Golden Helix Newsletter


Missing Heritability and the Future of GWAS
by Dr. Christophe Lambert, CEO & President Christophe Lambert

"Where is the missing heritability?" is a question asked frequently in genetic research, usually in the context of diseases that have large heritability estimates, say 60-80%, and yet where only perhaps 5-10% of that heritability has been found. The difficulty seems to come down to the common disease/common variant hypothesis not holding up. Or perhaps more accurately, that the frequency of the assayed markers are not in line with the frequency of the disease (or specific sub-phenotype thereof). Most of the technologies directed towards finding the genetic links to diseases - e.g., the first generation of major microarray platforms used in genome-wide association studies (GWAS) - were developed using this hypothesis as a premise... Continue reading on "Our 2 SNPs"

Increase Power and Data Quality with Advanced Genotyping and Imputation Methods
by Dr. Bryce Christensen, Director of Services and Statistical Geneticist

Accuracy and completeness of genotype data are among the most important factors for a successful genome-wide association study (GWAS), and must not be taken lightly. The Golden Helix team is always on the lookout for methods to improve data quality, and we have recently found the BEAGLE and BEAGLECALL software packages to be very useful in this regard. BEAGLE is particularly useful for inferring the genotypes of missing and untested SNPs. BEAGLECALL is a companion to BEAGLE that we have found to be the most accurate genotype calling tool available today... Continue reading on "Our 2 SNPs"

Enhanced ROH Analysis Improves Effectiveness to Identify Rare, Penetrant Recessive Loci
by Gabe Rudy, VP of Software Development

In 2007 Dr. Todd Lencz introduced a new way of doing association testing using SNP microarray platforms. The method, which he termed whole genome homozygosity association, first identifies patterned clusters of SNPs demonstrating extended homozygosity (runs of homozygosity or "ROHs") and then employs both genome-wide and regionally-specific statistical tests on ROH clusters for association to disease. This approach is powerful for identifying chromosomal segments that harbor rare, penetrant recessive loci.

An especially important contribution to this approach has been the addition of more advanced filtering criteria for ensuring that algorithmically detected ROHs are true population variants and not due to: random chance, the result of genotype calling anomalies, or low marker coverage over certain regions of the genome... Continue reading on "Our 2 SNPs"

   Featured Tutorial
Comparing CNVs Between Tumors and Normals Using the Affymetrix MIP Array

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   New Add-On Scripts
  • SNP Density
  • Rare Variant SNP
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7.3 Release Webcast
Interested in what's new in SVS 7.3? Download the webcast and find out!

SVS now available in China
We are proud to announce that Golden Helix has entered into an agreement with CloudScientific to act as a distributor of SVS in China. Read more

Where will we see you?
AMATA 2010
Tasmania, Australia  |  Sept 14-17

International Genetic Epidemiology Society Meeting
Boston, MA  |  Oct 10-12

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


Recent Customer Success Highlights

08.15.10  |  Nature Genetics
Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease
Hamza, T. et al
New York State Department of Health Wadsworth Center
Read the abstract

08.11.10  |  European Journal of Human Genetics
Nicotinic a5 receptor subunit mRNA expression is associated with distant 5' upstream polymorphisms
Smith, R. et al
Ohio State University
Read the abstract

07.30.10  |  Nature Biotechnology
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
MAQC Consortium
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


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