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Open Access Research article

An experimental assessment of in silico haplotype association mapping in laboratory mice

Sarah L Burgess-Herbert12, Shirng-Wern Tsaih1, Ioannis M Stylianou13, Kenneth Walsh1, Allison J Cox1 and Beverly Paigen1*

Author affiliations

1 The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA

2 Current address: San Diego Zoo Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA

3 Current address: University of Pennsylvania, School of Medicine, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104, USA

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Citation and License

BMC Genetics 2009, 10:81  doi:10.1186/1471-2156-10-81

Published: 9 December 2009



To assess the utility of haplotype association mapping (HAM) as a quantitative trait locus (QTL) discovery tool, we conducted HAM analyses for red blood cell count (RBC) and high density lipoprotein cholesterol (HDL) in mice. We then experimentally tested each HAM QTL using published crosses or new F2 intercrosses guided by the haplotype at the HAM peaks.


The HAM for RBC, using 33 classic inbred lines, revealed 8 QTLs; 2 of these were true positives as shown by published crosses. A HAM-guided (C57BL/6J × CBA/J)F2 intercross we carried out verified 2 more as true positives and 4 as false positives. The HAM for HDL, using 81 strains including recombinant inbred lines and chromosome substitution strains, detected 46 QTLs. Of these, 36 were true positives as shown by published crosses. A HAM-guided (C57BL/6J × A/J)F2 intercross that we carried out verified 2 more as true positives and 8 as false positives. By testing each HAM QTL for RBC and HDL, we demonstrated that 78% of the 54 HAM peaks were true positives and 22% were false positives. Interestingly, all false positives were in significant allelic association with one or more real QTL.


Because type I errors (false positives) can be detected experimentally, we conclude that HAM is useful for QTL detection and narrowing. We advocate the powerful and economical combined approach demonstrated here: the use of HAM for QTL discovery, followed by mitigation of the false positive problem by testing the HAM-predicted QTLs with small HAM-guided experimental crosses.