GenomeBrowse is here!

         September 13, 2012

Golden Helix announced it would offer a complimentary genome browser for visualizing DNA and RNA-Seq data back in October of 2011; however no release date was disclosed at that time. Well, after much blood, sweat, and tears, we are VERY excited to announce that GenomeBrowseTM is here! GenomeBrowse raises the bar on the on the experience of exploring and finding… Read more »

New Tools to Simplify the Workflow for Identifying Candidate Functional Polymorphisms in SVS

         September 5, 2012

Dr. Ken Kaufman’s extremely popular webinar inspired us to build new tools that would simplify the process of analyzing whole-exome DNA sequencing data even further.  First I’ll describe the tools showcased in the webcast.  Then I’ll detail the new tools we created to allow for a revised and simplified workflow. Subset Informative Genotypes by Category The Subset Informative Genotypes by… Read more »

Introducing GenomeBrowse: A revolutionary visual experience for genomic data

         August 29, 2012

As first announced in October 2011 and previewed in a blog post last month, Golden Helix has been hard at work for the last year developing a free genome browser called GenomeBrowseTM. We are now beyond excited to announce that GenomeBrowse will be available to the public on September 12th on our website. (Did we mention it’s free?) GenomeBrowse raises… Read more »

Peter K. Gregersen, MD Puts Analytical Power in the Hands of the Biologist with SVS

         August 21, 2012

Dr. Peter K. Gregersen, head of the Robert S. Boas Center for Genomics and Human Genetics at the Feinstein Institute for Medical Research, utilizes GWAS, targeted arrays, and sequencing technologies to identify genes associated with human autoimmune disorders. The arrival of the GWAS platform in the mid-2000’s greatly accelerated the pace of gene discovery—as well as accelerating the number of… Read more »

Learning vs. Doing (or why that Ph.D. took 10 years)

         August 15, 2012

What prevents scientists from being more productive and if we knew, could we do anything about it? I’d like to look at an often overlooked, but huge productivity inhibitor — bad multitasking. Many people put “excellent multitasker” on their resume as a badge of honor. We laud the efficiency of a good multitasker — they are rarely idle — someone… Read more »

Dr. Ken Kaufman’s Webcast on Exome Sequencing Wildly Successful

         August 9, 2012

Thank you to everyone who joined us yesterday for a webcast by Dr. Ken Kaufman of Cincinnati Children’s Hospital: “Identification of Candidate Functional Polymorphism Using Trio Family Whole Exome DNA Data.” Over 750 people registered for this event and 430 attended – a new Golden Helix record! If you missed the webcast (or would like to watch it again), the… Read more »

One Track to Rule Them All: Close but not quite from the 1000 Genomes Project

         July 31, 2012

I recently curated the latest population frequency catalog from the 1000 Genomes Project onto our annotation servers, and I had very high hopes for this track. First of all, I applaud 1000 Genomes for the amount of effort they have put in to providing the community with the largest set of high-quality whole genome controls available. My high hopes are… Read more »

Announcing Technical Support Bulletins

         July 20, 2012

Last month I was inspired to create a new way to keep our customers apprised of the latest information on Golden Helix software without cluttering inboxes and overwhelming our blog. I happened to receive a link to an article for one of Illumina’s bulletins and realized that was exactly what we needed at Golden Helix as well! On Wednesday, we… Read more »

My 23andMe Trio Exomes Arrived: Sneak Peek

         July 18, 2012

There is nothing cooler than having something arrive that you have been excitedly waiting for: last week I got an email notification that my 23andMe exome results were ready. Actually, I got 3 emails that my exome results were ready. You see, I lucked out. It all began two years ago on DNA day when Hacker News reported that 23andMe… Read more »

New 1kG, dbNSFP, and ESP6500 Annotation Tracks and Associated Filters

         July 16, 2012

SVS 7.6.7 features new tools for filtering sequencing data based on functional predictions and allele frequencies. To complement these new features, new annotations tracks have been uploaded to our data server and are now available for our customers! Below you will find descriptions of the new tools and the related annotations track(s).

“Easy-to-Use” SNP & Variation Suite Assists John Curtin, PhD in Uncovering Genetic Associations for Asthma and Allergies

         July 10, 2012

Dr. John Curtin is a Lecturer in Functional Genomics at the University of Manchester where he works with a large team studying the development of asthma in a birth cohort. This group has received data on study subjects periodically for over a decade including before birth. Given how much data there is, data management is a big deal to Dr…. Read more »

What is Bioinformatic Filtering?

         June 29, 2012

Recently I gave a presentation on bioinformatic filtering: the process of using quality scores, annotation databases, and functional prediction scores to intelligently and quickly reduce your variant search space. View the recording here» In this webcast, I mention that filtering is something we have been doing for a long time, and that there are some great examples that use exome… Read more »

New Analysis and Spreadsheet Manipulation Tools in SVS!

         June 28, 2012

The script development team at Golden Helix has been hard at work these past few months and this means several new and exciting tools for our SVS customers!  The scripts featured in this blog post vary in function, from expanding the analytical options currently offered in SVS to transforming and editing spreadsheets.  As always, we invite you to visit our… Read more »

New Technical Support Bulletins (Forthcoming!), and a Known Bug with Filter Samples by Call Rate

         June 27, 2012

As Product Quality Manager, I have been spending quite a bit of time lately thinking about the best way to communicate with our Golden Helix customers with regards to product quality and customer support issues. Most of our customers at this point have already seen several emails from me this year! Email is certainly one way to get an announcement… Read more »

Exaggerating your number of controls or being precise? “Variant not found in over 10,000 chromosomes from EVS…”

         June 22, 2012

Reading through the last release of AJHG I saw a couple papers mention that the putative rare variant they were investigating was “not present in over 10,000 control chromosomes from the EVS”. My first reaction was, “What? Do they mean the NHLBI 5400 Exome Sequencing Project? They only have 5,400 exomes not over 10,000! I wonder if there is some… Read more »

Admixture in Reference Populations: 1000 Genomes Uses African Americans in African Reference Group

         June 22, 2012

Today I ran into an interesting fact about how a prolifically used catalog of population controls classifies African Americans with potential impacts on research outcomes. The 1000 Genomes Project is arguably our best common set of controls used in genomic studies. They recently finished what was termed as “Phase 1” of the project, and they have been releasing full sets… Read more »

Have We Wasted 7 Years and $100 Million Dollars on GWAS Studies?

         June 21, 2012

Type 2 Diabetes, Rheumatoid Arthritis, Obesity, Chrohn’s Diseases and Coronary Heart Disease are examples of common, chronic diseases that have a significant genetic component. It should be no surprise that these diseases have been the target of much genetic research. Yet over the past decade, the tools of our research efforts have failed to unravel the complete biological architecture of… Read more »

Agrigenomic Researcher at U.C. Davis, Gonzalo Rincon, DVM, and Colleagues Publish 14 Articles and Obtain 2 Patents Using SVS

         June 13, 2012

Editor’s Note: This case study was written while Dr. Gonzalo Rincon was with the University of California, Davis. Dr. Rincon is now working as a Principal Investigator in Animal Genetics at Zoetis. Gonzalo Rincon, DVM is a Project Scientist in the Medrano Lab, part of the Department of Animal Science, at the University of California, Davis. While the lab works… Read more »