There is nothing cooler than having something arrive that you have been excitedly waiting for: last week I got an email notification that my 23andMe exome results were ready. Actually, I got 3 emails that my exome results were ready. You see, I lucked out. It all began two years ago on DNA day when Hacker News reported that 23andMe… Read more »
SVS 7.6.7 features new tools for filtering sequencing data based on functional predictions and allele frequencies. To complement these new features, new annotations tracks have been uploaded to our data server and are now available for our customers! Below you will find descriptions of the new tools and the related annotations track(s).
Dr. John Curtin is a Lecturer in Functional Genomics at the University of Manchester where he works with a large team studying the development of asthma in a birth cohort. This group has received data on study subjects periodically for over a decade including before birth. Given how much data there is, data management is a big deal to Dr…. Read more »
Recently I gave a presentation on bioinformatic filtering: the process of using quality scores, annotation databases, and functional prediction scores to intelligently and quickly reduce your variant search space. In this webcast, I mention that filtering is something we have been doing for a long time, and that there are some great examples that use exome sequencing data along with… Read more »
The script development team at Golden Helix has been hard at work these past few months and this means several new and exciting tools for our SVS customers! The scripts featured in this blog post vary in function, from expanding the analytical options currently offered in SVS to transforming and editing spreadsheets. As always, we invite you to visit our… Read more »
As Product Quality Manager, I have been spending quite a bit of time lately thinking about the best way to communicate with our Golden Helix customers with regards to product quality and customer support issues. Most of our customers at this point have already seen several emails from me this year! Email is certainly one way to get an announcement… 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 »
Editor’s Note: This case study was written while Dr. Gonzalo Rincon was with the University of California, Davis. Dr. Rincon is now working as a Principal Investigator in Animal Genetics at Zoetis. Gonzalo Rincon, DVM is a Project Scientist in the Medrano Lab, part of the Department of Animal Science, at the University of California, Davis. While the lab works… Read more »
My work in the GHI analytical services department gives me the opportunity to handle data from a variety of sources. I have learned over time that every genotyping platform has its own personality. Every time we get data from a new chip, I tend to learn something new about the quirks of genotyping technology. I usually discover these quirks the… 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 »
I’m a huge supporter of the Free and Open Source Software movement. I’ve written more about R than anything else on my blog, all the code I post on my blog is free and open-source, and a while back I invited you to steal my blog under a cc-by-sa license. Every now and then, however, something comes along that just might be worth paying… Read more »
Dr. Julia Pinsonneault is a Research Scientist at The Ohio State University where she works to find biomarkers that guide effective treatment. Published recently in Neuropsychopharmacology, Julia has found success using SVS to find novel associations that move her research forward. Usually managing 3-5 research projects at a time from various cohorts, she found time in her busy schedule this… Read more »
As most in the Golden Helix community are aware, SNP & Variation Suite (SVS) can handle all sorts of data including files from Affymetrix, Illumina, Agilent, and Complete Genomics with its powerful data management capabilities. Announced in February, SVS is now part of the Pacific Biosciences Partner Program and has the ability to analyze PacBio files.
In the last couple of weeks, the SVS Script Repository has seen a handful of new additions. This blog post highlights three new scripts, but as always, we welcome you to check out our repository regularly to enjoy the new and exciting functionality made possible by our Python integration in SVS! (To get these, or any other scripts, simply go… Read more »
Allow me to introduce you to Blaine Bettinger. Blaine is a patent attorney who holds a PhD in Biochemistry with a concentration in genetics. He is also a family history enthusiast who writes the Genetic Genealogist blog, where he gives commentary on applications of genomic science for advancing personal and family history research. I first learned about Blaine last May… 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 »
Speaking as somebody with a long history in data analysis, there are few things I find more exciting and tantalizing than new analysis methods that might apply to a problem I am trying to solve or was unable to solve in the past. Whenever I make a breakthrough in one project, I find I want to abandon the current project… 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 »
Sander van der Laan is like many Ph.D. students in the genomic analysis space. He has a lot of data and a lot of ideas about how to analyze it. His professor wants results. He’s the only one doing genetics (everyone else in his department is doing proteomics), so there’s always too much to do. And he finds command-line tools… Read more »
