Biostat 580B - Statistical Genetics Seminar

Instructor: Ellen Wijsman
Instructor: Katie Kerr
Instructor: Elizabeth Thompson
Instructor: Stephanie Monks

1 credit

Winter Quarter 2004
Seminar: Tuesday 3:45-4:45, in F643 HSB

This is a participatory seminar! Students, postdocs, faculty all present their own work and/or papers from the literature.

Remember the important questions:

Why? What? Why? How? Why? What next? and WHY?

(Why is this question important? What did they do? Why did they choose this approach? How did they do it? Why did they choose these methods? What should come next? Why is this the next logical step?)

Reminder: Everyone should read the papers for weeks in which we read a journal article. If the paper is available electronically, we will provide the reference, and you may download your own copy from the healthlinks web site, or through the UW e-journals page.
If the paper is not available electronically, the discussion leaders should make 2 copies, and should put one copy in each of the stat mailbox and the biostat 580B homework folder, preferably a week ahead of time. The stat mailbox is in the mail room in statistics; the biostat 580B homework folder is in the top left drawer underneath the biostat mailboxes in a folder to the far left as you face the mailboxes. Others should then make their copies from one of these two copies.

Discussion leaders are only expected to spend 20-30 minutes (jointly) presenting the assigned paper(s). If you don't understand everything, focus on what you can, and try to think about what is important about the papers, and what open questions you are left with. KEEP THE NUMBER OF PREPARED TRANSPARENCIES TO A SMALL NUMBER (AROUND 6), TO ENCOURAGE DISCUSSION.

MAKE SURE YOU LEAVE ADEQUATE TIME FOR DISCUSSION!!!

Statistical Genetics Computing in Biostat

For lists of previously suggested topics, click here .

WINTER 2004 SCHEDULE

Jan 6: CANCELLED BY UW DUE TO SNOW

Please email thompson@stat.washington.edu asap if you still need an entry code, or if you have one, but forgot it, and have not yet registered.

Jan 13: Lixuan Qin

• Lixuan will talk about her work with Katie Kerr on microarray experiments. Two suggested overview papers are:
  • Statistical tests for differential expression in cDNA microarray experiments", Cui and Churchill http://genomebiology.com/content/pdf/gb-2003-4-4-210.pdf
  • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments, Dudoit, Yang, Callow, and Speed http://www.stat.berkeley.edu/users/sandrine/Docs/Papers/sinica.final.pdf
  Please come prepared to asked all your questions about microarrays -- Lixuan fears the seminar may be too short, but, if it is, it is the other participants' fault, not hers.
  
  
• Everyone should please also bring a topic that they want to learn something about (relevant to statistical genetics). written down on a piece of paper -- Ellen has volunteered to collect the bits of paper, and Bill and Paul have each volunteered to get them to my mail box. (Thanks!). For previous lists of topics, see links on this web page.

Jan 20: Paul Scheet

• The first half will be organizational. Here is the NEW list of proposed topics
  
• 2 nd. half: Paul will lead discussion on:
  Storey & Tibshirani, 2003, PNAS 100: 9440-9445.

(Jan 21: COMBI seminar (1.30 p.m.) Elizabeth Thompson )

Jan 27: Elisabeth Rosenthal, Terri Kim

• Kaplan, N; Morris, R
  Prospects for association-based fine mapping of a susceptibility gene for a complex disease
  THEORETICAL POPULATION BIOLOGY, 60 (3): 181-191 NOV 2001

Feb 3: Garrett Hellenthal, Ying Huang
Garrett and Ying will focus on the McVean theory paper. The other paper is the data paper that motivated this line of research, but we will probably not get into the data paper this week.

• Gilean A. T. McVean (2002)
  A genealogical interpretation of linkage disequilibrium
  Genetics 162, 987-991
• D E Reich, S F Schaffner, M J Daly, G McVean, J C Mullikin, J M Higgins, D J Richter, E S Lander and D Altshuler (2002)
  Human genome sequence variation and the influence of gene history, mutation and recombination
  Nature Genetics 32: 135-142

Feb 10: Rob Igo, with Mike Badzioch (et al?)

• Loki: Star Performer or Supporting Player?: Comparing Methods for Linkage Analysis on Complex Quantitative Traits

Feb 17: Caroline Cutting, Ting-Yuan Liu

• Anderson and Slatkin (2004)
  Population genetic basis of haplotype blocks in the 5q31 region.
  AJHG 74: 40-49.

Feb 24: Arindam RoyChoudhury, Joe Rothstein

• Pritchard and Cox (2002)
  The allelic architecture of human disease genes: common disease --common variant ... or not?
  Human Molecular Genetics 11: 2417--2423.

Mar 2: Audrey Fu, Saonli Basu

• Slatkin M. and Bertorelle G. (2002?)
  The use of intraallelic variability for testing neutrality and estimating population growth rate.
  Genetics 158: 865--874.

Mar 9: Professor Bruce Weir, NCSU

• A StatGen special guest lecture!
  Bruce will talk about the HapMap project, and some early analyses of the data.
  Hap map reference
  Lon Cardon paper, referenced by Bruce.

Mar 12 and Mar 17:

For those interested: Bill Stewart will give his exam preview talk in Mathgen, C301 PDL, 1.30 p.m. Fri, Mar 12:
better yet, come to his General Exam, SAV 245, 9.00 a.m. Wed March 17!

For a link to other seminars of related interest, click here.

For a link to previous schedules of the statistical genetics seminar, click here.

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