Statistical Methods in Genetic Epidemiology

Public Health Genetics 519
Epidemiology 516
Biostatistics 516

Autumn 2011


Class Meetings: Mondays/Wednesdays, Health Sciences Building T360, 1:30-2:50 PM

Instructor: Timothy Thornton, Ph.D.
Assistant Professor, Department of Biostatistics
Email: tathornt@u.washington.edu
Office: Health Science Building F644
Telephone: 543-8004

Course Information

Syllabus


Announcements

  • (12/5/11)
    The data for the final exam as well as R commands to help you with the analysis of this data have been uploaded to the course website. Use the "Final Exam Data" link below to access the data. Class on Wednesday will including a demonstration in R to help you get started with the analysis of the data. Make sure that you are able to load the data files into R on your computer before class. Bring your laptop to class tomorrow with the data uploaded on your computer if you would like to follow along.


  • (12/5/11)
    Slides for the today's lectures on population structure and association testing with cryptic population structure have been posted. Homework 4 and Homework 5 solutions have been posted.

    The Nature Genetics article that introduced the EIGENSTRAT method discussed in class today for adjusting for cryptic population structure has been posted in the "Journal Articles" section of the course website (Use the "Journal Articles" link below.)



  • (12/5/11)
    R commands for the demonstration on population structure that we will cover in the begninnig of class on Wednesday can be found on the "Software" webpage for the course (use the Software link below). The input genotype and phenotype data files for the R demonstration can be downloaded from the "Data Set" webpage for the course (see the Data Set link below).



  • (11/30/11)
    Slides from today's lecture on Odds Ratios have been posted. Homework 6 has also been posted and is due next Wednesday, December 7th.


  • (11/29/11)
    Tommorow's lecture will include an R demonstartion on association testing and odds ratios. R commands for the demo have been posted on the Software webpage. Please bring your laptop tomorrow if you would like to follow along.


  • (11/28/11)
    Slides from today's lecture on case-control association testing have been posted.


  • (11/21/11)
    Slides from today's lecture on haplotype frequency estimation from genotype data with an EM algorithm have been posted. Homework 5 has also been posted.

    Reminder: There is no class on Wednesday, November 23rd. Happy Thanksgiving!


  • (11/16/10)
    The EM algorithm R script that we covered in class today for the ABO blood type example data has been posted and can be found on the course software webpage (use the Software link below).

    Also, there will be no class next Wednesday, November 23rd. Happy Thanksgiving!


  • (11/15/11)
    Please bring your laptop tomorrow with R installed on your machine if you would like to follow along. In addition to the R demo on programming, we will also implement the EM algorithm for the ABO blood type that we covered in class on Monday.


  • (11/14/11)
    Slides from today's lecture on the EM algorithm have been posted. Slides for the R programming demo that we will do in class on Wednesday have also been posted.


  • (11/19/11)
    Homework 4 has been posted.


  • (11/9/11)
    Today'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_location" files onto your computer which can found on the course Data Sets webpage (link is below).


  • (11/7/11)
    Homework 3 solutions have been posted. Slides from today's lecture have also been posted.


  • (11/2/11)
    Homework 2 solutions have been posted.


  • (10/26/11)
    Slides from today's lecture on Nonparametric Linkage Analysis have been posted. HW1 Solutions have been posted.


  • (10/25/11)
    Homework 3 has been posted. HW 3 is due on Wednesday, November 2. In the homework you will need to plot a LOD score as a function of the recombination fraction, theta. Commands to plot a function in R have been posted. Use the "Software" link below.


  • (10/25/11)
    The take home midterm exam will be given on Wednesday, November 2.


  • (10/24/11)
    Slides from today's lecture on Parametric Linkage Analysis have been posted.


  • (10/19/11)
    Slides from today's lecture on Linkage have been posted. R commands for plotting the log-liklihood function for the Sweet Pea Linkage Analysis example that we did in class have also been posted and can be found by going to the course software webpage (use the Software link below).


  • (10/18/11)
    The R software package can be downloaded by going to the course software webpage (use the Software link below). A link to an introduction to R can be also found by going to the software webpage.


  • (10/18/11)
    Tomorrow's class (October 19th) 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).


  • (10/12/11)
    Homework 2 has been posted. HW 2 is due on Monday, October 24th.


  • (10/10/11)
    Slides from today's lecture on HWE testing have been posted. The journal article on Exact HWE testing has also been posted. Click on the link below in the "Journal Articles" section to access it.


  • (10/10/11)
    For question 1 of HW 1, remember that the two parental strains of white flowers that are intially crossed must have different homozygous genotypes from each other at the genes.


  • (10/4/11)
    Homework 1 has been posted. Click on the link below in the "Homework Assignments" section to access it. HW 1 is due on Monday, October 17th.


  • (10/3/11)
    Slides from today's lecture on segregation and aggregation analysis have been posted.


  • (9/29/11)
    Slides from yesterday's lecture have been posted. Click on the link below in the "Lecture Notes and Handouts" section to access the slides.




Final Exam Data




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.