Recent Customer Success

         November 3, 2016
customer

We closed October with a record number of publications from our customers! Topics ranged widely from root traits in tropical maize to pretreatment depression severity. We hope you’ll enjoy reviewing some of our favorites: Bradley Aouizerat of NYU and colleagues published Human leucocyte antigen class I and II imputation in a multiracial population in the International Journal of Immunogenetics which considered… Read more »

Agrigenomics 2.0 Webcast

         October 27, 2016
genetic variants

This month’s webcast, Agrigenomics 2.0 – Advanced Analysis to Accelerate Discovery, will feature two well known Agrigenomic researchers and long-time Golden Helix customers, Christopher Seabury of Texas A&M and Holly Neiburgs of Washington State University. These two will join our own Gabe Rudy for a look at advanced workflows in SVS to advance mammalian genetic research. We hope you can join us! Wednesday,… Read more »

Final thoughts on ASHG 2016

         October 25, 2016
Customer Success

ASHG 2016 is in our rear mirror. Again, it was bigger and better than the previous year. The conference hosted over 9,000 visitors from 66 countries. This gave the event a level of vibrancy that was evenly matched by the wonderful ambiance of the city of Vancouver. Nestled in between the two conference centers was a little pier offering spectacular… Read more »

Using GWAS to investigate neurodevelopmental disorders

         October 18, 2016
Sergey Kornilov

Dr. Sergey Kornilov, a Duncan Scholar in Molecular and Human Genetics at Baylor College of Medicine, combines his broad psychology background with genetics to research the genetic basis of neurodevelopmental disorders with a unique dual perspective. Neuro-developmental disorders, for example, those of the spoken and written language, affect many worldwide – up to 10% of preschool children. In most cases, these… Read more »

See you in Vancouver for ASHG 2016!

         October 13, 2016
ASHG 2016

It’s hard to believe that summer has already faded into fall and that ASHG 2016 is right around the corner! 2016 has been quite a busy year for us so far at Golden Helix. We have been working hard to bring our community the very best tools available for variant interpretation and SNP analysis. This year at ASHG, you can… Read more »

Why Call CNVs: Getting More from your NGS Data

         October 11, 2016
CNV Call

Copy Number Variants have been important to clinical genetics for quite a while now. So, what has made now the right time to be looking at calling CNVs from NGS data? Well, there are a number of good reasons. The dominant one is simply that the NGS data you are already creating for calling variants can be used in many cases… Read more »

CADD, OMIM and OncoMD added to SVS

         October 6, 2016
CAD, OMIM and OncoMD

In our SVS 8.6.0 release, we updated our Annotate and Filter Variants feature to utilize our powerful VarSeq annotations. Annotations can be run against gene, interval, variant, and tabular tracks, including RefSeq, ClinVar, CADD, OMIM and OncoMD. The new streamlined dialog allows users to select track specific options and to set up custom filters. While our public annotation repository has… Read more »

50 Most Creative CEOs to Watch

         October 5, 2016

We are excited to announce that our CEO & President, Dr. Andreas Scherer, was featured in “The 50 Most Creative CEOs to Watch” issue of Insights Success magazine this month. The article is focused on how Dr. Scherer is leading Golden Helix to deliver top bioinformatics solutions to further enable Precision Medicine. Please take a look at the article here.

Recent Customer Publications

         October 4, 2016
published

Many of our customers published throughout September using our SVS software, and we love sharing their work with you. There’s bound to be a topic among the wide variety we’ve highlighted here that will spark your interest! Maurico Arcos Burgos, Claudio Mastronardi and colleagues of the Australian National University published Mutations modifying sporadic Alzheimer’s disease age of onset in the American Journal of Medical… Read more »

Upcoming Webcast on CNV Calling of Target Regions

         September 27, 2016
CNV calling

Copy Number Variations (CNVs) play an important role in human health and disease, and the detection of CNVs in clinical samples has the potential to improve clinical diagnoses and inform treatment decisions. Yet until now, if you wanted to have CNVs on your targeted gene samples, you would need an alternative assay such as Chromosomal Microarrays (CMAs). In this webcast,… Read more »

Big Data Webcast Q&A

         September 22, 2016
Big Data Q&A

Gabe Rudy’s webcast yesterday, Big Data at Golden Helix: Scaling to Meet the Demand of Clinical and Research Genomics, was a huge success with well over 300 registered. In today’s blog post, I wanted to recap the Q&A session with Gabe. If you missed the webcast, check it out! Question:  What is the end goal for an application like Warehouse? Answer:  The… Read more »

Genomic eBooks Series reached 10k Downloads!

         September 21, 2016
10 k Downloads

Today we reached an important milestone. We have registered over 10,000 confirmed eBook downloads. Of course we are thrilled! Over the years, we aimed to contribute relevant content to the community. For some time, we have blogged and conducted webinars on the latest technology, methods and best practices. Our eBooks were the latest addition to this mix. We received a… Read more »

NGS-Based Clinical Testing: Part V

         September 20, 2016
Quality Managment

Any validated bioinformatics pipeline must be continuously monitored. Quality management in clinical testing labs ensures that any divergence from predefined quality metrics during the analysis of clinical samples is investigated. For example: There is an insufficient number of sequence reads that passed the predefined base quality score threshold The number of variants identified in a data set may deviate substantially… Read more »

Let There Be Genomes: Big Data Genomics Webcast Teaser

         September 15, 2016
Big Data Genomics

Big data is here, but fear not, you don’t need a Hadoop cluster to analyze your genomes or your cohorts of tens of thousands of samples! It turns out, for the kind of algorithms employed in variant annotation and filtering, running optimized local programs is often faster anyway. As we support our diverse customer base, we have definitely seen the… Read more »

Determining the best LD Pruning options

         September 13, 2016
LD Pruning

Pruning your data based on Linkage Disequilibrium (LD) values is an important quality assurance step for GWAS analysis. In particular, some tests such as Identity by Descent Estimation (IBD), Inbreeding Coefficient Estimation (f) and Principal Component Analysis (PCA) will obtain better results if the markers used are not in linkage disequilibrium with each other. Therefore, Golden Helix’s SVS provides the… Read more »

Webcast on Big Data in Genomics

         September 8, 2016

Wednesday, September 21st @ 12:00 pm EDT Every day, the trove of genomic data is growing. Clinics are sequencing targeted genes at high read depths to report out genetic tests. Research groups are adding new exomes and genomes to their disease-specific cohorts. Agricultural breeders are genotyping their herds and flocks by the thousands of thousands. The conventional attitude to big… Read more »

NGS-Based Clinical Testing: Part IV

         September 6, 2016
clinical testing

After the Wet Lab process has been completed, the bioinformatics analysis of the sequencing data work begins. The next three blogs will focus on three aspects of this process. The building blocks of a bioinformatics pipeline, documentation and validation (today’s topic) Quality Management Clinical Reporting The Building Blocks of an NGS PipelineThe bioinformatics process to analyze NGS data occurs in three… Read more »

NGS-Based Clinical Testing: Part III

         September 1, 2016
DNA sequencing

Getting the NGS wet bench process right is not a small undertaking. Targeted NGS assays such as multigene panels or exome sequencing allow for the targeted analysis of genomic regions that are of particular interest. For every sample type, e.g. blood, formalin-fixed paraffin-embedded specimens, saliva etc, there must be a detailed protocol in place outlining how each sample type is going… Read more »

Recent Customer Publications

         August 30, 2016
published

For many of you this might be a busy week with school starting up again! However, even though school is just starting, many of our customers have been publishing all summer long. Here are a few highlights from our most recent publications this August: Evaline Ibeagha-Awemu and Xin Zhao of Agriculture and Agri-Food Canada, along with colleagues, published High density genome wide… Read more »