Category Archives: Clinical genetics

Unique Labs, Common Tool: Making VarSeq Ready for Clinical Workflows

         April 9, 2015

As VarSeq has been evaluated and chosen by more and more clinical labs, I have come to respect how unique each lab’s analytical use cases are. Different labs may specialize in cancer therapy management, specific hereditary disorders, focused gene panels or whole exomes. Some may expect to spend just minutes validating the analytics and the presence or absence of well-characterized… Read more »

Precision Medicine – Part I

         April 7, 2015

Precision Medicine Initiative On January 30, 2015, the Precision Medicine Initiative was announced by President Obama. Many in our field, researchers and clinicians alike, recognize that such a program would bring additional funding into our space to design, develop and implement new diagnostic tests that are aiding physicians in their practice of precision medicine. Here is what we know. Led by the National Institutes of Health (NIH),… Read more »

Question and Answers: Cancer Gene Panels Webcast

         March 17, 2015

Last week we conducted a webcast on “Cancer Gene Panels”; you can find the recording here. We had some excellent questions which we answered during the webcast and a few more that we didn’t get to in the allotted time. Please find answers to those questions here: 1. Are Cancer Gene Panels just another stepping stone on the way to… Read more »

Analyzing a Unique Family Structure in VarSeq 1.1.1

         March 12, 2015

I am constantly on the lookout for fun or interesting datasets to analyze in SVS or VarSeq and recently came across a study looking into inherited cardiac conduction disease in an extended family (Lai et al. 2013). The researchers sequenced the exomes from five family members including three affected siblings and their unaffected mother and an unaffected child of one… Read more »

Introducing Phenotype Gene Ranking in VarSeq

         March 3, 2015

Personal genome sequencing is rapidly changing the landscape of clinical genetics. With this development also comes a new set of challenges. For example, every sequenced exome presents the clinical geneticist with thousands of variants. The job at hand is to find out which one might be responsible for the person’s illness. In order to reduce the search space, clinicians use various methods… Read more »

PreventionGenetics to Use GoldenHelix’s VarSeq for Dx Test Offering

         February 9, 2015

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 »

Genetic Testing for Cancer

         January 20, 2015

In 1914 the German cytologist Theodor Boveri coined the phrase “Cancer is a disease of the genome”. At this time his ideas were equally revolutionary as they were highly contested. Fast forward. More than hundred years later, Next-Generation Sequencing effectively permits a highly sensitive analysis of cancer cells. It can help us to understand mutations associated with cancer development and… Read more »

Dr. Andreas Scherer to speak at ITI 2015

         January 15, 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

         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 »

6 Population Catalogs Compared with the ExAC 61,486 Exomes

         November 13, 2014

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 »

Leveraging SVS for NGS Workflows

         August 19, 2014

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 »

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 »

Why You Should Go To TCGC

         June 12, 2013

In a couple of short weeks, Gabe is headed off to TCGC in San Francisco where he will be giving part of a short course. He was super excited about it last year and is even more so this year. I sat down with him yesterday to find out why. Jessica: What’s TCGC? Gabe: Last year I got to attend… 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 »

To Find a Killer Variant: Successes and Challenges on the Journey to Mass Adoption of NGS in the Clinic

         October 22, 2012

Recently, I have been spending some time analyzing real patient data. I’m preparing for a webcast I’ll be giving in which I will walk through the process of replicating the findings of Dr. Gholson Lyon‘s study on the novel disease diagnosis he named Ogden Syndrome. Being so close to data that comes directly from clinical settings got me thinking about… Read more »