Today is a big day for us. Today we are announcing a major release of our flagship product, SNP & Variation Suite (SVS), to the general public. SVS 8 is a substantial improvement over the previous release in a number of dimensions (see detailed discussion on our What’s New page). We’ve come a long way. Over five years ago, in… Read more »
Time goes by fast. With the completion of the Human Genome Project in 2003, scientists worldwide were trying to understand the cause and effect of variations in the genome as they relate to functionalities, traits and disease. Along the way, we at Golden Helix helped researchers analyze data, discover variations and draw conclusions. It turns out that the real bottleneck… Read more »
Recently, Dr. Christophe Lambert joined the esteemed Theral Timpson over at Mendelspod to talk a bit about the big picture of bioinformatics. This 37 minute podcast references a recent blog post by Christophe on Illumina competing with its customers, the notion that if the end user isn’t buying that no one is selling, and learning from our GWAS mistakes. One… Read more »
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 »
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 »
What prevents scientists from being more productive and if we knew, could we do anything about it? I’d like to look at an often overlooked, but huge productivity inhibitor — bad multitasking. Many people put “excellent multitasker” on their resume as a badge of honor. We laud the efficiency of a good multitasker — they are rarely idle — someone… Read more »
Type 2 Diabetes, Rheumatoid Arthritis, Obesity, Chrohn’s Diseases and Coronary Heart Disease are examples of common, chronic diseases that have a significant genetic component. It should be no surprise that these diseases have been the target of much genetic research. Yet over the past decade, the tools of our research efforts have failed to unravel the complete biological architecture of… Read more »
The prevalence of open-source bioinformatic tools in the genetic research space is enormous. According to The North Shore LIJ Research Institute, there are over 500 genetic analysis software packages – the great majority of which are free – as of August 2010. Open-source tools are incredibly important in genetics. They allow new methodologies to be created and expanded. They tie… Read more »
Have you ever chosen to do something yourself instead of paying money for the alternative, when, in the long run, the alternative is not really that expensive? We all have, as we all have limited budgets. One particular example comes to mind in my own life. My boyfriend, Ben, and I bought a house in April. Unfortunately, it wasn’t properly… Read more »
While there is a lot of excitement in the industry about Next-Generation Sequencing, questions remain as to whether it will be “the answer” to the ails of the genetic research industry. I recently had the opportunity to sit down with three of Golden Helix’s thought leaders and ask a few questions about NGS – Gabe Rudy, Vice President of Product… Read more »
On September 16-17th, I attended the Asia-Pacific Economic Cooperative (APEC) Health Systems Innovation Policy Dialog in San Francisco. It was a stimulating opportunity to look at global healthcare concerns from the perspective of developing and developed economies. There was much opportunity to dialog and frame the issues around transforming healthcare systems to meet pressing problems such as aging populations, the… Read more »
The advances in DNA sequencing are another magnificent technological revolution that we’re all excited to be a part of. Similar to how the technology of microprocessors enabled the personalization of computers, or how the new paradigms of web 2.0 redefined how we use the internet, high-throughput sequencing machines are defining and driving a new era of biology. Biologists, geneticists, clinicians,… Read more »
When you think about the cost of doing genetic research, it’s no secret that the complexity of bioinformatics has been making data analysis a larger and larger portion of the total cost of a given project or study. With next-gen sequencing data, this reality is rapidly setting in. In fact, if it hasn’t already, it’s been commonly suggested that the… Read more »
If you have had any experience with Golden Helix, you know we are not a company to shy away from a challenge. We helped pioneer the uncharted territory of copy number analysis with our optimal segmenting algorithm, and we recently handcrafted a version that runs on graphical processing units that you can install in your desktop. So it’s probably no… Read more »
Over the past 3 years, Golden Helix has analyzed dozens of public and customer whole-genome and candidate gene datasets for a host of studies. Though genetic research certainly has a number of complexities and challenges, the number one problem we encounter, which also has the greatest repercussions, is born of problematic experimental design. In fact, about 95% of the studies… Read more »
“Where is the missing heritability?” is a question asked frequently in genetic research, usually in the context of diseases that have large heritability estimates, say 60-80%, and yet where only perhaps 5-10% of that heritability has been found. The difficulty seems to come down to the common disease/common variant hypothesis not holding up. Or perhaps more accurately, that the frequency… Read more »
As Andy Ferrin and I drove the five-hour car ride home from a cytogenetics conference, we had a lot of time to reflect on the persistent themes we heard in presentations and dialog among conference attendees. Taking somewhat of an outsider view, we traced each complaint, each sigh of frustration, and the unverbalized assumptions behind opposing viewpoints, and they all… Read more »
