Skip to main content
SpringerLink
Log in
Book cover

Cardiovascular Genomics pp 175–188Cite as

Quantitative Trait Locus Analysis Using J/qtl

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 573))

Abstract

Quantitative trait locus (QTL) analysis is a statistical method to link phenotypes with regions of the genome that affect the phenotypes in a mapping population. R/qtl is a powerful statistical program commonly used for analyzing rodent QTL crosses, but R/qtl is a command line program that can be difficult for novice users to run. J/qtl was developed as an R/qtl graphical user interface that enables even novice users to utilize R/qtl for QTL analyses. In this chapter, we describe the process for analyzing rodent cross data with J/qtl, including data formatting, data quality control, main scan QTL analysis, pair scan QTL analysis, and multiple regression modeling; this information should enable new users to identify QTL affecting phenotypes of interest within their rodent cross datasets.

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

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   139.00
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. Doerge, RW. (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3(1): 43–52.

    Article  PubMed  CAS  Google Scholar 

  2. Broman, KW. (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Anim 30(7): 44–52.

    CAS  Google Scholar 

  3. Broman, KW, Wu, H, Sen, S, et al. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19(7): 889–890.

    Article  PubMed  CAS  Google Scholar 

  4. Churchill, GA, Doerge, RW. (1994) Empirical threshold values for quantitative trait mapping. Genetics 138(3): 963–971.

    PubMed  CAS  Google Scholar 

  5. Dempster, AP, Laird, NM, Rubin, DB (1977) Maximum likelihood from incomplete data via Em algorithm. J R Stat Soc Ser B-Methodol 39(1): 1–38.

    Google Scholar 

  6. Sen, S, Churchill, GA, (2001) A statistical framework for quantitative trait mapping. Genetics 159(1): 371–387.

    PubMed  CAS  Google Scholar 

  7. Haley, CS, Knott, SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315–324.

    Article  PubMed  CAS  Google Scholar 

  8. Soller, M, Brody, T, Genizi, A (1976) Power of experimental designs for detection of linkage between marker loci and quantitative loci in crosses between inbred lines. Theor Appl Gen 47(1): 35–39.

    Article  Google Scholar 

Download references

Acknowledgments

We are grateful to Sharon Tsaih and Qian Li for preparing the summary table and several figures.

Author information

Authors and Affiliations

  1. The Jackson Laboratory, Bar Harbor, ME, USA

    Randy Smith, Keith Sheppard & Gary Churchill

  2. Novartis Institutes for BioMedical Research and Novartis Pharmaceutical Corporation, East Hanover, NJ, USA

    Keith DiPetrillo

Authors
  1. Randy Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Keith Sheppard
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Keith DiPetrillo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gary Churchill
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Research, Novartis Institute for Biomedical, Health Plaza 1, East Hanover, 07936, U.S.A.

    Keith DiPetrillo

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Smith, R., Sheppard, K., DiPetrillo, K., Churchill, G. (2009). Quantitative Trait Locus Analysis Using J/qtl. In: DiPetrillo, K. (eds) Cardiovascular Genomics. Methods in Molecular Biology™, vol 573. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-247-6_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-247-6_10

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-246-9

  • Online ISBN: 978-1-60761-247-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation