Optimal Design of Genetic Studies of Gene Expression With Two-Color Microarrays in Outbred Crosses
Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes. Efficient use of microarrays is paramount in experimental design as the cost of conducting this type...
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Published in | Genetics (Austin) Vol. 180; no. 3; pp. 1691 - 1698 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
United States
Genetics Soc America
01.11.2008
Genetics Society of America |
Subjects | |
Online Access | Get full text |
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Summary: | Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes. Efficient use of microarrays is paramount in experimental design as the cost of conducting this type of study is high. For those organisms where recombinant inbred lines are available for mapping, the "distant pair design" maximizes the number of informative contrasts over all marker loci. Here, we describe an extension of this design, named the "optimal pair design," for use with F2 crosses between outbred lines. The performance of this design is investigated by simulation and compared to several other two-color microarray designs. We show that, for a given number of microarrays, the optimal pair design outperforms all other designs considered for detection of expression quantitative trait loci (eQTL) with additive effects by linkage analysis. We also discuss the suitability of this design for outbred crosses in organisms with large genomes and for detection of dominance. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Communicating editor: R. W. Doerge Corresponding author: Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, United Kingdom. E-mail: alex.lam@roslin.ed.ac.uk |
ISSN: | 0016-6731 1943-2631 1943-2631 |
DOI: | 10.1534/genetics.108.090308 |