Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees

Sang Hong Lee; Julius Herman Van Der Werf

Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees

Sang Hong Lee
, Julius Herman Van Der Werf

School of Environmental & Rural Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Linkage disequilibrium (LD) information from closely linked markers has been widely used to fine-map quantitative trait loci (QTL). Steps needed for fine-mapping of QTL include inferring inheritance state of markers (haplotyping), estimating identity by descent (IBD) at QTL, and implementing the covariance structure based on IBD into a statistical model. Appropriate pedigree-genotype analysis can estimate more accurate inheritance state and haplotype configuration, which results in more accurate IBD probabilities. A variance component approach can implement covariance coefficients based on IBD probabilities in a mixed linear model to fit additive, dominance and epistasis QTL effects. We have also implemented a reversible jump Markov chain Monte Carlo (MCMC) method for multiple QTL mapping to account for confounding effects between closely linked QTL. Simulation results have shown that this method can improve the precision of mapping QTL.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	AAABG: Association for the Advancement of Animal Breeding, Genetics
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	376-382
Volume	17
ISBN (Print)	1921208139
Publication status	Published - 2007
Event	AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics - University of New England, Armidale, Australia Duration: 23 Sept 2007 → 26 Sept 2007

Conference

Conference	AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Armidale, Australia
Period	23/09/07 → 26/09/07

Keywords

Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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https://hdl.handle.net/1959.11/4107

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Lee, S. H., & Van Der Werf, J. H. (2007). Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees. In AAABG. Association for the Advancement of Animal Breeding, & Genetics (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 17, pp. 376-382). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/4107

Lee, Sang Hong ; Van Der Werf, Julius Herman. / Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / AAABG: Association for the Advancement of Animal Breeding ; Genetics. Vol. 17 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2007. pp. 376-382

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title = "Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees",

abstract = "Linkage disequilibrium (LD) information from closely linked markers has been widely used to fine-map quantitative trait loci (QTL). Steps needed for fine-mapping of QTL include inferring inheritance state of markers (haplotyping), estimating identity by descent (IBD) at QTL, and implementing the covariance structure based on IBD into a statistical model. Appropriate pedigree-genotype analysis can estimate more accurate inheritance state and haplotype configuration, which results in more accurate IBD probabilities. A variance component approach can implement covariance coefficients based on IBD probabilities in a mixed linear model to fit additive, dominance and epistasis QTL effects. We have also implemented a reversible jump Markov chain Monte Carlo (MCMC) method for multiple QTL mapping to account for confounding effects between closely linked QTL. Simulation results have shown that this method can improve the precision of mapping QTL.",

keywords = "Quantitative Genetics (incl Disease and Trait Mapping Genetics)",

author = "Lee, \{Sang Hong\} and \{Van Der Werf\}, \{Julius Herman\}",

year = "2007",

language = "English",

isbn = "1921208139",

volume = "17",

pages = "376--382",

editor = "\{Association for the Advancement of Animal Breeding\}, AAABG: and Genetics",

booktitle = "Proceedings of the Association for the Advancement of Animal Breeding and Genetics",

publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

note = "AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 23-09-2007 Through 26-09-2007",

}

Lee, SH & Van Der Werf, JH 2007, Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees. in AAABG Association for the Advancement of Animal Breeding & Genetics (eds), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 17, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 376-382, AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics, Armidale, Australia, 23/09/07. <https://hdl.handle.net/1959.11/4107>

Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees. / Lee, Sang Hong; Van Der Werf, Julius Herman.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / AAABG: Association for the Advancement of Animal Breeding; Genetics. Vol. 17 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2007. p. 376-382.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees

AU - Lee, Sang Hong

AU - Van Der Werf, Julius Herman

PY - 2007

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N2 - Linkage disequilibrium (LD) information from closely linked markers has been widely used to fine-map quantitative trait loci (QTL). Steps needed for fine-mapping of QTL include inferring inheritance state of markers (haplotyping), estimating identity by descent (IBD) at QTL, and implementing the covariance structure based on IBD into a statistical model. Appropriate pedigree-genotype analysis can estimate more accurate inheritance state and haplotype configuration, which results in more accurate IBD probabilities. A variance component approach can implement covariance coefficients based on IBD probabilities in a mixed linear model to fit additive, dominance and epistasis QTL effects. We have also implemented a reversible jump Markov chain Monte Carlo (MCMC) method for multiple QTL mapping to account for confounding effects between closely linked QTL. Simulation results have shown that this method can improve the precision of mapping QTL.

AB - Linkage disequilibrium (LD) information from closely linked markers has been widely used to fine-map quantitative trait loci (QTL). Steps needed for fine-mapping of QTL include inferring inheritance state of markers (haplotyping), estimating identity by descent (IBD) at QTL, and implementing the covariance structure based on IBD into a statistical model. Appropriate pedigree-genotype analysis can estimate more accurate inheritance state and haplotype configuration, which results in more accurate IBD probabilities. A variance component approach can implement covariance coefficients based on IBD probabilities in a mixed linear model to fit additive, dominance and epistasis QTL effects. We have also implemented a reversible jump Markov chain Monte Carlo (MCMC) method for multiple QTL mapping to account for confounding effects between closely linked QTL. Simulation results have shown that this method can improve the precision of mapping QTL.

KW - Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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M3 - Conference contribution

SN - 1921208139

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BT - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

A2 - Association for the Advancement of Animal Breeding, AAABG:

A2 - Genetics, null

PB - Association for the Advancement of Animal Breeding and Genetics (AAABG)

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Y2 - 23 September 2007 through 26 September 2007

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Lee SH, Van Der Werf JH. Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees. In Association for the Advancement of Animal Breeding AAABG, Genetics, editors, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 17. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2007. p. 376-382

Fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage with general pedigrees

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