ArticlePloS one2008
Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysis.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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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Who cites it
26 citing papers in PubMed, 38 citations in OpenAlex.
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- Fine-mapping QTLs in advanced intercross lines and other outbred populations.Mammalian genome : official journal of the International Mammalian Genome Society · 2014Review
- Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice.Genome biology · 2014Article
- MAPfastR: quantitative trait loci mapping in outbred line crosses.G3 (Bethesda, Md.) · 2013Article
- Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding.Rice (New York, N.Y.) · 2013Article
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- Location-dependent empirical thresholds for quantitative trait mapping.G3 (Bethesda, Md.) · 2012Article
- Identification of novel mouse genes conferring posthypoxic pauses.Journal of applied physiology (Bethesda, Md. : 1985) · 2012Article
- A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during domestication.PLoS genetics · 2012Article
- Identification of quantitative trait loci influencing skeletal architecture in mice: emergence of Cdh11 as a primary candidate gene regulating femoral morphology.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2011Article
- Exercise, weight loss, and changes in body composition in mice: phenotypic relationships and genetic architecture.Physiological genomics · 2011Article
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Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundAdvanced intercross lines (AIL) are segregating populations created using a multi-generation breeding protocol for fine mapping complex trait loci (QTL) in mice and other organisms. Applying QTL mapping methods for intercross and backcross populations, often followed by naïve permutation of individuals and phenotypes, does not account for the effect of AIL family structure in which final generations have been expanded and leads to inappropriately low significance thresholds. The critical problem with naïve mapping approaches in AIL populations is that the individual is not an exchangeable unit. METHODOLOGY/PRINCIPAL
findingsThe effect of family structure has immediate implications for the optimal AIL creation (many crosses, few animals per cross, and population expansion before the final generation) and we discuss these and the utility of AIL populations for QTL fine mapping. We also describe Genome Reshuffling for Advanced Intercross Permutation, (GRAIP) a method for analyzing AIL data that accounts for family structure. GRAIP permutes a more interchangeable unit in the final generation crosses - the parental genome - and simulating regeneration of a permuted AIL population based on exchanged parental identities. GRAIP determines appropriate genome-wide significance thresholds and locus-specific P-values for AILs and other populations with similar family structures. We contrast GRAIP with naïve permutation using a large densely genotyped mouse AIL population (1333 individuals from 32 crosses). A naïve permutation using coat color as a model phenotype demonstrates high false-positive locus identification and uncertain significance levels, which are corrected using GRAIP. GRAIP also detects an established hippocampus weight locus and a new locus, Hipp9a. CONCLUSIONS AND SIGNIFICANCE: GRAIP determines appropriate genome-wide significance thresholds and locus-specific P-values for AILs and other populations with similar family structures. The effect of family structure has immediate implications for the optimal AIL creation and we discuss these and the utility of AIL populations.
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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.