The new Annotate and Filter algorithm is now available with the release of SVS 8.6.0, see the release notes for full details on all new and updated features. To access this new functionality, you simply need to update your SVS installation to the new version. The update can be done by clicking the Update Available link at the bottom of… Read more »
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 »
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 »
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 »
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 »
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 »
Question: Now that I’ve added annotation sources for my sample, filtered down to a list of interesting variants, flagged those variants and generated a clinical report, can I save or copy the annotation sources and filters for use on another sample? Short Answer: Yes! Long Answer: VarSeq was created with ease and efficiency in mind. In VarSeq, once you’ve defined… Read more »
Every month hundreds of clinicians and researchers access the variety of free resources on the Golden Helix website. Our resource library hosts eBooks, webcasts and tutorials to keep the community apprised of new methods, informed on best practices and to help our customers get the most out of their software purchase. Here is a list of the 5 most watched webcasts… Read more »
The Bioinformatics Program at Rutgers Cancer Institute of New Jersey, the state’s only National Cancer Institute-designated Comprehensive Cancer Center, plays an integral part in the center’s precision medicine program helping to bring personalized medicine to patients in a timely manner. The Program needs to determine what mutations from a tumor are relevant to a particular therapeutic option, bringing the right… Read more »
Whole exome sequencing workflows using SNP & Variation Suite (SVS) was presented in a recent webcast, by Dr. Robert Hamilton from the Hospital for Sick Kids. In particular, he performed some filtering on his data to look for only heterozygous variants in his sample of interest, removed variants with allele frequency less than 0.005% based off of the ExAC Variant Frequency… Read more »
King Abdulaziz Medical City (KAMC) in Riyadh commenced its operations in May 1983. Since then, it has continued expanding, while providing services for a rapidly growing patient population in all of its catchments areas. Today, King Fahad National Guard Hospital has evolved to be part of the King Abdulaziz Medical City with many other prominent medical centers. Since its inauguration… Read more »
I’m very glad I had the chance to attend ESHG 2016 in Barcelona and talk to so many people about Golden Helix and our software at our booth. ESHG may be the little sibling in size compared to ASHG, but my impression is that it punches above its weight in terms of advancing human genetics applicability to human health and… Read more »
Using Whole Exome Sequencing in distant relationships to identify cardiomyopathy genes Wednesday, June 8th 12:00 pm EDT Cardiomyopathy (DCM; MIM 115200) are myocardial diseases that are frequently hereditary, yet remain gene-elusive for 60% of affected families. Traditional gene discovery techniques dependent on multigenerational samples are difficult to apply. This is because 1. Disease is often impenetrant in the youngest generation,… Read more »
There used to be much energy expended at conferences, bioinformatics forums and even publications about what was the better strategy for interpreting variants of clinical significance: Rule-based filtering and classification mechanisms or rank-based prioritization through all-encompassing “pathogenicity” scores. Both have shown to be effective. Rule-based systems, as exemplified in this filtering diagram in Baylor’s ground-breaking paper on clinical whole-exome sequencing… Read more »
During the webcast yesterday, I demonstrated a few ways of customizing de Novo Candidate and Compound Heterozygous Candidate workflows to consider family structure that was slightly different from the default trio workflow. The families included additional affected and unaffected siblings added to a trio as well as looking at what could be done if there were only two affected siblings… Read more »
Wednesday, April 6th 12:00 pm EDT As the number of samples and associated data volume in a testing lab increases, it becomes imperative for labs to leverage state of the art warehousing technology that not only organizes data, but also aides and enables researchers and clinicians to perform further analysis, and ongoing research. Built on the algorithms and high-performance storage… Read more »
Wednesday, March 2nd 12:00 pm EST Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will show how VarSeq and VSReports can be used to go… Read more »
As VarSeq continues its adoption amongst clinical labs and researchers looking for reproducible workflows for variant annotation, filtering and interpretation, we have continued to prioritize the addition of features to assess the quality of the upstream data at a variant, coverage and now sample level. The Importance of Quality Assurance Sample prep and sequencing problems are difficult to detect through the analysis… Read more »
Yesterday, it was my pleasure to share in a live webcast our integrated solution for genetic data warehousing, VSWarehouse. Although we had a great set of questions at the end of our presentation, we didn’t have time to answer all of them, so here is a selection of the remaining representative questions and my answers. We can provide a hosted version… Read more »
So, why are we launching a new data warehouse product? Why did we build VSWarehouse? According to Grand View Market Research, the next generation sequencing (NGS) market size was $2.0 billion (USD) globally in 2014. This number is expected to grow from 2015 to 2022 at an annual rate of about 40%. What drives this phenomenon is the increasing number… Read more »
