I've been using GenABEL for some time now for GWAS analysis using related individuals. It has an excellent set of functions for estimating a kinship matrix from a dense marker panel and then using this in a linear mixed effects model to allow for related individuals in the analysis of a quantitative trait.
A new paper in Nature by the Wellcome Trust Case Control Consortium examining 16,000 cases of 8 common diseases and 3000 shared controls finds that common CNVs probed on existing arrays are well tagged by SNPs and are unlikely to contribute much to common human disease.
*** Update April 25, 2011: This code has gone through a major revision. Please see the updated code and tutorial here. *** A few months ago I showed you in this post how to use some code I wrote to produce manhattan plots in R using ggplot2. The qqman() function I described in the previous post actually calls another function, manhattan(), which has a few options you can set.
Vanderbilt Epidemiology Center, Institute for Medicine and Public Health presents: "Pathway-based analysis for genome-wide association studies" Steven Chen Ph.D Assistant Professor of Biostatistics Tuesday, March 16, 2010 9:00 AM - 10:00 AM 2525 West End Avenue 6th Floor BoardroomGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Suppose you have billions of reads from a hot new sequencing machine and you want to simultaneously align these reads and call SNPs very quickly on the cheap. Check out an open source tool called Crossbow and the recent paper in Genome Biology.
Time for a little shameless self-promotion. I'll be giving a talk in genetics interest group next week. "Using GWAS in an EMR-linked biobank to explore genetic and environmental determinants of HDL cholesterol" Thursday, March 11, 2010 Noon-1pm 206 PRBGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
The first post on Getting Genetics Done was one year ago today. To celebrate, here are the top 10 most viewed posts since GGD launched last year. Incidentally, nine of the ten are tutorials on how to do something in R. Thanks to all the readers and all the commenters for sharing your thoughts!
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.
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.