ArticlePLoS genetics2008
How to perform meaningful estimates of genetic effects.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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.
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Who cites it
15 citing papers in PubMed.
- Article
- Analysis of Epistasis in Natural Traits Using Model Organisms.Trends in genetics : TIG · 2018Review
- Natural and orthogonal model for estimating gene-gene interactions applied to cutaneous melanoma.Human genetics · 2014Article
- Article
- Two-stage genome-wide search for epistasis with implementation to Recombinant Inbred Lines (RIL) populations.PloS one · 2014Article
- MAPfastR: quantitative trait loci mapping in outbred line crosses.G3 (Bethesda, Md.) · 2013Article
- Article
- Current applications of models of genetic effects with interactions across the genome.Current genomics · 2012Article
- Natural and orthogonal interaction framework for modeling gene-environment interactions with application to lung cancer.Human heredity · 2012Article
- Multiallelic models of genetic effects and variance decomposition in non-equilibrium populations.Genetica · 2011Article
- Evolution of pleiotropy: epistatic interaction pattern supports a mechanistic model underlying variation in genotype-phenotype map.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2011Article
- Article
- Epistasis--the essential role of gene interactions in the structure and evolution of genetic systems.Nature reviews. Genetics · 2008Review
- Dissection of the genetic architecture of body weight in chicken reveals the impact of epistasis on domestication traits.Genetics · 2008Article
- Estimation of genetic effects and genotype-phenotype maps.Evolutionary bioinformatics online · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the genotype-phenotype map plays a central role both in Quantitative and Evolutionary Genetics, the formalization of a completely general and satisfactory model of genetic effects, particularly accounting for epistasis, remains a theoretical challenge. Here, we use a two-locus genetic system in simulated populations with epistasis to show the convenience of using a recently developed model, NOIA, to perform estimates of genetic effects and the decomposition of the genetic variance that are orthogonal even under deviations from the Hardy-Weinberg proportions. We develop the theory for how to use this model in interval mapping of quantitative trait loci using Halley-Knott regressions, and we analyze a real data set to illustrate the advantage of using this approach in practice. In this example, we show that departures from the Hardy-Weinberg proportions that are expected by sampling alone substantially alter the orthogonal estimates of genetic effects when other statistical models, like F2 or G2A, are used instead of NOIA. Finally, for the first time from real data, we provide estimates of functional genetic effects as sets of effects of natural allele substitutions in a particular genotype, which enriches the debate on the interpretation of genetic effects as implemented both in functional and in statistical models. We also discuss further implementations leading to a completely general genotype-phenotype map.
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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.