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 »

Is Illumina Aiming to Compete with its Customers?

         February 12, 2013

In a recent GenomeWeb article by Tony Fong, “Sequenom’s CEO ‘Puzzled’ by Illumina’s Buy of Verinata, Lays out 2013 Goals at JP Morgan,” Harry Hixson, Sequenom’s CEO, expresses puzzlement over why its major supplier, Illumina, is acquiring a Sequenom competitor in Non-Invasive Prenatal Testing (NIPT), and thus apparently competing with one of its major customers. In a JP Morgan interview… Read more »

Upcoming webcast: New Study Identifies High-Risk Variants Associated with Autism Spectrum Disorders

         January 24, 2013

Twenty-four new variants discovered, each conferring more than a 2-fold risk of developing ASD Date: January 29, 2013, Noon EST, 90 minutes Presenters: Dr. Hakon Hakonarson, Director of the Center for Applied Genomics, Children’s Hospital of Philadelphia Dr. Mark F. Leppert, Professor of Human Genetics at the University of Utah and Chief Science Advisor at Lineagen Dr. Michael Paul, President… Read more »

Three New Scripts and Two Updated Ones

         January 16, 2013

We are excited to let you know about new scripts to aid in filtering rows/columns and identifying unique values in a column, as well as two updated scripts. Don’t forget about the Technical Support Bulletins which keep you up-to-date on all the latest script news. You can stream this feed via an RSS reader, receive email updates, or see the… Read more »

Meet Autumn Laughbaum: Biostatistician

         January 9, 2013

As a senior studying statistics at Montana State University, I was fortunate to be granted the opportunity to intern with the development team at a local software company.  I was even more fortunate when this internship turned into full-time employment after I graduated. Working on a team with extremely talented individuals, I realized the significant impact our company makes through… Read more »

New Plant and Animal Genomes and Tracks Now Available!

         January 3, 2013

Happy new year! We hope all of our readers, clients, and users had a great holiday season filled with friends and family! While Golden Helix did take a break from blogging in December, we’ve still been pretty busy bringing you new and exciting things. We’re pleased to announce the addition of genome maps and annotation tracks for two new plant… 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: 23andMe Variant Analysis of My Personal Exome

         November 28, 2012

Join me on December 5th for a one-hour webcast as I explore my personal exome provided by the Exome Pilot project of 23andMe. Exome sequencing has seen many success stories in the realm of diagnosing highly penetrant monogenic disorders as well as in informing treatment of certain cancers. As the use of exome sequencing expands to more complex polygenic disorders… Read more »

SVS 7.7 is here!

         November 19, 2012

After much anticipation, we are excited to announce that SVS 7.7 is available! It’s been a lot of work, but we are pleased with the result and know you will be too! SVS 7.7 includes: Improved RNA-Seq Analysis Package for mRNA Expression Profiling Import tabularized quantification data from the Golden Helix pipeline or other sources. Utilize DESeq to perform differential… 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 »

Dr. Folefac Aminkeng Saves Time and Increases Productivity with SVS to Study the Pharmacogenomics of Adverse Drug Reactions in Cancer Therapy

         October 17, 2012

Dr. Folefac Aminkeng is a Postdoctoral Fellow at The Centre for Molecular Medicine and Therapeutics (CMMT) at the University of British Columbia in Vancouver, BC, Canada. He utilizes GWAS studies to identify single-nucleotide polymorphisms (SNPs) that might be associated with serious adverse drug reactions (ADRs) in cancer therapeutics. The field of pharmacogenomics—how one’s genetic makeup affects drug response—has grown exponentially… 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 »

Guest Post: Next Generation Variant Calling

         September 26, 2012

Editor’s Note by Gabe Rudy: I’ve had the chance to exchange thoughts, emails, and blog post comments for a while now with Jeff as he has written posts on NGS Leaders and engaged with me on 23andMe. He has also worked with Golden Helix software as part of Dr. Todd Lencz’s research efforts at Zucker Hillside Hospital until he recently… Read more »

Election Season: Which Exome Chip Wins?

         September 19, 2012

It has now been about a year since Illumina and Affymetrix announced their respective exome genotyping arrays.  Both products were launched with ambitious visions of how they would enable researchers to learn significantly more about the cause of human diseases. Sales of the Illumina chip exceeded expectations, and the company said that it sold enough exome chips through the first… Read more »

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 »