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Cardiovascular Genomics pp 175–188Cite as

Quantitative Trait Locus Analysis Using J/qtl

Part of the Methods in Molecular Biology™ book series (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.

Key words

  • Quantitative trait locus analysis
  • QTL

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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
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  2. Keith Sheppard
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  3. Keith DiPetrillo
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  4. Gary Churchill
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Editor information

Editors and Affiliations

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

    Keith DiPetrillo

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

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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

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

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-246-9

  • Online ISBN: 978-1-60761-247-6

  • eBook Packages: Springer Protocols

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