Biostat 580B - Statistical Genetics Seminar
1 credit
Spring Quarter 2000
Seminar: Tuesday 4:00-5:00 T360 ***** NOTE LOCATION
Reminder: Everyone should read the papers (make a copy from the copy left in
the stat mailbox, or the purple biostat 580B homework folder under the biostat
mailboxes). Discussion leaders are only expected to spend 15-20 minutes
presenting the assigned papers. 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.
Remember the important questions:
Why? What? Why? How? Why? What next? and WHY?
Spring Schedule
March 28:
Elizabeth Thompson
See subject (2) from last two quarters -- overview!
Linkage 1934-1999; IBD; Complex traits; a case study (that works ?)
Also, we'll discuss the topics/schedule for this quarter.
We decided to continue with the same three topics, bascically!
Focusing maybe a bit more on disequilibria, population issues, etc.
April 4:
Anne-Louise Leutenegger
Kruglyak, L. and Daly, M. J. and Reeve-Daly, M. P. and Lander, E.S. (1996)
Parametric and nonparametric linkage analysis: a unified multipoint approach.
AJHG 58: 1347--1363.
This one not on web, so Anne-Louise will make copies for Stat and Biostat.
April 11:
Maureen Reiner, Jessica Maia
Templeton AR, Clark AG, Weiss KM, Nickerson DA,
Boerwinkle E. and Sing CF (2000)
Recombinational and Mutational Hotspots within the Human Lipoprotein
Lipase Gene
Am.J.Hum.Genet 66:69-83, 2000.
April 18:
Warwick Daw, Solly Sieberts
Starting with the background to MCMC on pedigrees:
Lange K. and Matthysse S, (1989)
"Simulation of Pedigree Genotypes by Random Walks."
AJHG, 1989 Dec;45(6):959-70
and maybe progressing to more recent developments, such as
Note from Warwick:
Note that there are options to the left of the text to download PDF or PS
versions.
Those with no experience of MCMC should read the first paper.
Those who know about MCMC should try to read the second one (also?)
April 25:
France Gagnon, Hao Liu
Lonjou C., Collins A., and Morton N.E. (1999)
Allelic association between marker loci.
PNAS 96: 1621-1626.
(This paper is available via PUBMED, France.)
May 2:
Erin Conlon, Eric Anderson
What is the outcome of a GAW like?
(This is the GAW10 summary paper for the simulated data GAW10 problem)
Also, Eric and Erin will discuss, on the same GAW problem:
Todorov et al., "Probabilities of IBD patterns in sibships when the
parents are not genotyped." Genetic Epi. 14:909--913,
and
Goldin and Chase, "Improvement of the power to detect complex disease
genes by regional inference procedures" Genetic Epi. 14:785--789
There are
copies of the readings in the purple statgen folder in
biostat, and in the statgen box in the statdept mail room. The web ref is
Genetic Epidemiology, Vol 14, Issue 6.
May 9:
Lindsey Dubb, Gosia Bogdan
What is known about genetic epidemiology of asthma?
Francesca Sampogna, Florence Demenais, Joelle Hochez, Marie-Pierre
Oryszczyn, Jean Maccario, Francine Kauffmann, Josue' Feingold,
Marie-He'le'ne Dizier (2000)
Segregation analysis of IgE levels in 335 French families (EGEA) using
different strategies to correct for the ascertainment through a
correlated trait (asthma).
Genetic Epidemiology
Volume: 18, Issue: 2, Date: February 2000, Pages: 128-142
Well, that web ref isn't quite right either --- it seems to be the next paper
in the journal. However, that paper might be of interest also!
Also, two other papers, in the StatGen boxes (or soon):
Abramson M. J. and Harrap S. B. (1998)
The new asthma genetics and its implications for public health
Public Health Rev. 1998, 26: 127--144.
and
S. Holgate (1997)
Asthma genetics: waiting to exhale.
Nat. Genet. 1997,15: 227--229.
The first of these will also be discussed. The other is for general information.
May 16:
Nicky Chapman, Ellen Goode
1) the unpublished letter by ellen w. and I about sib pair analysis vs
single locus association tests - pretty short and sweet. (and you can
all tell me why it was not-publishable. slightly embarassing.)
2) Anthony D. Long and Charles H. Langley
LETTER:
The Power of Association Studies to Detect the Contribution of Candidate
Genetic Loci to Variation in Complex Traits.
Genome Research: Vol. 9, Issue 8, 720-731, August 1999
Or, go to www.genome.org, and search for C. Langley.
May 23:
Do Peterson, Michael Li
Rybicki BA, Elston RC. (2000)
The relationship between the sibling
recurrence-risk ratio and genotype relative risk.
Am.J.Hum.Genet. 66:593-604.
May 30:
Mike Badzioch
Collins A, Lonjou C, Morton NE (1999)
Genetic epidemiology of single-nucleotide polymorphisms
Proc Natl Acad Sci U S A 1999 Dec 21;96(26):15173-7
Available here
Other seimars etc;
April 11:
1.00 p.m. Nicky Chapman's general exam; probably in Biostat conference room.
April 21;
3.30 p.m. Eric Anderson wil give the
ACMS seminar