Category Archives: Big picture

PreventionGenetics to Use GoldenHelix’s VarSeq for Dx Test Offering

Today, we at Golden Helix announced our collaboration with PreventionGenetics as they prepare to implement the VarSeq software into their exome sequencing pipeline. The VarSeq software will allow PreventionGenetics to offer an exome test by dramatically speeding up the analysis process. VarSeq will narrow down sequence data into gene(s) of interest based on inheritance patterns, facilitating the identification of clinically relevant… Read more »

Final Thoughts on PAGXXIII

      Andreas Scherer    January 22, 2015    No Comments on Final Thoughts on PAGXXIII

The Plant & Animal Genome XXIII Conference (PAG) was again a success. It’s the venue for leading genetic scientists and researchers involved in plant and animal research to meet with their peers. If anything the event continues to grow. The largest population of registrations tend to be from an Academic background (64%), with Industry (25%) and Government (11%) sectors comprising… Read more »

Dr. Andreas Scherer to speak at ITI 2015

The Integrative Therapies Institute is soon hosting the annual, ITI 2015 conference January 23rd through the 25th in sunny San Diego and our own Dr. Andreas Scherer has been invited to speak. Some of the most prominent genomic and integrative medicine specialists will gather at ITI 2015 to share case studies and protocols with the community. Attendees can expect to… Read more »

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

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 »

What to expect from Golden Helix in 2015

There is a lot we can be grateful for at Golden Helix. The past year was marked by two major breakthrough launches. Earlier in 2014, we shipped SVS 8 which unified SVS with our GenomeBrowse product. We were able to improve SVS’ data management and visualization capabilities. In addition we added a number of new methods in SVS, such as SKAT-O, MM-KBAC, and various genomic prediction algorithms.

Golden Helix Gives Back – The Winners

Last month, I announced our Golden Helix Gives Back Campaign. During times like this, when funding is tight, we wanted to make a statement to our community. We at Golden Helix are committed to empower researchers and practitioners in the life science field. For those hard working people it is nice to catch a break from time to time. After… Read more »

Genomic Prediction

      Andreas Scherer    December 16, 2014    No Comments on Genomic Prediction

The major interest in genomic prediction is best understood by looking at the growth of the human population. Over the last few hundred years we have experienced an increase in population due to medical advances and massive increase in agricultural productivity. The planet’s population continues to explode: from 1 billion in 1820 to 2 billion in 1930, 3 billion in… Read more »

Bridging the gap between genetics and organic chemistry at UIUC

As Dr. Andreas Scherer mentioned in a blog post earlier this year, Golden Helix is committed to supporting the education of the next generation of genetic researchers. And as such, over the course of 2014, we at Golden Helix are working with education programs across the US and Canada to make teaching and learning bioinformatics easier. This fall semester at the… Read more »

Announcing the 2015 Abstract Challenge

Last year, as part of our ongoing commitment to empower genetic research, we hosted our first research competition. The competition was very successful and now we will make the competition an annual event. Here at Golden Helix, we are dedicated to creating powerful software that enables researchers to complete complex analysis. This competition allows us to enable discovery by awarding… Read more »

6 Population Catalogs Compared with the ExAC 61,486 Exomes

To say the announcement of Dan MacArthur’s group’s release of the Exome Aggregation Consortium (ExAC) data was highly anticipated at ASHG 2014 would be an understatement. Basically, there were two types of talks at ASHG. Those that proceeded the official ExAC release talk and referred to it, and those that followed the talk and referred to it. Why is this… Read more »

Final thoughts on ASHG14

      Andreas Scherer    October 28, 2014    No Comments on Final thoughts on ASHG14

To make a long story short, we had a blast at ASHG14. The traffic at our booth was terrific. Every day we had scheduled presentations on VarSeq, SVS, and GenomeBrowse which were very well attended. And of course, there were our new t-shirts. The new designs were well received. If anything we promise to bring more next year. In particular more… Read more »

Variant Notation: In simplicity we find complexity

Recently, I have been thinking a lot about Human Genome Variation Society (HGVS) notation — you know “G dot”, “P dot”, and “C dot”. HGVS has quickly become one of the most common ways to represent variants.  It’s no wonder that HGVS nomenclature is used so widely. It provides an easily readable, compact representation of a variant. Since it is… Read more »

Looking forward to ASHG

      Andreas Scherer    October 2, 2014    1 Comment on Looking forward to ASHG

The 64th annual ASHG meeting is coming up in just a few short weeks in San Diego. This year’s event will be an exciting one for Golden Helix as we present VarSeq, with the first demonstration on Sunday at 11:30 am in booth 422. After the demonstration we will have some great VarSeq t-shirts to give away – you will not… Read more »

VarSeq: Making Variant Discovery and Gene Panels Easy

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 »

Entering the Clinical Testing Market with VarSeq

The adoption of genetic services is key to our ability to provide personalized medicine in the future. The goal is to better diagnose diseases, predict their outcomes, and to choose the best possible care option for a patient. Our part here at Golden Helix is to essentially build the equivalent of an MRI for the genome. In this process the latest… Read more »

Exciting News for ASHG!

      Delaina Hawkins    September 23, 2014    No Comments on Exciting News for ASHG!

With ASHG only four weeks away, the hype has only continued to grow. The 64th Annual Meeting of the American Society of Human Genetics is shaping up to be one of the best with some amazing abstracts, including one from our very own Greta Linse Peterson. Greta will be presenting Monday, October 20th in room 20A at 6:15 PM in… Read more »

A few thoughts from IGES

      Golden Helix    September 18, 2014    No Comments on A few thoughts from IGES

Late last month I had the opportunity to attend one of my favorite events: the annual meeting of the International Genetic Epidemiology Society (IGES).  This year’s conference was held in Vienna, in conjunction with the Genetic Analysis Workshop (GAW) and the International Society for Clinical Biostatistics (ICBS).  The program at IGES this year was very diverse, with content ranging from… Read more »

False Positives in Big Data Analytics

We had a lot to celebrate recently. Last year was the 300th anniversary of Jacob Bernoulli’s Ars Conjectandi. In this book he consolidated central ideas in probability theory, such as the very first version of the law of large numbers. It was also the 250th anniversary of  Bayes theorem named after Thomas Bayes (1701–1761), who first suggested using the theorem to update beliefs.

Leveraging SVS for NGS Workflows

Over the last decade, DNA sequencing has made vast technological improvements. With the cost of sequencing decreasing significantly, sequencing technology has become a product for the masses. The sequencing technology and programs that were once used exclusively by major research institutions are now becoming available in many research facilities around the globe. These tools produce large amounts of data sets… Read more »

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

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 »