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Mammalian Genome

, Volume 17, Issue 6, pp 565–574 | Cite as

A comprehensive mouse IBD database for the efficient localization of quantitative trait loci

  • Alessandra C.L. CervinoEmail author
  • Mark Gosink
  • Mohammad Fallahi
  • Bruce Pascal
  • Christopher Mader
  • Nicholas F. Tsinoremas
Article

Abstract

Traditional fine-mapping approaches in mouse genetics that go from a linkage region to a candidate gene are very costly and time consuming. Shared ancestry regions, along with the combination of genetics and genomics approaches, provide a powerful tool to shorten the time and effort required to identify a causative gene. In this article we present a novel methodology that predicts IBD (identical by descent) regions between pairs of inbred strains using single nucleotide polymorphism (SNP) maps. We have validated this approach by comparing the IBD regions, estimated using different algorithms, to the results derived using the sequence information in the strains present in the Celera Mouse Database. We showed that based on the current publicly available SNP genotypes, large IBD regions (>1 Mb) can be identified successfully. By assembling a list of 21,514 SNPs in 61 common inbred strains, we inferred IBD regions between all pairs of strains and confirmed, for the first time, that existing quantitative trait genes (QTG) and susceptibility genes all lie outside of IBD regions. We also illustrated how knowledge of IBD structures can be applied to strain selection for future crosses. We have made our results available for data mining and download through a public website ( http://www.mouseibd. florida.scripps.edu).

Keywords

Single Nucleotide Polymorphism Inbred Strain Single Nucleotide Polymorphism Frequency Single Nucleotide Polymorphism Selection Celera Assembly 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors thank Ariel Darvasi for critical reading of the manuscript. This work was supported by the Florida Funding Corporation.

Supplementary material

supp.pdf (58 kb)

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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Alessandra C.L. Cervino
    • 1
    Email author
  • Mark Gosink
    • 1
  • Mohammad Fallahi
    • 1
  • Bruce Pascal
    • 1
  • Christopher Mader
    • 1
  • Nicholas F. Tsinoremas
    • 1
  1. 1.Department of InformaticsScripps FloridaJupiterUSA

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