Golden Helix Newsletter


A Hitchhiker's Guide to Next Generation Sequencing - Part 1
by Gabe Rudy, VP of Product Development A Hitchhikers Guide to Next Generation Sequencing  Part 1

If you have had any experience with Golden Helix, you know we are not a company to shy away from a challenge. We helped pioneer the uncharted territory of copy number analysis with our optimal segmenting algorithm and we recently hand crafted a version that runs on graphical processing units that you can install in your desktop. So it’s probably no surprise to you that the R&D team at Golden Helix has been keeping an eye on the developments of next generation sequencing technologies. But what may have surprised you, as it certainly did us, was the speed in which these sequencing hardware platforms and services advanced. In a matter of a few short years, the price dropped and the accuracy improved to reach today’s standards where acquiring whole exome or whole genome sequence data for samples is both affordable and accurate. Continue reading on "Our 2 SNPs" »

CNV Analysis Tips for Illumina Data
by Dr. Bryce Christensen, Director of Services

The following statement is representative of a common question that is posed to the Golden Helix support team:

"I followed all of the steps in the SVS7 CNV analysis tutorial, but my results seem kinda funny. The segment means are skewed to the left and it doesn't look like I have any copy number gains. Can you tell me what to do? By the way, I'm using Illumina data."

Let's face it: CNV analysis is not easy. While SNP-based GWAS follows a largely standardized process, there are few conventions for CNV analysis. CNV studies typically require extensive craftsmanship to fully understand the contents of the data and explain the findings. As much as we would like to automate the process, there are always factors that require the researcher to make informed decisions or educated guesses about how to proceed. Illumina data has some unique features that require special attention. Continue reading on "Our 2 SNPs" »

   Featured Tutorial
Quantitative Haplotype Association and Haplotype Trend Regression

View tutorial »

ASHG 2010 Presentation
Check it out: Improving the Power of Your Study with Advanced Genotype Calling, Imputation, and Next-Generation Sequencing by Dr. Bryce Christensen
View webcast »

Did you know that GHI offers Genetic Research Services?
Having collaborated on dozens of genome-wide association studies with some of the top research organizations in the field, our experience and expertise will help you get more meaningful results from your data, faster, and with fewer headaches.
Find out more »


Congratulations to the winners of SVS Server Licenses!

Golden Helix is thrilled to announce the winners of our IGES and ASHG contests for a free SVS server license for their entire department!

Yi-Hsiang Hsu  

Congratulations to our IGES winner, Yi-Hsiang Hsu, an Assistant Scientist at the Hebrew SeniorLife Institute for Aging Research and Harvard Medical School. Dr. Hsu's research focuses on genome-wide association studies (GWAS), copy number variation and deep re-sequencing on musculoskeletal traits in large consortia, such as CHARGE and GEFOS. He also works on the methodological development of multi-phenotype GWAS meta-analysis to identify pleiotropic genetic effects on reproductive phenotypes and musculoskeletal phenotypes as well as metabolic syndrome risk factors and the musculoskeletal phenotypes.

Stephen Turner  

The winner from ASHG is Stephen Turner, a graduate student finishing a Human Genetics doctoral program at the Vanderbilt University Center for Human Genetics Research. He specializes in genetic epidemiology and development of novel statistical and bioinformatics methodology for understanding the complex relationship between genes, environment, and human disease. Stephen is also a registered patent agent, and blogs about genetic analysis on

Recent Customer Success Highlights


11.1.10  |  PLoS ONE
Flavopiridol Pharmacogenetics: Clinical and Functional Evidence for the Role of SLCO1B1/OATP1B1 in Flavopiridol Disposition
Ni, W. et al
Ohio State University, Columbus, Ohio, USA
Read the abstract »


11.6.10  |  Genomics
Genome-wide association study of copy number variations associated with pulmonary function measures in Korea Associated Resource (KARE) next term cohorts
Lee, B. et al
Seoul National University, Seoul, Republic of Korea
Read the abstract »

11.9.10  |  BMC Plant Biology
A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.)
Emanuelli, E. et al.
Istituto Agrario di San Michele all'Adige, Italy
Read the abstract »

11.10.10  |  BMC Medical Genetics
Association Analysis of Nine Candidate Gene Polymorphisms in Indian Patients with Type 2 Diabetic Retinopathy
Balasubbu, S. et al.
Aravind Medical Research Foundation, India & National Eye Institute, Maryland, US
Read the abstract »

11.24.10  |  Clinical Cancer Research
Impact of ABCB1 allelic variants on QTc interval prolongation
Sissung, T. et al.
NIH, National Cancer Institute, Maryland, US
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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