Search Results for: Catalog

New and Updated Annotation Tracks Now Available!

         June 11, 2015

In recent months we have been updating our public annotation library to include the most recent versions of existing sources as well as include new sources. Each of these annotation sources are compatible with our three major products (SVS, GenomeBrowse and VarSeq) and can be used for visualization, annotation and filtering. NHLBI ESP6500SI-V2-SSA137 Exomes Variant Frequencies 0.0.30, GHI Annotations are… Read more »

VarSeq is a better ANNOVAR, snpEff and VEP

         June 9, 2015

Yes, I said it. “Them be fighting words” you may say. Well, it’s worth putting a stake in the ground when you have worked hard to have a claim worth staking. We have explored the landscape, surveyed the ravines and dangerous cliffs, laboriously removed the boulders and even dynamited a few tree stumps. Stake planted. Ok, so now I’m going… Read more »

Precision Medicine – Part V – Bioinformatics Pipelines and Systems Infrastructure

         May 7, 2015
bioinformatics

Bioinformatics Pipelines and Systems Infrastructure The genetics industry is undergoing a fundamental shift from a clinical science focus to a bioinformatics focus. Genetic services require a greater level of data analytics sophistication than is required for other laboratory testing. Currently, data generated by new tests overwhelms current information technology systems and human interpretation capabilities. This is one of the reasons… Read more »

Supercentenarian Variant Annotation: Complex to Primitive

         March 19, 2015

In a previous blog post, I demonstrated using VarSeq to directly analyze the whole genomes of 17 supercentenarians. Since then, I have been working with the variant set from these long-lived genomes to prepare a public data track useful for annotation and filtering. Well, we just published the track last week, and I’m excited to share some of the details… Read more »

New and Updated Annotation Tracks Now Available!

         January 29, 2015

In recent months we have been updating our public annotation library to include the most recent versions of existing sources, as well as include new sources. All of these annotation sources are compatible with our three major products, VarSeq, SVS, and GenomeBrowse, and can be used for visualization, annotation, and filtering. dbNSFP NS Functional Predictions 2.8, GHI and dbNSFP Predictions… Read more »

SVS, Population Genetics, and 1000 Genomes Phase 3

         January 27, 2015

One frequent question I hear from SVS customers is whether whole exome sequence data can be used for principal components analysis (PCA) and other applications in population genetics. The answer is, “yes, but you need to be cautious.” What does cautious mean? Let’s take a look at the 1000 Genomes project for some examples.

In Pursuit of Longevity: Analyzing the Supercentenarian Whole Genomes with VarSeq

         January 13, 2015

If you haven’t been closely watching the twittersphere or other headline sources of the genetics community, you may have missed the recent chatter about the whole genome sequencing of 17 supercentenarians (people who live beyond 110 years). While genetics only explains 20-30% of the longevity of those with average life-spans, it turns out there is a number of good reasons… Read more »

VarSeq: Making Variant Discovery and Gene Panels Easy

         September 29, 2014

Last week, our CEO Andreas Scherer announced our entrance into the clinical testing market with VarSeq. This week, I will be giving a webcast on Wednesday introducing this new tool and demonstrating its capabilities. (Register for the webcast) VarSeq’s focused purpose is making NGS gene testing and variant discovery efficient, scalable and accessible to users with a broad range of backgrounds and specialties. In this blog post, we will examine the use cases that VarSeq supports in more detail,… Read more »

Updates to ClinVar and dbSNPs: Fresh charts for Cromonaughts!

         August 28, 2014

I’m sitting in the Smithsonian Air and Space Museum basking in the incredible product of human innovation and the hard work of countless engineers. My volunteer tour guide started us off at the Wright brother’s fliers and made a point of saying it was only 65 years from lift off at Kitty Hawk to the landing of a man on the moon…. Read more »

RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care

         August 14, 2014

You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product. But in fact, there is more complexity here than you ever really wanted to know about. Andrew Jesaitis covered some of this… Read more »

The New Human Genome Reference and Clinical Grade Annotations: It’s All About the Coordinates

         February 17, 2014

On my flight back from this year’s Molecular Tri-Conference in San Francisco, I couldn’t help but ruminate over the intriguing talks, engaging round table discussions, and fabulous dinners with fellow speakers. And I kept returning to the topic of how we aggregate, share, and update data in the interest of understanding our genomes. Of course, there were many examples of… Read more »

Turning SRA Files Into Usable BAMs and VCFs

         January 21, 2014

In our recent webcast, Advancing Agrigenomic Discoveries with Sequencing and GWAS Research, Greta Linse Peterson featured bovine data which she download from the NCBI website. The data was downloaded in SRA format and in order to analyze the data in SVS, the files had to be converted to BAMs and then merged into a single VCF file. Since many of… Read more »

What Can Exomes Tell Us About the Pathology of Complex Disorders?

         February 26, 2013

My investigation into my wife’s rare autoimmune disease I recently got invited to speak at the plenary session of AGBT about my experience in receiving and interpreting my Direct to Consumer (DTC) exomes. I’ve touched on this before in my post discussing my own exome and a caution for clinical labs setting up a GATK pipeline based on buggy variants… Read more »

GATK is a Research Tool. Clinics Beware.

         December 3, 2012

In preparation for a webcast I’ll be giving on Wednesday on my own exome, I’ve been spending more time with variant callers and the myriad of false-positives one has to wade through to get to interesting, or potentially significant, variants. So recently, I was happy to see a message in my inbox from the 23andMe exome team saying they had… Read more »

Upcoming Webcast – Reproducing a DNA-Seq Discovery: Finding the Causal Variant of a Novel X-Linked Disorder

         October 10, 2012

Date: Wednesday, October 24th, 12:00 pm EDT | 4:00 pm UTC Presenter: Gabe Rudy, VP of Product Development Abstract Next-generation sequencing of DNA has shown to be a successful tool to discover causal variants of rare, highly penetrant mendelian diseases. In this webinar, we will analyze clinical samples to demonstrate the bioinformatic workflows and visualization techniques used to reproduce the… Read more »

Streamlined Workflow for Identifying Candidate Functional Polymorphisms

         October 4, 2012

Since Dr. Ken Kaufman gave his webcast on Identifying Candidate Functional Polymorphisms in SVS, we’ve been working  with Dr. Kaufman to simplify and automate many of the steps in his workflow.  I touched on this in my last blog post, and I’m excited to report that with Ken’s help, we’ve been able to simplify the workflow even more. In particular… 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 »

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 »

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).

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 »