Search Results for: Report

Variant Notation: In simplicity we find complexity

         October 9, 2014

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 »

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 »

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 »

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 added value of GenomeBrowse

         July 17, 2014

We released GenomeBrowse 2.0 earlier this year, allowing users to review all types of genomic data. Since then, it has received rave reviews from thousands of users around the world. Essentially, it’s the Google Earth app for genomic data. GenomeBrowse allows a user to sift through vast amounts of genomic data, and make it easy to focus on a single part… Read more »

The State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP

         June 25, 2014

Up until a few weeks ago, I thought variant classification was basically a solved problem. I mean, how hard can it be? We look at variants all the time and say things like, “Well that one is probably not too detrimental since it’s a 3 base insertion, but this frameshift is worth looking into.” What we fail to recognize is… Read more »

Guest Post: Uncovering the Genetic Mechanisms of Common Language Disabilities, by John Eicher

         May 20, 2014

When many people think of learning disabilities such as dyslexia and language impairment, they typically do not think of a biological or medical condition. Even more rarely do people think of these conditions as being the result of biological and genetic phenomena. However, that is exactly what I have thought of every day during my doctoral training in the Department… Read more »

Genomics in the City of Brotherly Love

         April 30, 2014

Philadelphia. The City of Brotherly love, home of the Philadelphia cheesesteak, and home to the Children’s Hospital of Philadelphia, who took the No. 1 spot in this year’s U.S. News & World Report’s Best Children’s Hospitals Honor Roll. We are honored (and excited!) to sponsor this year’s Mid-Atlantic Epidemiology and Statistics (MAGES) Conference at the University of Pennsylvania. MAGES will… Read more »

Adding Value Through Golden Helix Services

         April 9, 2014

As I write this article, Golden Helix has hundreds of clients in top research institutions world-wide. The adoption of our product at these institutions ranges from a few individual users to site licenses used by entire organizations. Because of the quality of SNP & Variation Suite (SVS) and GenomeBrowse, our competence in the field is recognized, and increasingly our clients… 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 »

“Intriguing Findings Are for Romance Novels”

         October 29, 2013

A report from the World Congress of Psychiatric Genetics Earlier this month, while much of the genetics community was scrambling to edit and print their posters for ASHG, I had the opportunity to attend WCPG, the World Congress of Psychiatric Genetics, in Boston.  This was my second trip to WCPG and it is becoming one of my favorite events to… Read more »

Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory Usage

         July 17, 2013

Genotype imputation is a common and useful practice that allows GWAS researchers to analyze untyped SNPs without the cost of genotyping millions of additional SNPs. In the Services Department at Golden Helix, we often perform imputation on client data, and we have our own software preferences for a variety of reasons. However, other imputation software packages have their own advantages… 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 »

The Murky Waters of Variant Nomenclature – You Could Be Missing Vital Information

         May 6, 2013

When researchers realized they needed a way to report genetic variants in scientific literature using a consistent format, the Human Genome Variation Society (HGVS) mutation nomenclature was developed and quickly became the standard method for describing sequence variations. Increasingly, HGVS nomenclature is being used to describe variants in genetic variant databases as well. There are some practical issues that researchers… Read more »

Population Structure + Genetic Background + Environment = Mixed Model

         March 22, 2013

A few months ago, our CEO, Christophe Lambert, directed me toward an interesting commentary published in Nature Reviews Genetics by authors Bjarni J. Vilhjalmsson and Magnus Nordborg.  Population structure is frequently cited as a major source of confounding in GWAS, but the authors of the article suggest that the problems often blamed on population structure actually result from the environment… Read more »

Follow Along on an Analyst’s Journey to Filter Whole Genome Data to Four Candidate Variants in SVS

         March 14, 2013

Last week Khanh-Nhat Tran-Viet, Manager/Research Analyst II at Duke University, presented the webcast: Insights: Identification of Candidate Variants using Exome Data in Ophthalmic Genetics. (That link has the recording if you are interested in viewing.) In it, Khanh-Nhat highlighted tools available in SVS that might be under used or were recently updated. These tools were used in his last three… 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 »

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 »

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 »