ArticleGenetics2005
Quantitative trait locus study design from an information perspective.
Article in Genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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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.
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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
19 citing papers in PubMed.
- Genetic mapping in collaborative cross mouse strains identifies loci that affect initial sensitivity to cocaine.Psychopharmacology · 2026Article
- Diversity Outbred Mice Reveal the Quantitative Trait Locus and Regulatory Cells of HER2 Immunity.Journal of immunology (Baltimore, Md. : 1950) · 2020Article
- Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L.) Merr.] Seed Protein and Oil QTLs.G3 (Bethesda, Md.) · 2016Article
- Genetic, morphometric, and behavioral factors linked to the midsagittal area of the corpus callosum.Frontiers in genetics · 2012Article
- Multiple Quantitative Trait Loci Influence the Shape of a Male-Specific Genital Structure in Drosophila melanogaster.G3 (Bethesda, Md.) · 2011Article
- Article
- Genetic analysis of genome-scale recombination rate evolution in house mice.PLoS genetics · 2011Article
- Combining DNA pooling with selective recombinant genotyping for increased efficiency in fine mapping.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- Quantitative trait loci for exercise training responses in FVB/NJ and C57BL/6J mice.Physiological genomics · 2009Article
- Aging in inbred strains of mice: study design and interim report on median lifespans and circulating IGF1 levels.Aging cell · 2009Article
- Article
- Mapping quantitative trait loci from a single-tail sample of the phenotype distribution including survival data.Genetics · 2007Article
- R/qtlDesign: inbred line cross experimental design.Mammalian genome : official journal of the International Mammalian Genome Society · 2007Article
- Sequential quantitative trait locus mapping in experimental crosses.Statistical applications in genetics and molecular biology · 2007Article
- Heritability and tissue specificity of expression quantitative trait loci.PLoS genetics · 2006Article
- Mapping quantitative trait loci by an extension of the Haley-Knott regression method using estimating equations.Genetics · 2006Article
- A review of statistical methods for expression quantitative trait loci mapping.Mammalian genome : official journal of the International Mammalian Genome Society · 2006Review
- Article
- Integrated analysis of genetic data with R.Human genomics · 2006Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We examine the efficiency of different genotyping and phenotyping strategies in inbred line crosses from an information perspective. This provides a mathematical framework for the statistical aspects of QTL experimental design, while guiding our intuition. Our central result is a simple formula that quantifies the fraction of missing information of any genotyping strategy in a backcross. It includes the special case of selectively genotyping only the phenotypic extreme individuals. The formula is a function of the square of the phenotype and the uncertainty in our knowledge of the genotypes at a locus. This result is used to answer a variety of questions. First, we examine the cost-information trade-off varying the density of markers and the proportion of extreme phenotypic individuals genotyped. Then we evaluate the information content of selective phenotyping designs and the impact of measurement error in phenotyping. A simple formula quantifies the information content of any combined phenotyping and genotyping design. We extend our results to cover multigenotype crosses, such as the F(2) intercross, and multiple QTL models. We find that when the QTL effect is small, any contrast in a multigenotype cross benefits from selective genotyping in the same manner as in a backcross. The benefit remains in the presence of a second unlinked QTL with small effect (explaining <20% of the variance), but diminishes if the second QTL has a large effect. Software for performing power calculations for backcross and F(2) intercross incorporating selective genotyping and marker spacing is available from http://www.biostat.ucsf.edu/sen.
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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.