Statistical Genetics

Time: Mondays, 10am - noon (Please arrive on time so we can end on time to give enough between-calss time to students who are taking the Math Stat. II).
Location: HSB 790.
HSB: Health Sciences Building, 155 College Street (South on College and West of University).

Mondays 11:50-12:30pm (other personal on-demand time slots can also be arranged, particularly for students who are taking the Math Stat. II).
There is no TA for the course.

This is a graduate course with the following prerequisites.
- Statistics at the graduate level or consent of instructor.
- There will be one or more simulation studies (no tutorial) and use of GENEHUNTER and PLINK software packages (with tutorial).
All participating students must register! This is a graduate school policy.
- January 23: The final date to enroll the course.
- February 27: The final date to withdraw from the course.

Teaching objectives
This course is for students of biostatistics, epidemiology and statistics with little genetics background but with some knowledge of probability and statistics. This course covers the fundamental statistical problems in genetics, with an emphasis on human genetics. The aim of the course is to provide students necessary background and prepare them for advanced study and research in the area of statistical genetics.
Format of instruction
Lectures and computing labs
Evaluation
Student evaluation will be based on homework problem sets and lab projects and overall participation in the classes.
Recommended books (no formal text book but lecture notes in .pdf are provided)
- For basic genetics background
  - Gonick L, Wheelis M (1991). Cartoon guide to genetics. Revised edition. HarperCollins.
  - Virtually any genetics textbook.
- For statistical genetics
  - Sham P (1998). Statistics in Human Genetics. Arnold, London.
  - Zieglier A, Koenig I (2006). A Statistical Approach to Genetic Epidemiology: Concepts and Applications. Wiley-VCH, .
  - Thomas DC (2004). Statistical Methods in Genetic Epidemiology. Oxford University Press.
  - Lange K (2002). Mathematical and Statistical Methods for Genetic Analysis. 2nd edition. Springer-Verlag, New York.
  - Ott J (1999). Analysis of Human Genetic Linkage. 3rd edition. Johns Hopkins University Press, Baltimore.

January 9: session 1 (Wei Xu).
Introduction and overview, and administrative work.
January 16: session 2 (Lei Sun).
Basic genetic terms and principles of population genetics.
January 24: session 3 (Wei Xu).
Familial aggregation, single locus inheritance, and segregation analysis.
January 30: session 4 (Lei Sun).
Multiple locus inheritance, map, and linkage.
February 6: session 5 (Lei Sun).
Linkage mapping I (full-parametric method and allele-sharing method).
February 13: session 6 (Lei Sun).
Computing lab I - application using GENEHUNTER.
February 20: University reading week, no class.
February 27: session 7 (Wei Xu).
Association analysis I (LD, case-control study and TDT).
March 5: session 8 (Wei Xu).
Association analysis II (Genome wide association study, haplotype analysis).
March 12: session 9 (Wei Xu).
Computing lab II - application using PLINK.
March 19: session 10 (Laura Faye and Lei Sun).
Principal component analysis
March 26: session 11 (Lei Sun).
Mutiple hypothesis testing.
April 02: session 12 (Lei Sun; Lat One!).
GWAS and related statistical issues.