ranking probability approach and its usage in design and analysis of large-scale studies.PloS one · 2013Article
- A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder.Human genetics · 2012Article
- An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error.Molecular vision · 2012Article
- The AVPR1A gene and substance use disorders: association, replication, and functional evidence.Biological psychiatry · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
With the recent advances in high-throughput genotyping techniques, it is now possible to perform whole-genome association studies to fine map causal polymorphisms underlying important traits that influence susceptibility to human diseases and efficacy of drugs. Once a genome scan is completed the results can be sorted by the association statistic value. What is the probability that true positives will be encountered among the first most associated markers? When a particular polymorphism is found associated with the trait, there is a chance that it represents either a "true" or a "false" association (TA vs. FA). Setting appropriate significance thresholds has been considered to provide assurance of sufficient odds that the associations found to be significant are genuine. However, the problem with genome scans involving thousands of markers is that the statistic values of FAs can reach quite extreme magnitudes. In such situations, the distributions corresponding to TAs and the most extreme FAs become comparable and significance thresholds tend to penalize TAs and FAs in a similar fashion. When sorting between true and false associations, the "typical" place (i.e., rank) of TAs among the most significant outcomes becomes important, ordered by the association statistic value. The distribution of ranks that we study here allows calculation of several useful quantities. In particular, it gives the number of most significant markers needed for a follow-up study to guarantee that a true association is included with certain probability. This can be calculated conditionally on having applied a multiple-testing correction. Effects of multilocus (e.g., haplotype association) tests and impact of linkage disequilibrium on the distribution of ranks associated with TAs are evaluated and can be taken into account.
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Registered trials
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