RT Journal
A1 Aylor, David L.
A1 Valdar, William
A1 Foulds-Mathes, Wendy
A1 Buus, Ryan J.
A1 Verdugo, Ricardo A.
A1 Baric, Ralph S.
A1 Ferris, Martin T.
A1 Frelinger, Jeff A.
A1 Heise, Mark
A1 Frieman, Matt B.
A1 Gralinski, Lisa E.
A1 Bell, Timothy A.
A1 Didion, John D.
A1 Hua, Kunjie
A1 Nehrenberg, Derrick L.
A1 Powell, Christine L.
A1 Steigerwalt, Jill
A1 Xie, Yuying
A1 Kelada, Samir N.P.
A1 Collins, Francis S.
A1 Yang, Ivana V.
A1 Schwartz, David A.
A1 Branstetter, Lisa A.
A1 Chesler, Elissa J.
A1 Miller, Darla R.
A1 Spence, Jason
A1 Liu, Eric Yi
A1 McMillan, Leonard
A1 Sarkar, Abhishek
A1 Wang, Jeremy
A1 Wang, Wei
A1 Zhang, Qi
A1 Broman, Karl W.
A1 Korstanje, Ron
A1 Durrant, Caroline
A1 Mott, Richard
A1 Iraqi, Fuad A.
A1 Pomp, Daniel
A1 Threadgill, David
A1 Pardo-Manuel de Villena, Fernando
A1 Churchill, Gary A.
T1 Genetic analysis of complex traits in the emerging Collaborative Cross
JF Genome Research 
JO Genome Research 
YR 2011 
FD August 01 
VO 21 
IS 8 
SP 1213 
OP 1222 
DO 10.1101/gr.111310.110 
UL http://genome.cshlp.org/content/21/8/1213.abstract 
AB The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites—all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping approaches. Analysis based on inferred haplotypes improves power, reduces false discovery, and provides information to identify and prioritize candidate genes that is unique to multifounder crosses like the CC. The number of expression QTLs discovered here exceeds all previous efforts at eQTL mapping in mice, and we map local eQTL at 1-Mb resolution. We demonstrate that the genetic diversity of the CC, which derives from random mixing of eight founder strains, results in high phenotypic diversity and enhances our ability to map causative loci underlying complex disease-related traits.