Golden Helix Blog

Influencing the Global Dialog on Healthcare

Sep 28, 2011

On September 16-17th, I attended the Asia-Pacific Economic Cooperative (APEC) Health Systems Innovation Policy Dialog in San Francisco. It was a stimulating opportunity to look at global healthcare concerns from the perspective of developing and developed economies. There was much opportunity to  dialog and frame the issues around transforming healthcare…

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Wondering what SVS can do for a PhD student? Just ask Sander.

Sep 14, 2011

Sander van der Laan is like many Ph.D. students in the genomic analysis space. He has a lot of data and a lot of ideas about how to analyze it. His professor wants results. He’s the only one doing genetics (everyone else in his department is doing proteomics), so there’s…

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Marker Map Manipulation Improvements in SVS 7.5

Aug 31, 2011

Manipulating a marker map in SVS has never been easier, thanks to expanded functionality in SVS 7.5.  Have you ever wanted to view annotation data next to marker map data?  Or expand the current marker map with spreadsheet data to create a custom map?  SVS 7.5 features two new functions…

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SVS 7.5 Now Available!

Jul 28, 2011

More powerful rare variant analysis and visualization techniques We are proud to unveil SNP & Variation Suite (SVS) 7.5! The fifth installment of SVS delivers the most powerful rare variant analysis tools with the latest advances in tertiary or “sense making” methods for DNA next-gen sequencing. This release also adds…

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Please Help Me Get My Regression Model Set Up!

Jul 6, 2011

Golden Helix’ SNP & Variation Suite (SVS) has a Regression Module to enable researchers with varying degrees of statistical knowledge to interrogate their data using regression models to account for potential confounding effects of covariates and interaction terms. While these tools are labeled “basic”, they can be difficult to use…

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Going Coast to Coast for the Latest NGS News

Jun 23, 2011

Last week I was able to attend two very interesting conferences about the latest developments in the analysis of sequence data.  I started the week in San Diego at the Illumina iDEA Conference and finished it in Philadelphia at Children’s Hospital of Philadelphia’s (CHOP) Third Annual Next-Generation Sequencing Symposium.  The…

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SVS 7.5 Feature Sneak Peek: Grouping and Filtering in the Genome Browser

Jun 8, 2011

Ever since the release of SNP & Variation Suite (SVS) 7.4 back in January, our software engineers have been hard at work developing new functionality for the next version, to enable researchers to have even more control over their data. (Okay, well really, they started working on it before 7.4…

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NGS Tools and Formats for Secondary Analysis: A Primer

Apr 20, 2011

In a series of previous blog posts, I gave an overview of Next Generation Sequencing trends and technologies. In Part Two of the three part series, the range of steps and programs used in the bioinfomatics of NGS data was defined as primary, secondary and tertiary analysis. In Part Three…

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I Want a GPU for Computational Analysis! Which One Should I Get?

Apr 14, 2011

A GPU can produce an enormous boost in performance for many scientific computing applications. Since we announced the availability of SNP & Variation Suite’s incorporation of GPUs to dramatically speed up copy number segmentation, we’ve received numerous inquiries on recommendations for what GPU to purchase. Unfortunately the technical terminology and…

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Recent Publications on Polycystic Ovary Syndrome, Bovine Calving Ease, Systemic Lupus Erythematosus, and much more

Mar 29, 2011

We’ve had another busy few weeks for Golden Helix customers who have been hard at work publishing in all sorts of journals on all sorts of topics. (All abstracts below.) First off, from the Cedars-Sinai Medical Center in LA, “Replication of association of a novel insulin receptor gene polymorphism with…

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Updates to CNAM Make SVS the Fastest and Most Accurate Copy Number Tool for Common and Rare CNVs

Mar 16, 2011

A recent email from a user of SVS: “Your CNAM Optimal Segmentation algorithm is by far the best I ever used and believe me, I’ve tried many. Great use of the GPU for segmentation – it is 3x faster than using my 8 CPUs alone and 25x faster compared to…

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Getting Your Research Questions Answered Quickly with the Various Golden Helix Support Mediums

Mar 9, 2011

From the Customer Support Desk… At Golden Helix, we place a strong emphasis on customer support and helping our customers use the software to the best of their abilities to answer any research questions they have. Due to such a strong emphasis on customer and technical support, there are numerous…

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Recent Publications on Asthma, Schizophrenia, Peripheral Neuropathy, Rheumatoid Arthritis, Alzheimer Disease, and Esophageal Cancer

Feb 17, 2011

As you may have guessed from the title of this post, we’ve had a lot of customers publishing in the first six weeks of 2011. We are always excited to hear about about our customers’ findings and how they were able to use SNP & Variation Suite to accelerate their…

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A Hitchhiker’s Guide to Next Generation Sequencing – Part 3

Jan 19, 2011

The advances in DNA sequencing are another magnificent technological revolution that we’re all excited to be a part of. Similar to how the technology of microprocessors enabled the personalization of computers, or how the new paradigms of web 2.0 redefined how we use the internet, high-throughput sequencing machines are defining…

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Recent Publications on Schizophrenia, Cocaine Abuse, Childhood IgA Nephropathy, CNV Regions, and Genetic Variants in Metabolic Traits

Jan 5, 2011

Happy New Year! Golden Helix customers published 92 papers in 2010 unveiling new associations and novel findings using SNP and Variation Suite – a great feat for all! We anticipate an even more “significant” 2011. Wrapping up last year, congrats to Subba Rao Indugula, Guangyun Sun, and Ranjan Deka over…

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A Hitchhiker’s Guide to Next Generation Sequencing – Part 2

Dec 9, 2010

When you think about the cost of doing genetic research, it’s no secret that the complexity of bioinformatics has been making data analysis a larger and larger portion of the total cost of a given project or study. With next-gen sequencing data, this reality is rapidly setting in. In fact,…

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Recent Publications on Type 2 Diabetic Retinopathy, Grapevine Flavor, Pulminary Function, and Pharmacogenetics Testing

Nov 30, 2010

Let’s kick off this month’s recognition with Audrey Papp and Wolfgang Sadee at Ohio State University for their work on “Flavopiridol Pharmacogenetics: Clinical and Functional Evidence for the Role of SLCO1B1/OATP1B1 in Flavopiridol Disposition” just published in PLoS ONE. (All abstracts below.) Also in pharmacogenetics (albeit in mice) this month…

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CNV Analysis Tips for Illumina Data

Nov 24, 2010

Please see our updated tutorials for CNV Analysis by visiting: https://www.goldenhelix.com/resources/SNP_Variation/tutorials/index.html 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…

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A Hitchhiker’s Guide to Next Generation Sequencing – Part 1

Nov 15, 2010

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 handcrafted a version that runs on graphical processing units that…

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Recent Publications on Bladder Cancer, Schizophrenia, Childhood IgA Nephropathy, and Ancestry Markers

Nov 5, 2010

Recognition this month begins with Eric Londin at Coriell Institute for Medical Research for his publication in PLoS ONE: “CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins.” (Abstract below). Also recently published in PLoS ONE is Chiara Magri with Brescia University School of Medicine on her…

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