A Population‐based Latent Variable Approach for Association Mapping of Quantitative Trait Loci

@article{Wang2006APL,
  title={A Population‐based Latent Variable Approach for Association Mapping of Quantitative Trait Loci},
  author={Tao Wang and Bruce S. Weir and Zhao-Bang Zeng},
  journal={Annals of Human Genetics},
  year={2006},
  volume={70}
}
A population‐based latent variable approach is proposed for association mapping of quantitative trait loci (QTL), using multiple closely linked genetic markers within a small candidate region in the genome. By incorporating QTL as latent variables into a penetrance model, the QTL are flexible to characterize either alleles at putative trait loci or potential risk haplotypes/sub‐haplotypes of the markers. Under a general likelihood framework, we develop an EM‐based algorithm to estimate genetic… 
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Author Index
  • Biology
  • 2006
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High-Resolution mtDNA Studies of the Indian Population: Implications for Palaeolithic Settlement of theIndian Subcontinent, 42 Bastos-Rodrigues, L., Pimenta, J. R., Pena, S. J. see Wheeler et al.
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References

SHOWING 1-10 OF 65 REFERENCES
A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis.
TLDR
A new statistical method for mapping quantitative trait loci (QTL) of additive, dominant, and epistatic effects in equilibrium natural populations and can detect marker-QTL disequilibria of different orders and QTL epistatic interactions of various kinds on the basis of a multilocus analysis is presented.
Modeling and inferring quantitative trait loci using linkage disequilibrium in natural populations.
TLDR
The main research of the thesis is on development of an exact multipoint likelihood approach to infer QTL in natural populations and discusses the advantages as well as limitations of the approach developed in this thesis.
Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci.
  • Z. Zeng
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1993
It is now possible to use complete genetic linkage maps to locate major quantitative trait loci (QTLs) on chromosome regions. The current methods of QTL mapping (e.g., interval mapping, which uses a…
Estimating the genetic architecture of quantitative traits.
TLDR
One application of the analysis is to improve genome-wide marker-assisted selection, particularly when the information about epistasis is used for selection with mating, as well as other areas that require further investigation.
On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals
TLDR
SPTA controls for population stratification through a set of genomic markers by first deriving a genetic background variable for each sampled individual through his/her genotypes at a series of independent markers, and then modeling the relationship between trait values, genotypic scores at the candidate marker, and genetic background variables through a semiparametric model.
Modeling Quantitative Trait Loci and Interpretation of Models
TLDR
A quantitative genetic model relates the genotypic value of an individual to the alleles at the loci that contribute to the variation in a population in terms of additive, dominance, and epistatic effects and proposes a number of models to describe this relationship.
Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci.
TLDR
A multimarker linkage disequilibrium mapping method was developed for the fine mapping of quantitative trait loci (QTL) using a dense marker map, which showed that a QTL was correctly positioned within a region of 3, 1.5, or 0.75 cM.
Inferring linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations.
TLDR
Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas thePower of ANVA and regression analyses is relatively independent from the allelic frequency.
A classical setting for associations between markers and loci affecting quantitative traits.
TLDR
It is considered that this greater-than-usual level of generality leads to additional insights, in a way reminiscent of Cockerham's decomposition of genetic variance into five terms: three terms in addition to the usual additive and dominance terms.
Precision mapping of quantitative trait loci.
  • Z. Zeng
  • Biology, Medicine
    Genetics
  • 1994
TLDR
A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression, an interval test in which the test statistic on a marker interval is made to be unaffected by QTLs located outside a defined interval.
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