- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Nielsen, D. M.
- Articles by Weir, B. S.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Nielsen, D. M.
- Articles by Weir, B. S.
Genetics, Vol. 168, 1029-1040, October 2004, Copyright © 2004
doi:10.1534/genetics.103.022335
Effect of Two- and Three-Locus Linkage Disequilibrium on the Power to Detect Marker/Phenotype Associations
Dahlia M. Nielsen*,1,
Margaret G. Ehm
,
Dmitri V. Zaykin and
Bruce S. Weir*
* Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695-7566
Department of Population Genetics, GlaxoSmithKline, Research Triangle Park, North Carolina 27709-3398
1 Corresponding author: 1503 Partners II Bldg., 840 Main Campus Dr., Raleigh, NC 27606.
E-mail: dahlia{at}statgen.ncsu.edu
There has been much recent interest in describing the patterns of linkage disequilibrium (LD) along a chromosome. Most empirical studies that have examined this issue have concentrated on LD between collections of pairs of markers and have not considered the joint effect of a group of markers beyond these pairwise connections. Here, we examine many different patterns of LD defined by both pairwise and joint multilocus LD terms. The LD patterns we considered were chosen in part by examining those seen in real data. We examine how changes in these patterns affect the power to detect association when performing single-marker and haplotype-based case-control tests, including a novel haplotype test based on contrasting LD between affected and unaffected individuals. Through our studies we find that differences in power between single-marker tests and haplotype-based tests in general do not appear to be large. Where moderate to high levels of multilocus LD exist, haplotype tests tend to be more powerful. Single-marker tests tend to prevail when pairwise LD is high. For moderate pairwise values and weak multilocus LD, either testing strategy may come out ahead, although it is also quite likely that neither has much power.
This article has been cited by other articles:
 |
|
 |
|
  D. V. Zaykin, A. Pudovkin, and B. S. Weir Correlation-Based Inference for Linkage Disequilibrium With Multiple Alleles Genetics, September 1, 2008; 180(1): 533 - 545. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Li, Y. Li, S. Wu, K. Han, Z. Wang, W. Hou, Y. Zeng, and R. Wu Estimation of Multilocus Linkage Disequilibria in Diploid Populations With Dominant Markers Genetics, July 1, 2007; 176(3): 1811 - 1821. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. H. Zhao, R. L. Fernando, and J. C. M. Dekkers Power and Precision of Alternate Methods for Linkage Disequilibrium Mapping of Quantitative Trait Loci Genetics, April 1, 2007; 175(4): 1975 - 1986. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Soller, S. Weigend, M. N. Romanov, J. C. M. Dekkers, and S. J. Lamont Strategies to Assess Structural Variation in the Chicken Genome and its Associations with Biodiversity and Biological Performance Poult. Sci., December 1, 2006; 85(12): 2061 - 2078. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. V. Zaykin and L. A. Zhivotovsky Ranks of Genuine Associations in Whole-Genome Scans Genetics, October 1, 2005; 171(2): 813 - 823. [Abstract] [Full Text] [PDF]
|
|