ANOVA, Nonparametric Tests, and More Added to SVS via New Python Capabilities

         March 3, 2011

Our recent blog post about the release of  SNP & Variation Suite v7.4 gave you a sneak peek into what can be achieved with the revamped SVS/Python integration, which includes the incorporation of NumPy and SciPy libraries and new graphical layout capabilities. A Python package (such as SciPy) is similar to an R package, which you may be more familiar… Read more »

Recent Publications on Asthma, Schizophrenia, Peripheral Neuropathy, Rheumatoid Arthritis, Alzheimer Disease, and Esophageal Cancer

         February 17, 2011

As you may have guessed from the title of this post, we’ve had a lot of customers publishing in the first six weeks of 2011. We are always excited to hear about about our customers’ findings and how they were able to use SNP & Variation Suite to accelerate their research. (All abstracts below.) First, in the pharma world, congrats… Read more »

Checking Relatedness and/or Inbreeding in Samples as a Quality Assurance Measure

         February 10, 2011
James' whiteboard with IBD calculations

Almost every statistic that is used for significance testing in scientific research comes with a set of assumptions. If the test is applied to data that does not meet those assumptions, then the results of the test may not be valid. The statistics commonly used in genome-wide association studies (GWAS), such as the Fisher’s Exact Test or the Chi-Square Test,… Read more »

A Hitchhiker’s Guide to Next Generation Sequencing – Part 3

         January 19, 2011

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 »

Recent Publications on Schizophrenia, Cocaine Abuse, Childhood IgA Nephropathy, CNV Regions, and Genetic Variants in Metabolic Traits

         January 5, 2011

Happy New Year! Golden Helix customers published 92 papers in 2010 unveiling new associations and novel findings using SNP and Variation Suite – a great feat for all! We anticipate an even more “significant” 2011. Wrapping up last year, congrats to Subba Rao Indugula, Guangyun Sun, and Ranjan Deka over at the University of Cincinnati College of Medicine for their… Read more »

A Hitchhiker’s Guide to Next Generation Sequencing – Part 2

         December 9, 2010

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 »

Recent Publications on Type 2 Diabetic Retinopathy, Grapevine Flavor, Pulminary Function, and Pharmacogenetics Testing

         November 30, 2010

Let’s kick off this month’s recognition with Audrey Papp and Wolfgang Sadee at Ohio State University for their work on “Flavopiridol Pharmacogenetics: Clinical and Functional Evidence for the Role of SLCO1B1/OATP1B1 in Flavopiridol Disposition” just published in PLoS ONE. (All abstracts below.) Also in pharmacogenetics (albeit in mice) this month is Tristan Sissung at the NIH National Cancer Research. His… Read more »

CNV Analysis Tips for Illumina Data

         November 24, 2010

Please see our updated tutorials for CNV Analysis by visiting: http://goldenhelix.com/resources/SNP_Variation/tutorials/index.html The following statement is representative of a common question that is posed to the Golden Helix support team: “I followed all of the steps in the SVS7 CNV analysis tutorial, but my results seem kinda funny. The segment means are skewed to the left and it doesn’t look like… Read more »

Recent Publications on Bladder Cancer, Schizophrenia, Childhood IgA Nephropathy, and Ancestry Markers

         November 5, 2010

Recognition this month begins with Eric Londin at Coriell Institute for Medical Research for his publication in PLoS ONE: “CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins.” (Abstract below). Also recently published in PLoS ONE is Chiara Magri with Brescia University School of Medicine on her study locating new CNVs in schizophrenia. (Abstract below) Skipping over… Read more »

ASHG 2010 is here!

         November 2, 2010

Well, it’s that time of year again, when the genetics world convenes for the American Society of Human Genetics Annual Meeting. This year, we have the privilege of heading to the nation’s capital for the week of November 2-6. ASHG is always a highlight of our year as Golden Helix employees get the opportunity to talk to so many researchers… Read more »

Conference Report: International Genetic Epidemiology Society and Genetic Analysis Workshop

         October 27, 2010

The week of October 10-16th was a busy time in our industry.  Hundreds of biostatisticians, genetic epidemiologists, and statistical geneticists gathered in Cambridge, MA for the annual conference of the International Genetic Epidemiology Society (IGES) on October 10-12, followed by the biennial Genetic Analysis Workshop (GAW) on October 13-16.  I had the opportunity to participate in both conferences, and I… Read more »

Video Graphics and Genomics: A Real Game Changer?

         October 20, 2010

Why should a genetic researcher care about the latest in video gaming technology? The answer is video graphics cards or Graphics Processing Units (GPUs). For certain computational tasks, a single GPU can perform as well as an entire cluster of CPUs for only a fraction of the cost. And because video gaming has grown into a highly competitive multi-billion dollar… Read more »

Four New Add-on Scripts Available for Strand Flipping, Histogram Means, and Chi-Squared Calculation

         October 14, 2010

The scripting environment in SVS 7 allows for cross-communication between the powerful Python scripting language and the tools used in data analysis. Scripting is often the most effective way to make new features available to customers prior to new software releases. We often write scripts based on a specific customer’s need and then expand availability to all customers, many who… Read more »

Best Practices for Incorporating Public Genotype Data in Your Study

         October 12, 2010

The Golden Helix sales team recently came to me for recommendations regarding best practices for incorporating public controls in SNP GWAS.  It seems that there has been a surge of questions regarding this practice over the past few weeks from our customers.  Initially, I laughed at the irony of being asked to outline the best practices for what I see… Read more »

Recent Publications on Ankylosing Spondylitis, Asthma, Heroin Dependence, and Lupus

         October 6, 2010

It’s been a busy month for the genetics community, and Golden Helix customers are no exception. First in the line up, congrats to Marta Artieda with Progenika Biopharma in Spain for her work on “Association of the Intergenic Single-Nucleotide Polymorphism rs10865331 (2p15) with Ankylosing Spondylitis in a Spanish Population” in the Journal of Rheumatology (abstract below). Next up, kudos to… Read more »

Stop Ignoring Experimental Design (or my head will explode)

         September 29, 2010
Stop Ignoring Experimental Design (or my head will explode)

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 »

Report from Capita Selecta in Complex Disease Analysis Conference in Belgium

         September 14, 2010

How much fun is a person allowed to have when going to a conference? That kind of sums up my personal experience going to the first ever Capita Selecta in Complex Disease Analysis (bi-annual) conference in Leuven, Belgium. Not only was it fun, but the conference program was packed with interesting talks and short courses. Dr. Kristel van Steen and… Read more »

New Add-on Scripts Available: BEAGLE & BEAGLECALL Scripts Package

         September 8, 2010

In the ongoing quest to empower our customers with the latest in genetic analysis methods, we are continually releasing new functionality for SNP & Variation Suite 7 in the form of add-on scripts. Add-on scripts are written in Python, a clear and powerful object-oriented programming language similar to Java or Perl. Python provides fully-programmatic access to most aspects of the… Read more »