Golden Helix Blog

New 1kG, dbNSFP, and ESP6500 Annotation Tracks and Associated Filters

Jul 16, 2012

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…

Read more →

“Easy-to-Use” SNP & Variation Suite Assists John Curtin, PhD in Uncovering Genetic Associations for Asthma and Allergies

Jul 10, 2012

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…

Read more →

What is Bioinformatic Filtering?

Jun 29, 2012

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…

Read more →

New Analysis and Spreadsheet Manipulation Tools in SVS!

Jun 28, 2012

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…

Read more →

New Technical Support Bulletins (Forthcoming!), and a Known Bug with Filter Samples by Call Rate

Jun 27, 2012

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…

Read more →

Have We Wasted 7 Years and $100 Million Dollars on GWAS Studies?

Jun 21, 2012

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…

Read more →

Agrigenomic Researcher at U.C. Davis, Gonzalo Rincon, DVM, and Colleagues Publish 14 Articles and Obtain 2 Patents Using SVS

Jun 13, 2012

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,…

Read more →

Why You Should Care About Segmental Duplications

Jun 6, 2012

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…

Read more →

Is Free Software Really Free?

May 23, 2012

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…

Read more →

Guest Post: Stepping Outside My Open-Source Comfort Zone: A First Look at Golden Helix SVS

May 16, 2012

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,…

Read more →

Researcher Uses SVS for Pharmacogenetic Associations for 10 Years

Apr 11, 2012

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…

Read more →

Analyzing PacBio Data with SNP & Variation Suite

Mar 21, 2012

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…

Read more →

New Features in SVS: Accounting for Sex Chromosomes and Filter Columns by Variant Type

Feb 29, 2012

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…

Read more →

Admixture and Blaine Bettinger

Jan 25, 2012

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…

Read more →

Leaky Sprinklers and “The Future of NGS Market Study 2011”

Nov 23, 2011

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…

Read more →

Is NGS the Answer?

Nov 9, 2011

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…

Read more →

Sequence Analysis Methods Not Just for Sequence Data

Oct 12, 2011

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…

Read more →

Influencing the Global Dialog on Healthcare

Sep 28, 2011

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…

Read more →

Wondering what SVS can do for a PhD student? Just ask Sander.

Sep 14, 2011

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…

Read more →

Marker Map Manipulation Improvements in SVS 7.5

Aug 31, 2011

Manipulating a marker map in SVS has never been easier, thanks to expanded functionality in SVS 7.5.  Have you ever wanted to view annotation data next to marker map data?  Or expand the current marker map with spreadsheet data to create a custom map?  SVS 7.5 features two new functions…

Read more →