ArticlePLoS genetics2016
Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 918 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
918 citing papers in PubMed.
- An IRAT109 NAM population: Genetic characterization and mapping utility for trait dissection in japonica rice (Oryza sativa L.).The plant genome · 2026Article
- Genome-wide association analysis of resistance to scald in an adapted multiparent winter malting barley population.The plant genome · 2026Article
- Genomic prediction of single cross families of perennial ryegrass under two nitrogen managements.The plant genome · 2026Article
- A multi-race blast resistance locus identified and validated in US elite rice via association and biparental mapping.The plant genome · 2026Article
- Article
- Genome-wide characterisation of leaf rust resistance loci in an Eastern European barley collection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Common genetic control for grain filling duration and kernel weight in grain sorghum.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- High-resolution GWAS and diagnostic functional marker development for leaf shape in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genome-Wide Association Study of Body Measurement Traits at Birth in Cattle.Animals : an open access journal from MDPI · 2026Article
- Genetic identification and characterization of a locus controlling productive tiller number with breeding value in Chinese endemic wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Review
- Genome-Wide Association Mapping of Ear Traits in Early-Maturing Maize Under Contrasting Planting Densities.International journal of molecular sciences · 2026Article
- Identification of septoria nodorum blotch susceptibility genes in hard winter wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Unlocking the potential of spring wheat genetic resources: uncovering resistance sources against leaf rust and yellow rust.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- High-Density Genome-Wide Association Mapping Identifies Candidate Loci Associated with Maize Stalk Cell Wall Composition.Plants (Basel, Switzerland) · 2026Article
- A yield-reducing introgression linked to sd1 in rice.The plant genome · 2026Article
- Genome-wide variation analysis of two Salvia hispanica L. genotypes and implication for associations with metabolic and adaptive traits.Journal, genetic engineering & biotechnology · 2026Article
- Integrative genomics and zero-shot deep learning-based phenotyping reveal the genetic architecture of seed traits in mungbean (Vigna radiata L.).The plant genome · 2026Article
- JanusX: an integrated and high-performance platform for scalable genome-wide association studies and genomic selection.The Plant journal : for cell and molecular biology · 2026Article
858 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
False positives in a Genome-Wide Association Study (GWAS) can be effectively controlled by a fixed effect and random effect Mixed Linear Model (MLM) that incorporates population structure and kinship among individuals to adjust association tests on markers; however, the adjustment also compromises true positives. The modified MLM method, Multiple Loci Linear Mixed Model (MLMM), incorporates multiple markers simultaneously as covariates in a stepwise MLM to partially remove the confounding between testing markers and kinship. To completely eliminate the confounding, we divided MLMM into two parts: Fixed Effect Model (FEM) and a Random Effect Model (REM) and use them iteratively. FEM contains testing markers, one at a time, and multiple associated markers as covariates to control false positives. To avoid model over-fitting problem in FEM, the associated markers are estimated in REM by using them to define kinship. The P values of testing markers and the associated markers are unified at each iteration. We named the new method as Fixed and random model Circulating Probability Unification (FarmCPU). Both real and simulated data analyses demonstrated that FarmCPU improves statistical power compared to current methods. Additional benefits include an efficient computing time that is linear to both number of individuals and number of markers. Now, a dataset with half million individuals and half million markers can be analyzed within three days.
Indexed as
Identifiers
What OpenQuestion holds
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.