ArticleGenetics2014
Recovering power in association mapping panels with variable levels of linkage disequilibrium.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 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
59 citing papers in PubMed.
- Comparative genomic analysis of QTL for resistance to Aphanomyces euteiches between pea, lentil, faba bean, and the model species Medicago truncatula.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Multi-environment GWAS uncovers markers associated to biotic stress response and genotype-by-environment interactions in stone fruit trees.Horticulture research · 2025Article
- Genome-wide association for agro-morphological traits in a triploid banana population with large chromosome rearrangements.Horticulture research · 2025Article
- Genetic variability of aquaporin expression in maize: From eQTLs to a MITE insertion regulating PIP2;5 expression.Plant physiology · 2024Article
- Envirotyping within a multi-environment trial allowed identifying genetic determinants of winter oilseed rape yield stability.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Multi-trait association mapping for phosphorous efficiency reveals flexible root architectures in sorghum.BMC plant biology · 2024Article
- Genomic and phenomic predictions help capture low-effect alleles promoting seed germination in oilseed rape in addition to QTL analyses.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Maize green leaf area index dynamics: genetic basis of a new secondary trait for grain yield in optimal and drought conditions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Different wheat loci are associated to heritable free asparagine content in grain grown under different water and nitrogen availability.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Plasticity QTLs specifically contribute to the genotype × water availability interaction in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Identifying QTLs involved in hybrid performance and heterotic group complementarity: new GWAS models applied to factorial and admixed diallel maize hybrid panels.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2023Article
- Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-ProducingMicroorganisms · 2023Article
- Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola.The plant genome · 2022Article
- COMPILE: a GWAS computational pipeline for gene discovery in complex genomes.BMC plant biology · 2022Article
- A major-effect genetic locus, ApRVII, controlling resistance against both adapted and non-adapted aphid biotypes in pea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- A multi-environment framework to evaluate the adaptation of wheat (Triticum aestivum) to heat stress.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Identification of QTLs affecting post-anthesis heat stress responses in European bread wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Efficient ReML inference in variance component mixed models using a Min-Max algorithm.PLoS computational biology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Association mapping has permitted the discovery of major QTL in many species. It can be applied to existing populations and, as a consequence, it is generally necessary to take into account structure and relatedness among individuals in the statistical model to control false positives. We analytically studied power in association studies by computing noncentrality parameter of the tests and its relationship with parameters characterizing diversity (genetic differentiation between groups and allele frequencies) and kinship between individuals. Investigation of three different maize diversity panels genotyped with the 50k SNPs array highlighted contrasted average power among panels and revealed gaps of power of classical mixed models in regions with high linkage disequilibrium (LD). These gaps could be related to the fact that markers are used for both testing association and estimating relatedness. We thus considered two alternative approaches to estimating the kinship matrix to recover power in regions of high LD. In the first one, we estimated the kinship with all the markers that are not located on the same chromosome than the tested SNP. In the second one, correlation between markers was taken into account to weight the contribution of each marker to the kinship. Simulations revealed that these two approaches were efficient to control false positives and were more powerful than classical models.
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.