Golden Helix Newsletter

 

Stop Ignoring Experimental Design (or my head will explode)
by Dr. Christophe Lambert, CEO & President Stop Ignoring Experimental Design (or my head will explode)

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

CSCDA 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" »


 
   Featured Tutorial
Regression with Covariates

View tutorial »


   New Add-On Script
Chi-Squared Contingency Table

Access script »


   SNP-ITS

CSCDA Conference Presentation Available
On August 25th, Dr. Christophe Lambert presented "Design and Analysis of GWAS using CNVs" at CSCDA in Belgium.
Download the recording »



Harvard Steps Up Collab-oration with Golden Helix
We are excited to share the news that Harvard School of Public Health (HSPH) and Golden Helix have been working together on refactoring PBAT, HSPH's software for studying disease heritability in families.
Read more »



GHI YouTube Channel
Yep, that's right - Golden Helix now has a YouTube channel. Check it out for software demonstrations, live presentation recordings, and more!
View the channel »



Where will we see you?
International Genetic Epidemiology Society Meeting
Boston, MA  |  Oct 10-12

American Society of Human Genetics 60th Annual Meeting
Washington DC  |  Nov 2-6

XGen Congress
San Diego, CA  |  Mar 14-18

 

Recent Customer Success Highlights

09.16.10  |  Arthritis & Rheumatism
Genetically determined amerindian ancestry correlates with increased frequency of risk alleles for systemic lupus erythematosus
Sanchez, E. et al
Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
Read the abstract »


09.13.10  |  Journal of Asthma
Putative association of SMAP1L polymorphisms with risk of aspirin intolerance in asthmatics
Kim, J. et al
Sogang University, Seoul, Korea
Read the abstract »


09.03.10  |  Pharmacogenetics and Genomics
A possible association of the norepinephrine transporter gene in the development of heroin dependence in Han Chinese
Yeh, Y. et al
Tri-Service General Hospital, Taiwan, China
Read the abstract »


09.01.10  |  Journal of Rheumatology
Association of the Intergenic Single-Nucleotide Polymorphism rs10865331 (2p15) with Ankylosing Spondylitis in a Spanish Population
Sanchez, A. et al
Puerta de Hierro University Hospital, Madrid, Spain
Read the abstract »


07.30.10  |  Carcinogenesis
Genetic Variations in MicroRNA-Related Genes Are Associated with Survival and Recurrence in Patients with Renal Cell Carcinoma
Lin, J. et al
The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
Read the abstract »



 
About Golden Helix
We are inspired by significance. Not only statistical, but technological, scientific, and personal significance. It's embodied in everything we and our customers do. And we believe the only way to achieve significance is by transcending the status quo. Every day we strive for extraordinary analytic and technological advancements that empower scientists around the world to pursue that which is truly significant: from uncovering the genetic causes of disease and transforming drug discovery to developing genetic diagnostics and advancing the quest for personalized medicine. To learn more about how we are accelerating the quest for significance visit www.goldenhelix.com.

 


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