Statistical Genomics Syllabus
Numbers in parentheses after topic area signify chapter(s) in Liu's book.
Subtopics in parentheses are not covered in the text, but are of related interest.
We can discuss papers and/or books that extend coverage as needed.
This syllabus at present overlooks important statistical issues in
DNA/RNA Sequence Analysis and in Molecular Evolution, in which the
genome is studied at a much finer scale. This could be incorporated
as a minor or major component of such a course depending on interest.
Fall 1998 Semester
- Genomics: Basic Biology (1-3)
- Mendelian genetics
- Hardy-Weinberg equilibrium, gene & allele frequency
- single gene model, trait models, & heritability
- molecular genetics: DNA to RNA to protein
- genomics: genome, mapping populations, markers
- Likelihood-Based Methodology (4)
- commonly used distributions
- likelihood ratio principle
- least squares vs. maximum likelihood
- hypothesis tests, estimation & sample size
- profile likelihood & the EM method
- Single- & Two-Locus Models (5-8)
- segregation ratios, marker screening
- linkage & estimation of recombination fraction
- linkage phase, random mating populations
- linkage disequilibrium & recombination
- Multi-Point Linkage & Linkage Maps (9-11)
- linkage groups, multilocus ordering
- map functions & map distance
- merging linkage maps
- (genetic vs. physical maps)
Spring 1999 Semester
- Complex Traits, QTLs & Polygenes (12-17)
- least squares approach
- interval mapping
- (Mapmaker/QTL and QTLCart programs)
- composite interval mapping
- (mixed models / polygenes)
- (multiple traits)
- Data Resampling & Simulation (19)
- Permutation Thresholds
- Nonparametric LODs
- Monte Carlo Simulation
- (Markov chain Monte Carlo)
- Pedigrees & Multiple Generations (11)
- (genetic identity / identity by state / identity by descent)
- comparing linkage maps
- (animal model / mixed models / polygenes)
- (multiple generation analysis / pedigree analysis)
Fall 1998 Semester
- Introduction
- Biology in Genomics
- Introduction to Genomics
- Statistics in Genomics
- Single-Locus Models
- Two-Locus Models: The Controlled Crosses
- Two-Locus Models: Natural Populations
- Two-Locus Models: Using Linkage Disequilibrium
- Linkage Grouping and Locus Ordering
- Multi-Locus Models
- Linkage Map Merging
Spring 1999 Semester
- QTL Mapping: Introduction
- QTL Mapping: Single-Marker Analysis
- QTL Mapping: Interval Mapping
- QTL Mapping: Natural Populations
- QTL Mapping: Statistical Power
- QTL Mapping: Future Considerations
Both Semesters
- Computer Tools
- Resampling and Simulation in Genomics
Return to Statistical Genomics.
Last modified: Tue Sep 1 12:38:25 1998 by Brian Yandell
(yandell@stat.wisc.edu)