Skip to main content

Complex Trait Analyses of the Collaborative Cross: Tools and Databases

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1488))

Abstract

The Collaborative cross (CC) is a powerful mouse resource for investigating complex genetic traits. Here we discuss various tools and techniques for gene mapping and identification using the CC. The data analyses procedures are illustrated with examples.

This is a preview of subscription content, log in via an institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Threadgill DW, Miller DR, Churchill GA, de Villena FP (2011) The collaborative cross: a recombinant inbred mouse population for the systems genetic era. ILAR J 52:24–31

    Article  CAS  PubMed  Google Scholar 

  2. Collaborative Cross Consortium (2012) The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 190:389–401

    Article  PubMed Central  Google Scholar 

  3. Morahan G, Balmer L, Monley D (2008) Establishment of “The Gene Mine”: a resource for rapid identification of complex trait genes. Mamm Genome 19:390–393

    Article  PubMed  Google Scholar 

  4. Chesler EJ, Miller DR, Branstetter LR, Galloway LD, Jackson BL, Philip VM, Voy BH, Culiat CT, Threadgill DW, Williams RW, Churchill GA, Johnson DK, Manly KF (2008) The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics. Mamm Genome 19:382–389

    Article  PubMed  PubMed Central  Google Scholar 

  5. Iraqi FA, Churchill G, Mott R (2008) The Collaborative Cross, developing a resource for mammalian systems genetics: a status report of the Wellcome Trust cohort. Mamm Genome 19:379–381

    Article  PubMed  Google Scholar 

  6. Threadgill DW, Churchill GA (2012) Ten years of the Collaborative Cross. Genetics 190:291–294

    Article  PubMed  PubMed Central  Google Scholar 

  7. Ram R, Mehta M, Balmer L, Gatti DM, Morahan G (2014) Rapid identification of major-effect genes using the collaborative cross. Genetics 198:75–86

    Article  PubMed  PubMed Central  Google Scholar 

  8. Ferguson B, Ram R, Handoko HY, Mukhopadhyay P, Muller HK, Soyer HP, Morahan G, Walker GJ (2015) Melanoma susceptibility as a complex trait: genetic variation controls all stages of tumor progression. Oncogene 34:2879–2886

    Article  CAS  PubMed  Google Scholar 

  9. Weerasekera LY, Balmer L, Ram R, Morahan G (2015) Characterization of retinal vascular and neural damage in a novel model of diabetic retinopathy. Invest Ophthalmol Vis Sci 56:3721–3730

    Article  CAS  PubMed  Google Scholar 

  10. Didion JP, Buus RJ, Naghashfar Z, Threadgill DW, Morse HC, de Villena FP (2014) SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy. BMC Genomics 15:847

    Article  PubMed  PubMed Central  Google Scholar 

  11. Durrant C, Tayem H, Yalcin B, Cleak J, Goodstadt L, de Villena FP, Mott R, Iraqi FA (2011) Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection. Genome Res 21:1239–1248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellåker C, Goodstadt L, Nicod J, Bhomra A, Hernandez-Pliego P, Whitley H, Cleak J, Dutton R, Janowitz D, Mott R, Adams DJ, Flint J (2011) Sequence-based characterization of structural variation in the mouse genome. Nature 477:326–329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178:1709–1723

    Article  PubMed  PubMed Central  Google Scholar 

  14. Mott R, Talbot CJ, Turri MG, Collins AC, Flint J (2000) A method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci 97:12649–12654

    Article  PubMed  PubMed Central  Google Scholar 

  15. Zheng C, Boer MP, Eeuwijk FA (2015) Reconstruction of genome ancestry blocks in multiparental populations. Genetics 200:1073–1087

    Article  PubMed  PubMed Central  Google Scholar 

  16. Broman KW, Sen S (2009) A guide to Qtl mapping with R/Qtl. Statistics for biology and health. Springer, Dordrecht

    Book  Google Scholar 

  17. Fernández JR, Etzel C, Beasley TM, Shete S, Amos CI, Allison DB (2002) Improving the power of sib pair quantitative trait loci detection by phenotype winsorization. Hum Hered 53:59–67

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from the Diabetes Research Foundation of Western Australia and the National Health and Medical Research Council (1069173), Australia.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Grant Morahan .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Ram, R., Morahan, G. (2017). Complex Trait Analyses of the Collaborative Cross: Tools and Databases. In: Schughart, K., Williams, R. (eds) Systems Genetics. Methods in Molecular Biology, vol 1488. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6427-7_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6427-7_5

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6425-3

  • Online ISBN: 978-1-4939-6427-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics