ArticleGenetics2010
Identity-by-descent matrix decomposition using latent ancestral allele models.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 20 citations in OpenAlex.
- How do the type of QTL effect and the form of the residual term influence QTL detection in multi-parent populations? A case study in the maize EU-NAM population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- Article
- Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships.Genetics · 2015Article
- PIGS: improved estimates of identity-by-descent probabilities by probabilistic IBD graph sampling.BMC bioinformatics · 2015Article
- Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield.Journal of experimental botany · 2014Article
- Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- QTL linkage analysis of connected populations using ancestral marker and pedigree information.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
Genetic linkage and association studies are empowered by proper modeling of relatedness among individuals. Such relatedness can be inferred from marker and/or pedigree information. In this study, the genetic relatedness among n inbred individuals at a particular locus is expressed as an n x n square matrix Q. The elements of Q are identity-by-descent probabilities, that is, probabilities that two individuals share an allele descended from a common ancestor. In this representation the definition of the ancestral alleles and their number remains implicit. For human inspection and further analysis, an explicit representation in terms of the ancestral allele origin and the number of alleles is desirable. To this purpose, we decompose the matrix Q by a latent class model with K classes (latent ancestral alleles). Let P be an n x K matrix with assignment probabilities of n individuals to K classes constrained such that every element is nonnegative and each row sums to 1. The problem then amounts to approximating Q by PP(T), while disregarding the diagonal elements. This is not an eigenvalue problem because of the constraints on P. An efficient algorithm for calculating P is provided. We indicate the potential utility of the latent ancestral allele model. For representative locus-specific Q matrices constructed for a set of maize inbreds, the proposed model recovered the known ancestry.
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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.