Doug Robinson (JMP Academic Division, SAS Institute) is giving a presentation of the JMP Genomics software from SAS illustrating data analysis for genetics, expression, and copy number variation studies. Agenda includes: CNV analysis, merging CNV data sets of continuous traits, and QC, analysis, and downstream applications of expression studies.

If you read the previously mentioned "synthetic associations" paper in PLoS Bio by Dickson et al. in David Goldstein's group, be sure to read this brief commentary written by Pat Sullivan at UNC offering a different point of view.

A tip of the hat to @JVJAI for pointing out this interesting looking paper in AJHG. ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure Timothy Thornton and Mary Sara McPeek Department of Biostatistics, University of Washington. Abstract: Genome-wide association studies are routinely conducted to identify genetic variants that influence complex disorders.

In my previous post about Q10 a commenter suggested a software called "The Journal" by davidRM for productively keeping track of experiments, datasets, projects, etc. I've never tried this software before, but about a year ago I ditched my pen and paper lab notebook for an electronic lab notebook in the form of a blog using Blogger, the same platform I use to write Getting Genetics Done.

Department of Biostatistics Seminar/Workshop Series: Statistical Methods for DNA Resequencing Analysis in Disease-Gene Studies Wenyi Wang, Ph.D., Faculty Candidate Stanford Genome Technology Center, UC Berkeley Statistics 2:00-3:00pm Monday, February 15, 2010 MRB III Room 1220 Intended Audience: Persons interested in applied statistics, statistical theory, epidemiology, health services research, clinical trials methodology, statistical

This is the first in a series of posts on how to use MySQL with genetic data analysis. MySQL is a very popular, freely available database management system that is easily installed on desktop computers (or Linux servers). The "SQL" in MySQL stands for Structured Query Language, which is by my humble estimation the most standardized way to store and access information in the known universe.

Update Friday, May 14, 2010: See this newer post on LocusZoom. If you caught Cristen Willer's seminar here a few weeks ago you saw several beautiful figures in the style of a manhattan plot, but zoomed in around a region of interest, with several other useful information overlays.

Here are the papers we talked about in yesterday's Journal Club: PLoS Biol. 2010 Jan 26;8(1):e1000294. Rare variants create synthetic genome-wide associations. See my previous coverage of this paper and the comments. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. PLoS Genet. 2010 Jan;6(1):e1000798.

Frank Harrell is teaching his 3-session short course on regression modeling strategies using R here at Vanderbilt next month. Frank is a professor and chair of the Vanderbilt Biostatistics Department, and the author of several massively popular R libraries, including Design, rms, and the indispensable Hmisc.

We're restarting the PCG Journal Club again Monday February 8 at 4pm in the CHGR conference room. Most of you who usually attend are familiar with the format, but if not, bring any papers you've read recently and give a brief (i.e. 2 minute) overview of the paper and why you thought it was interesting. No slides allowed.

If you were here for any of the talks Rick Myers has given here at Vanderbilt over the last few years you'll remember all the interesting biomedical research going on at his company, HudsonAlpha.  Their spring symposium is March 30, 8am-6pm, at the HudsonAlpha institute in Huntsville, AL. It's FREE, and poster sessions are open to all students and postdocs.