Cheryl Rogers

Introducing Dr. Heather J. Huson

Dr. Heather Huson

Dr. Heather Huson

It is with great excitement that we introduce our next webcast: Population Structure & Genetic Improvement in Livestock, presented by Dr. Heather J. Huson of Cornell University. Huson was one of the first place winners in this year’s research abstract competition. As part of the competition Huson has the opportunity to present her research in a webcast on Tuesday July 22nd.

Heather received a Bachelor’s in Animal Science from Cornell University in 1997 and went on to complete her Ph.D. in Molecular Genetics at the University of Alaska Fairbanks in 2011.

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Ashley Hintz

The Differences Between EMMA and EMMAX

I recently gave a webcast on GWAS in a model organism: Arabidopsis thaliana; a question was brought up about the differences between EMMA and EMMAX and why the results with each would differ. Continue reading

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Alyssa Burzynski

Join us for a GWAS in Arabidopsis Thaliana

Join us tomorrow, July 9th at 12PM EDT, for Ashley Hintz’s webcast on GWAS in a Model Organism: Arabidopsis Thaliana.

Joining the Golden Helix team as a Field Application Scientist in April of 2014, Hintz is the perfect candidate to present on Arabidopsis Thaliana given her background in zoology and phylogenetics of planigales. Continue reading

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Alyssa Burzynski

Last Chance to Submit Your T-Shirt Design

It’s coming down to the wire – if you have not submitted your Golden Helix T-shirt design please do so!! We have already had many great submissions but we are missing yours.

Once the contest closes tomorrow, July 3rd, our talented Golden Helix staff will narrow down the choices and display them to our community for voting. The designs with the most votes will be put into production and unveiled at our booth at ASHG in October. Continue reading

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Andrew Jesaitis

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

different ways

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 just how many assumptions went into the above statement. What transcript set are we using? In what part of the gene did the mutation occur? What subfeature of the gene are we looking at? Are there other ontologies for the variant? Why did we use the term we did? In order to develop a tool to annotate variants, rules to answer all these questions have to be codified into software. Enumerating these assumptions means that a process that is subject to a great deal of human interpretation, is now a rigidly defined objective framework. There are currently three major tools that attempt to classify variants: Annovar, SnpEff and Variant Effect Predictor (VEP). It is no surprise that these tools do not always agree since the way the rules have been defined differ slightly between each application. Continue reading

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Ashley Hintz

Update from MAGES 2014

The 2014 MAGES Conference hosted in Philadelphia brought out the shining stars in Statistical Genetics, along with a variety of approaches and difficulties researchers in the field are facing. Being my first MAGES event, I did not know what to expect; however, I was thoroughly impressed and am excited to go back next year.

Some of the topics that seemed to become more prevalent over the day included the use of BioBank data, algorithms taking advantage of Bayesian statistics, and talks addressing how complex disease actually is! Continue reading

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Alyssa Burzynski

2014 Golden Helix Summer School

We are incredibly excited to sponsor the 2014 Golden Helix Summer School (not directly affiliated with Golden Helix, Inc. (us)), hosted on the island of Aegina, Greece, from September 11th-15th, 2014.  This year’s theme is “Pharmacogenomics and Genomic Medicine: Bridging research and the clinic” and will focus on disciplines within genomic medicine.

The Golden Helix Summer School, conducted annually, is a collection of international educational activities surrounding the field of precision medicine and biomedical informatics. These activities create a unique opportunity for participants to increase their knowledge and understanding of the ever-changing field of genomic medicine, as well as discuss and nurture innovative ideas. Continue reading

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Cheryl Rogers

Here’s Your Chance to Design a Golden Helix T-shirt!

Copyright: falara / 123RF Stock Photo

Over the last few years, it’s clear that our t-shirts are loved. But the time has come for some fresh designs and we are looking to our customers and community for inspiration.

Do you have a brilliant idea in mind for a Golden Helix t-shirt? Great! You should enter our first ever t-shirt contest! It’s pretty easy really; draw it on a piece of paper, design it in your favorite software, or use your words to convey the message and enter to win here.

From the submissions, we will narrow it down to just a handful and send them out to the Golden Helix community for voting. The three designs with the most votes will be put into production and unveiled at this year’s ASHG in San Diego.
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Jami Bartole

Two New Regression Scripts

We are excited to let you know about two new scripts to aid in Numeric Regression analysis. Don’t forget about the Technical Support Bulletins which keep you up-to-date on all the latest script news. You can stream this feed via an RSS reader, receive email updates, or see the latest on the SVS splash screen.

Linear and Logistic Regression with Interactions

The Linear and Logistic Regression with Interactions script will output the results from either a Linear or Logistic Regression Analysis run with one dependent variable, multiple interacting, and non-interacting covariates on all numeric columns. This script uses the numpy, scipy, and statsmodels python packages to perform the regression. Continue reading

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

Bio_John_Eicheri

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 of Genetics at Yale University.

Here, my colleagues and I work to identify and examine the genes that contribute to common learning disabilities with an emphasis on those concerning language, such as dyslexia and language impairment. Dyslexia is characterized by unexpected difficulties with reading and written language, while language impairment involves deficits in expressive and receptive verbal language. Both dyslexia and language impairment are persistent impairments that affect an individual’s daily life, within or outside a school setting. Interestingly, these disorders commonly co-occur, meaning that children often have both dyslexia and language impairment. This has led my colleagues and I to hypothesize that these conditions may share genetic risk factors.
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