Stop Ignoring Experimental Design (or my head will explode)
by Dr. Christophe Lambert, CEO & President
Over the past 3 years, Golden Helix has analyzed dozens of public and customer whole-genome and candidate gene datasets for a host of studies. Though genetic research certainly has a number of complexities and challenges, the number one problem we encounter, which also has the greatest repercussions, is born of problematic experimental design. In fact, about 95% of the studies in which we have participated have major problems with experimental design. Namely, some aspect of data collection or experimental order (i.e. plating) is not randomized with respect to the phenotypes of interest. The unfortunate result is endless struggles with spurious associations due to confounding, to the point, in fact, where real associations cannot be distinguished from experimental artifacts. This confounding only gets worse when two or more poorly randomized experiments are combined with the goal of increasing power through mega-analyses. Continue reading on "Our 2 SNPs" »
SVS Tips and Tricks:
Using the split and filter feature in Plot Viewer
by Josh Forsythe, Chief Golden Helix Evangelist
As many of you know there are quite a few seemly little features in SVS that, once you know where they are and how to use them, can significantly increase the utility of the software. We discover new ways to use the software all the time and what better way to share what we learn than profiling them in the tips and tricks section of our blog.
September's post profiles the utility of the filter and split features in the Plot Viewer. These two buttons are great for filtering any view on a numeric threshold or categorical variable or splitting a plot into several colors to compare two or more groups of values. Some common use cases include: Manhattan plots, X heterozygosity, batch effect detection, population stratification, and genotype cluster plots. Continue reading on "Our 2 SNPs" »
Report from Capita Select in Complex Disease Analysis Conference in Belgium
by Rudy Parker, Solutions Advisor, Genetic Research
How much fun is a person allowed to have when going to a conference? That kind of sums up my personal experience going to the first ever Capita Selecta in Complex Disease Analysis (bi-annual) conference in Leuven, Belgium. Not only was it fun, but the conference program was packed with interesting talks and short courses. Dr. Kristel van Steen and her team did an excellent job organizing the meeting, with plenty of time for socializing and networking among the participants.
Scientifically, the conference also had plenty to offer. For those not quite familiar with GWAS, there were 2 (well attended) short courses offered on Wednesday. Dr. David Evans from the University of Bristol did a great job explaining the intricacies of Design and Analysis of GWAS with SNP data. If you think GWAS will soon die an ignominious death, don't hold your breath. GWAS will be with us for some time to come. What may change is how GWAS is conducted, in conjunction with Next Generation Sequencing, and how it will improve the effectiveness of these studies. Continue reading on "Our 2 SNPs" »