Statistical Methods in Genetic Epidemiology

Public Health Genetics 519
Epidemiology 516
Biostatistics 516

Autumn 2009


Class Meetings: Tues/Thurs Health Sciences Building T360, 10:30-11:50 AM

Instructor: Timothy Thornton
Assistant Professor, Department of Biostatistics
Email: tathornt@u.washington.edu
Office: Health Science Building F646
Telephone: 616-6846

Course Information

Syllabus


Announcements

  • (11/23/09)
    We will cover estimating relationships in tomorrow's lecture. The lecture will include an example using the R software package. If you would like to follow along with your laptop, then you will need to download the file "FINAL_ESTIMATING_RELATEDNESS.R" from the Software webpage for the course. You will also need to download the "GENO_RELATED.data" and "FREQ_RELATED.data" files which can found on the Data Sets webpage (links are below).


  • (11/20/09)
    Homework 5 has been posted. It is due on Tuesday, December 1, 2009.

  • (11/17/09)
    An article on the Transmission Disequilibrium Test (TDT) can be downloaded from the Journal Articles section. Read this article carefully and bring a written summary and discussion points of this article to Thursday's class (November, 19, 2009). We will have a journal club style discussion of this article on Thursday.


  • (11/17/09)
    Today's lecture notes on odds ratios have been posted. The commands for the R demonstration given in class are available on the Software webpage.


  • (11/10/09)
    HW 4 has been posted. Today's lecture notes on haplotype frequency estimation via the EM algorithm and the lecture notes for the R programming demonstration given in class have been posted. An article on estimating haplotypes is available in the Journal Articles section.


  • (11/9/09)
    Tomorrow's class will include a tutorial on how to write an R script that contains a loop. Please bring your laptop to class if you would like to follow along.


  • (11/03/09)
    Homework 3 solutions and slides from today's lecture have been posted.


  • (11/03/09)
    The last slide, page 14, for the Linkage Disequilibrium lecture slides has been changed.


  • (11/2/09)
    Tomorrow's class will include a tutorial on the Haploview software package. If you would like to follow along with your laptop, then you will need to download Haploview onto your computer. The link to download the package can be found on the software webpage for this course (use the Software link below). You will also need to download the "LD_FILE.geno" and "LD_FILE.snpnames" files onto your computer which can found on the course Data Sets webpage (link is below).


  • (10/29/09)
    The midterm due date has been changed to Thursday, November 5.


  • (10/27/09)
    An article on the topic of a unified approach for parametric and nonparametric linkage analysis from the American Journal of Human Genetics has been posted.


  • (10/27/09)
    Homework 2 solutions and slides for the lecture on linkage disequilibrium have been posted.


  • (10/25/09)
    Commands to plot a function in R have been posted. Use the "Software" link below.


  • (10/23/09)
    Homework 3 has been posted. It is due next Thursday, October 29, 2009.


  • (10/21/09)
    Homework 1 solutions have been posted.


  • (10/20/09)
    Parametric linkage analysis slides have been posted. A typo on page 16 in the HWE slides has been corrected.


  • (10/14/09)
    Homework 2 has been posted. It is due next Thursday, October 22, 2009.


  • (10/14/09)
    R commands for the HWE demo have been posted and can be found by going to the software webpage.


  • (10/12/09)
    Tomorrow's class will include a tutorial on HWE testing in R. If you would like to follow along with your laptop, then you will need to download the R "genetics" package onto your computer. Intructions on how to download the package can be found on the software webpage for this course (use the Software link below). You will also need to download the "HWE.geno" file onto your computer which can found on the course Data Sets webpage (link is below).


  • (10/12/09)
    An introduction to R can be found by going to the software webpage (link is below).


  • (10/12/09)
    Class will be held in T360 for the remainder of the quarter.


  • (10/07/09)
    An article on Hardy-Weinberg Equilibrium from the American Journal of Human Genetics has been posted. We will discuss some of the material in this article during the next lecture.


  • (10/07/09)
    Corrected a typo in HW1. In question 4, "affected parent and at least one affected offspring" has been changed to "affected parent and at least one offspring." This correction does not affect the statisitical analysis.


  • (10/06/09)
    Homework 1 has been posted. It is due at the beginning of class on Tuesday, October 13, 2009.




Lecture Notes and Handouts




Homework Assignments




Journal Articles



Software



Data Sets



Acknowledgements

Some of the course material was developed by Dr. Stephanie Monks and Dr. Katie Kerr, both of whom previously taught this course.