BMI 826-001: Statistical methods for QTL mapping (Fall, 2012)

Course summary

QTL are quantitative trait loci: genetic loci that contribute to variation in a quantitative trait (such as body weight or blood pressure). In this course, we will give an overview of statistical methods for mapping QTL in experimental crosses.

The course will focus largely on mouse genetics; however, it should also be valuable to students interested in human genetics or in animal and plant breeding. Mouse crosses are simple, and discussion of QTL mapping in this context can allow the basic principles to be elucidated with greater clarity.

The course will be aimed at PhD students in Biostatistics & Medical Informatics or Statistics, though we also welcome graduate students from the biological sciences. The statistical aspects should be accessible to any student with knowledge of analysis of variance and linear regression.

Prerequisites: Genetics 466 or equivalent; one of Statistics 310, 571, 610, or 710, or equivalent (that is, some basic statistics course); some knowledge of R


Karl Broman
Office: 4710 Medical Sciences Center [directions]
Email: kbroman at
Phone: 608-262-4633
Office hours: Tu 2-3pm, or by appointment


TR 9:30-10:45am, 1209 Engr Hall
Sep 4 - Nov 15, 2012, but no lecture Oct 4, Oct 30, and Nov 1


Here (as pdf)




KW Broman, Ś Sen (2009) A Guide to QTL Mapping with R/qtl. Springer. [Amazon | Online complements]


P Dalgaard (2008) Introductory Statistics with R, 2nd edition. Springer. [Amazon]
WN Venables, BD Ripley (2002) Modern Applied Statistics with S, 4th edition. Springer. [Amazon | Online complements]

Computer software

We will use R ( and R/qtl (

Basis for grading:

4 equally-weighted homeworks/labs

Last modified: Fri Nov 23 11:20:06 2012