Skip to main content

Model selection in binary trait locus mapping.

Publication ,  Journal Article
Coffman, CJ; Doerge, RW; Simonsen, KL; Nichols, KM; Duarte, CK; Wolfinger, RD; McIntyre, LM
Published in: Genetics
July 2005

Quantitative trait locus (QTL) mapping methodology for continuous normally distributed traits is the subject of much attention in the literature. Binary trait locus (BTL) mapping in experimental populations has received much less attention. A binary trait by definition has only two possible values, and the penetrance parameter is restricted to values between zero and one. Due to this restriction, the infinitesimal model appears to come into play even when only a few loci are involved, making selection of an appropriate genetic model in BTL mapping challenging. We present a probability model for an arbitrary number of BTL and demonstrate that, given adequate sample sizes, the power for detecting loci is high under a wide range of genetic models, including most epistatic models. A novel model selection strategy based upon the underlying genetic map is employed for choosing the genetic model. We propose selecting the "best" marker from each linkage group, regardless of significance. This reduces the model space so that an efficient search for epistatic loci can be conducted without invoking stepwise model selection. This procedure can identify unlinked epistatic BTL, demonstrated by our simulations and the reanalysis of Oncorhynchus mykiss experimental data.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Genetics

DOI

ISSN

0016-6731

Publication Date

July 2005

Volume

170

Issue

3

Start / End Page

1281 / 1297

Location

United States

Related Subject Headings

  • Oncorhynchus mykiss
  • Models, Statistical
  • Models, Genetic
  • Genes
  • Epistasis, Genetic
  • Developmental Biology
  • Computer Simulation
  • Chromosome Mapping
  • Animals
  • 3105 Genetics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Coffman, C. J., Doerge, R. W., Simonsen, K. L., Nichols, K. M., Duarte, C. K., Wolfinger, R. D., & McIntyre, L. M. (2005). Model selection in binary trait locus mapping. Genetics, 170(3), 1281–1297. https://doi.org/10.1534/genetics.104.033910
Coffman, Cynthia J., R. W. Doerge, Katy L. Simonsen, Krista M. Nichols, Christine K. Duarte, Russell D. Wolfinger, and Lauren M. McIntyre. “Model selection in binary trait locus mapping.Genetics 170, no. 3 (July 2005): 1281–97. https://doi.org/10.1534/genetics.104.033910.
Coffman CJ, Doerge RW, Simonsen KL, Nichols KM, Duarte CK, Wolfinger RD, et al. Model selection in binary trait locus mapping. Genetics. 2005 Jul;170(3):1281–97.
Coffman, Cynthia J., et al. “Model selection in binary trait locus mapping.Genetics, vol. 170, no. 3, July 2005, pp. 1281–97. Pubmed, doi:10.1534/genetics.104.033910.
Coffman CJ, Doerge RW, Simonsen KL, Nichols KM, Duarte CK, Wolfinger RD, McIntyre LM. Model selection in binary trait locus mapping. Genetics. 2005 Jul;170(3):1281–1297.

Published In

Genetics

DOI

ISSN

0016-6731

Publication Date

July 2005

Volume

170

Issue

3

Start / End Page

1281 / 1297

Location

United States

Related Subject Headings

  • Oncorhynchus mykiss
  • Models, Statistical
  • Models, Genetic
  • Genes
  • Epistasis, Genetic
  • Developmental Biology
  • Computer Simulation
  • Chromosome Mapping
  • Animals
  • 3105 Genetics