Golden Helix Newsletter

GenomeBrowse 2.0
RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care
by Gabe Rudy, VP of Product Development

You probably haven't spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product.

But in fact, there is more complexity here than you ever really wanted to know about. Andrew Jesaitis covered some of this in detail as he dove deep in the analysis of variant annotation against transcripts in his recent post The State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP. Continue reading »

New MM-KBAC Method Explaind
by Greta Linse Peterson, Director of Product Management

In June 2014, we announced a new method that Golden Helix developed–the now available MM-KBAC (Mixed Model Kernel Based Adaptive Clustering).

You can read Greta's blog about the new method here.

We are very excited to announce that we have been accepted to present this material at ASHG this October! Greta Linse Peterson will present the material Monday, October 20, at 6:15 pm in room 20A. (We'll be in booth 422! Stop by and say hi!) See a schedule of events here.

Have you ever had a bad experience with a VCF file?
by Bryce Christensen, Ph.D., Statistical Geneticist

Who has ever had a bad experience with a VCF file?" I like to ask that question to the audience when I present data analysis workshops for Golden Helix. The question invariably draws laughter as many people raise their hands in the affirmative. It seems that just about everybody who has ever worked VCF files has encountered some sort of difficulty with the format's complexity or practical limitations. Among other responsibilities at Golden Helix, I give frequent demonstrations of our SVS software and train people to use it. In this capacity I have observed many of the challenges people encounter with VCF files, and I'd like to discuss some of those issues. Continue reading »

Runs of Homozygosity Updated
by Alison Figueria, Software Engineer

For the SVS 8.2 release we decided to improve upon the existing ROH feature. The improvements include new parameters to define a run and a new clustering algorithm to aide in finding more stringent clusters of runs. The improvements were motivated by customer comments and a recent research paper by Zhang 2013, "cgaTOH: Extended Approach for Identifying Tracts of Homozygosity," that outlined a new approach to identify clusters of runs.

You will also notice that there are now two Runs of Homozygosity menu items. Under the DNA-Seq menu there will be Runs of Homozygosity for NGS and under the Genotype menu there will be Runs of Homozygosity for GWAS. The NGS option now allows for treating missing genotypes as homozygous reference calls and when searching for runs, it does not take into account the gap between variants or the variant density. Continue reading »
   Upcoming Webcast
Using Genomic Prediction for Trait Optimization
  Tues, Aug 26
12:00 pm EDT

Genomic estimated breeding values (GEBVs) can help a researcher determine which animals or plants to continue breeding due to high estimated breeding values for desired traits.

This webcast will discuss the benefits of genomic prediction for trait optimization, how to set up training and validation datasets, cover the highlights of the GBLUP method, and demonstrate genomic prediction and training/validation using GBLUP in Golden Helix's SNP and Variation Suite (SVS) software.

Webcast Registration

   Featured SVS Script
Extract Info from Regression Stats Viewer
Download » | Script repository »

Vitamin D Tied to Alzheimer's Risk
Low vitamin D is associated with an increased risk for Alzheimer's disease and other forms of dementia, according to a new report, though whether low vitamin D is a cause of the disorders remains unknown.
Continue reading »

What You Need to Know About the Ebola Outbreak
More than 1,975 people in Guinea, Liberia, Nigeria and Sierra Leone have contracted Ebola since March, according to the World Health Organization, making this the biggest outbreak on record. More than 1,050 people have died. Two American aid workers infected with Ebola while working in West Africa were taken to a containment unit in Atlanta for treatment.
Continue reading »

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About Golden Helix
Golden Helix has been delivering industry leading bioinformatics solutions for the advancement of life science research and translational medicine for over 15 years. Our innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from microarrays and next-generation sequencing. With our solutions, hundreds of the world's top pharmaceutical, biotech, and academic research organizations are able to harness the full potential of genomics to identify the cause of disease, improve the efficacy and safety of drugs, develop genomic diagnostics, and advance the quest for personalized medicine. Golden Helix products and services have been cited in over 800 peer-reviewed publications.


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