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doi:10.1534/genetics.105.052720
A more recent version of this article appeared on June 1, 2006.
REGULAR RESEARCH PAPERS |
Association mapping with Single-Feature Polymorphisms
Sung Kim 1, Keyan Zhao 1, Rong Jiang 1, John Molitor 1, Justin Borevitz 2, Magnus Nordborg 1 and Paul Marjoram 1*
1 USC
2 University of Chicago
* To whom correspondence should be addressed. E-mail: pmarjora{at}usc.edu.
Submitted on October 22, 2005
Revised on December 6, 2005
Accepted on 21 February 2006
We develop methods for exploiting "Single-Feature Polymorphism'' data, generated by hybridizing genomic DNA to oligonucleotide expression arrays. Our methods enable the use of such data, which can be regarded as very high density, but imperfect, polymorphism data, for genome-wide association or linkage disequilibrium mapping. We use a simulation-based power study to conclude that our methods should have good power for organisms like Arabidopsis thaliana, in which linkage disequilibrium is extensive, the reason being that the noisiness of Single-Feature Polymorphism data is more than compensated for by their great number. Finally, we show how power depends on the accuracy with which Single-Feature Polymorphisms are called.
Key Words: association mapping, linkage disequilibrium
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