STAT/BIOSTAT 550: Spring 2014
Statistical Genetics I; Discrete Mendelian traits
Instructor: Elizabeth Thompson
Time: MWF 8.30-9.20
Place: THO 211
SOME OF THE INFORMATION ON THIS (AND LINKED) PAGE(S) MAY NOT BE UPDATED FOR 2014
Single nucleotide polymorphisms are discrete Mendelian traits!
Here will be a draft schedule:
only partially updated for this year.
The draft schedule is usually the first place
I update and check links.
PLEASE LET ME KNOW ABOUT ANY NON-WORKING LINKS THAT YOU BELIEVE SHOULD BE
WORKING.
Course information
Grading:
Course will be graded 30% homework, 30% computing labs, 10% for participation
in class summaries and discussions of homeworks/labs, and 30% final
project (info to be posted).
There is no final exam, apart from the
project.
Homeworks and/or labs will be discussed in class (most) Fridays.
Also, I will drop your lowest-scoring homework in computing your overall
homework score. (But all labs count.)
Office hours
For brief questions, please see me after class.
If you need a longer time, please
feel free to email for an appointment. Also, feel free to email me questions
about course, lab, or homework material --
if the question is relevant to many in the class, I may respond to the
class email, including your query. If I do that, I may edit your query.
I am often available 4.00-5.30 Thursdays, B313-C PDLFD --
apologies to BIOST students.
Books
Here is the
official UW list for books for this course.
None of the books are necessary: some may be helpful.
-
My book might be most useful (except the relevant bits are mostly in notes
I'll provide on the web).
-
Weir's book is useful.
-
Ott's book will be very
useful for those going on through Stat/Biostat 552, but less so for this first
course.
-
Lange's book is more specialized, and contains a variety of topics.
It has some very good bits.
Email
is good, but is NOT an "instant-messaging" system.
Note my preferred email is eathomp@uw.edu.
Computing
We will use the Statistics computer
statgen.stat.washington.edu machine for this class. It will also be
possible to download and install your own copies of software if you prefer.
HERE is some information for 2014
There is also quite a bit of
Statistical Genetic software information. .
You will need your UWNet ID to access this page.
The software referred to is
installed in the
Biostatistics Computers, and this was extensively updated by Kirk Li
in 2012.
Course materials
- GENETICS BACKGROUND:
Elementary introduction to genetics
These web notes were written for undergraduates, by an undergraduate.
But they may be a useful summary review.
-
STATISTICS BACKGROUND:
Here is a summary of likelihood ideas and theory
(PDF version).
Here is a note about expectations
which may be
helpful to those with less probability and statistics background.
-
Chapter 1.1 to 1.4 (posted 3/29/2014; updated 4/08/2014)
-
Chapter 1.5 to 1.6 (posted 4/08/2014)
and
Stephens' ppt on Phasing
-
Chap 2.1, 2.2 (posted 4/13/2014).
An interesting pedigree from Wikipedia! (posted 04/19/2014)
-
Chap 2.3, 2.4, 2.5 (posted 4/19/2014;
updated 05/04/2014)
-
Chap 3.1, 3.2 (posted 05/04/2014)
-
Chap 3.3, 3.4, 3.5 (posted 05/11/2014, updates 05/20/2014, 05/22/2014)
-
Chap 4.1, 4.2, 4.3 (posted 5/22/2014,
updated 6/04/2014)
-
Chap 4.4, 4.5, 4.6 (posted 5/22/2014, updated 6/04/2014)
Homeworks and Labs
-
Week 1: Homework 1
(Posted 3/29/2014). Due after class, Friday April 4
-
Week 2: Homework 2
(Posted 4/01/2014) Due after class, Friday April 11.
-
Week 3: Homework 3, Q1 and Q4.
(Posted 4/08/2014)
and
Lab 1
(Checked on statgen.stat, 04/08/2014)
Both due after class, Friday April 18.
A note on Homework-3 Qu.1 (posted 04/19/2014)
- Week 4:
Homework 3, Q2 and Q3.
(Posted 4/08/2014)
and Lab 2 (Posted 04/15/2014).
Both due after class, Friday April 25.
NOTE: On statgen.stat, the linking
to all the MORGAN programs, including the Lab2 pedcheck program, is now fixed.
Here is (optional)
Pedfiddler information.
- Week 5:
Homework 4.
(Posted April 24, 2014). Due May 2, 2014.
- Week 6:
Lab 3 (Posted 04/28/2014)
Due May 9, 2014.
- Week 7;
Homework 5
(First 3 questions: Posted 05/01/2014.
Homework updated/finalized 05/07/2014).
Due May 16, 2014.
- Week 8:
Lab 4 (Posted 05/15/2014)
and
Half-Homework 6a (Posted 05/16/2014).
Due May 23 2014.
- Week 9:
Homework 7 (posted 05/23/2014)
Due May 30 2014.
- Week 10:
Lab 5
(posted 05/27/2014, updated and checked 05/29/2014) and
Half-Homework 6b
(posted 05/23/2014; checked 05/29/2014). Due June 6 2014.
Projects
Preliminary
information re the final project
is posted (May 6, 2014).
The list of papers is
posted, but currently these
are the 2013 papers -- updates will follow!! .
Note the full paper citations are in the last 3 pages of this document.
June 2 update:
All students have selected papers
and the list is now final
except there is one change to be updated.
Projects are due, Tuesday June 10, 11:59 p.m.,
as a PDF file by email.
