Special Topics in Genetics and Genomics (140.668)

Second Term, 2006-2007

Instructor:		Karl Broman
Office hours:		F 10:30-12:00 in E3612 Wolfe St
Topic:		Mapping quantitative trait loci in experimental crosses
Prerequisites:		140.651-654; knowledge of the computer package R.
Course time:		Monday and Wednesday, 10:30 - 11:50am
Course room:		W4007 SPH
Software:		R and R/qtl
Grades:		Class discussion and a final project.
Final project:		Visit the QTL archive, and register and select a data set. Analyze the data, and write a short (5-10 pages) paper describing the data, your analysis methods, and your results. If possible, compare your results to the other publications on the chosen data.

Syllabus

Date		Topic
Oct	30	Overview of QTL mapping
Nov	1	Meiosis, recombination, and crossover interference
	6	Discussion of readings
	8	Hidden Markov models
	13	Discussion of readings
	15	Standard interval mapping
	20	Discussion of readings
	22	Interval mapping variants
	27	Discussion of readings
	29	Interval mapping with other phenotype models
Dec	4	Discussion of readings Sample R/qtl code: [prepData.R | analysis.R]
	6	Covariates, composite interval mapping
	11	Discussion of readings
	13	2d scans, multiple QTL analysis
	18	Discussion of readings
	20	More modern things

Course home page

Last modified: Wed Apr 15 23:09:22 2009