QTL

Statistical Genomics Course Notes (Stat 692)
Spring 2003
Brian S. Yandell (yandell@stat.wisc.edu)
www.stat.wisc.edu/~yandell/statgen/course/

These are notes built around a text in preparation titled ``Statistical Methods for Quantitative Trait Loci in Experimental Crosses'' by KW Broman, GA Churchill, BS Yandell, ZB Zeng. Numbered chapter/notes are mine; indented subheadings are links to useful ancillary material. Citations within my notes are to Quantitative Trait Loci References.

0 Overview

1 General Biology Relevant to QTL

Central Dogma of Molecular Biology, Access Excellence

Central Dogma, MIT Biology Hypertextbook

Meiosis Tutorial, Biology Project, U AZ

Nobel e-Museum:

• DNA-RNA-Protein
• DNA the Double Helix

Meiotic Cytology, DG Peterson, MS Genome Exploration Lab, MS St U

Introduction to Recombination and Linkage Analysis, MS McPeek, Statistics, UC Berkeley

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

2 Key Statistical Ideas for QTL

3 Marker Regression Analysis

4 Interval Mapping for Single QTL

5 Sample Size, Power & Thresholds

Experimental Design and Sample Size Requirement for QTL Mapping, ZB Zeng (2003), NCSU Bioinformatics, PAG XI

6 Model Selection for Multiple QTL

Assessment of Model Selection, KW Broman, Johns Hopkins U, & TP Speed, UC Berkeley

Mapping and characterizing QTL in inbred line crosses, GA Churchill (2001), Jackson Laboratory

Sillanpaa MJ, Arjas E (2002) Model choice in gene mapping: what and why. Trends in Genetics 18: 301-307.

7 Multiple QTL Implementation

Mapping and characterizing QTL in inbred line crosses, GA Churchill (2001), Jackson Laboratory

8 QTL for Multiple Crosses

Experimental Design and Sample Size Requirement for QTL Mapping, ZB Zeng (2003), NCSU Bioinformatics, PAG XI

Hardy-Weinberg & Linkage Disequilibrium (Yandell 2001 notes based on Zeng 2000 book draft)

Transmission Disequilbrium Test, Statistical Genetics, UC Berkeley, TP Speed

Finding Disease Genes, Human Genetics 500, Yale U, R Lifton

9 Multiple Traits and Environments

Jiang & Zeng (1995) CIM approach (Yandell 2001 notes based on Zeng 2000 book draft)

Gene Mapping for High Throughput Expression Profiles: Lessons from Diabetes (Yandell talk in Genetics Colloquium, 2000) [1.3M]

10 Extensions of the Phenotype Model

QTL References

Return to Statistical Genomics Course Page.

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www.stat.wisc.edu/~yandell/statgen/course/ by Brian Yandell (yandell@stat.wisc.edu)