Current Book Outline (ZBZ, 21 aug 2000)

1. Introduction
2. QTL Mapping Data
3. Linkage Map Analysis
4. Quantitative Genetic Models
5. Single Marker Analysis
6. Interval Mapping (IM)
7. Composite Interval Mapping (CIM)
8. Multiple Interval Mapping (MIM)
9. A General View and Directions for Extension
10. Dominant and Missing Marker Analysis
11. Multiple Trait Analysis

Proposed Book Outline (ZBZ & BSY, 17 nov 2000)

1. Introduction
   • software intro
2. Experimental Design and QTL Data
   • computation
   • data management
   • internet databases
   • R interface tools
3. Linkage Map Analysis
   • segregation
   • linkage
   • linkage phase
   • map functions
   • ordering markers (simulated annealing; branch and bound)
   • map construction
   • missing data (Markov chain; Jiang Zeng 1997)
4. Quantitative Genetic Models
   • partition of variance
   • linkage disequilibrium; Hardy-Weinberg equilibrium
   • least squares model
   • variance components
   • inbred line cross
   • multiple crosses
   • general model
5. Single Marker Analysis
   • t-test, F-test
6. Interval Mapping (IM)
   • least squares (Haley-Knott)
   • likelihood analysis, LOD
   • threshold: theory and permutation test
   • Dominant and Missing Marker Analysis
7. Non-normal Interval Mapping
   • exponential family data (Kendziorski; Newton Hoff)
   • semi-parametric (Zou Fine Yandell 2000)
   • non-parametric (Kruglyak Lander 1995)
8. Composite Interval Mapping (CIM)
9. Multiple Interval Mapping (MIM)
   • likelihood
   • model selection
   • epistasis (Cockerham vs Mather-Jenks)
10. Bayesian Analysis
    • single QTL (Satagopan et al. 1996)
    • multiple QTL (SY 1996, SF 1998, SA 1998)
    • inferring the number of QTL
    • epistasis
11. Combining Multiple Crosses
    • F2 and backcrosses
    • diallele
    • full sib
    • outbred populations
    • Fisch, Ragot; YF Liu & Zeng; Zou & Yandell; Huang (TDT); Xu; Bernardo; Roeder; Hoeschele; Thompson
12. Multiple Trait Analysis
    • principle components
    • direct multiple traits
    • time course, developmental
    • multiple environments
13. Threshold and Power Calculations
    • Lander Botstein 1989
    • Dupuis; Ragot; Piepho; Zou
    • Churchill-Doerge permutation tests for IM
    • permutation tests in CIM, MIM
14. Microarrays and QTLs
    • gene expression arrays (review of biology)
    • comparing two conditions (Chen et al; Newton et al)
    • experimental design for microarrays (Kerr Churchill)
    • clustering methods for microarrays (Eisen et al; Dudoit et al)
    • principle components and microarray experiments (Alter et al)
    • microarrays in F2 and BC experiments
    • microarrays and congenic lines
15. Appendix
    • Software review