Tag Archives: VarSeq

Harmonizing Next-Generation Sequencing Data: VarSeq Liftover Tool

         June 15, 2021
genomeAsia

One of the inherent realities of next-generation sequencing is the ongoing updates to the human reference genome—one of the strongest recommendations to take the original sequencing data and remap to the latest genome assembly. However, there are several reasons why remapping may be impractical. So, an alternative solution is needed to convert the data running through an initial mapping to… Read more »

Variant Filtration and Interpretation

         June 3, 2021

I learned about Batten disease from a childhood friend’s Facebook post. Over the course of a few months, her 8-year-old, Eva, the oldest of 4 daughters – Emily, Lucy, and Carly – was rapidly going blind. Baffled, doctors ran a genetic panel that returned a devastating result – the diagnosis of Juvenile Neuronal Ceroid Lipofuscinosis or Batten disease. A broad… Read more »

Importing CNVs using VSPipeline

         June 2, 2021

VSPipeline is a command-line interface that will provide high throughput environments the ability to tap the full power of VarSeq’s algorithms and flexible project template system from any command-line context, including the existing bioinformatics pipeline. This feature is a great resource for analyzing large sample volumes as it automates importing and annotating your data, which can help streamline your analysis… Read more »

Summer 2021 Software Specials

         May 25, 2021
Special Offer

Summer is quickly approaching, which heralds the return of our summer software specials! Golden Helix will be offering a limited number of the following deals through June 30th, 2021. Here is a snapshot of what is being offered: VarSeq w/ CADD & OMIM (3-users) – $8,995 | (3 available) Our filtering and annotating product, VarSeq, paired with premium annotations. VSClinical,… Read more »

Easily Edit Algorithms in VarSeq Projects with a Quick Right-Click

         May 20, 2021

Thanks for checking out this blog on how to to get more out of your VarSeq projects! The best way to show off one of my favorite new features that have been incorporated into the latest VarSeq 2.2.3 release is with a scenario: You work in a lab that processes and analyzes multiple whole exome samples for copy number variations,… Read more »

Case Study – Hannover Medical School

         May 11, 2021
hannover

Dr. Auber is the team leader for the molecular genetic diagnosis of hereditary diseases at the Institute for Human Genetics at Hannover Medical School (MHH). MHH is one of the largest hospitals in northern Germany, with one of the largest outpatient clinics for individuals and families dealing with hereditary cancer and predisposition syndromes. Dr. Auber was in high school when… Read more »

VarSeq 2.2.3 Released!

         April 27, 2021

I want to take this opportunity to highlight and briefly discuss some of the key features and updates that have been incorporated into VarSeq 2.2.3. Some of you may have attended the webcast that covered the prominent new features added to VarSeq, which are the updates to improve whole-exome analysis workflows, namely improved CNV calling in whole-exome datasets. However, there… Read more »

Using Gene Preferences in VarSeq and VSClinical

         April 20, 2021

With the latest release of VarSeq, we have made significant updates to our handling of the interaction of variants and genes. This includes the support for non-coding transcripts, improved splice site predictions, and updates to gene and transcript annotations. We received several questions regarding how decisions are made in the software regarding genes and transcripts with these gene-related changes. This… Read more »

Webcast Recap: Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Capabilities

         April 8, 2021
Exome CNV webcast

Thank you to those who attended the recent webcast, “Exome Analysis with VS-CNV & VSClinical: Updated Strategies & Expanded Capabilities”. For those who could not attend but wish to watch, here is a link to the recording. In this webcast, we covered the capabilities and updates that have been incorporated into VarSeq that enhance whole exome sequencing workflows. The new… Read more »

GenomeAsia 100K Variant Frequency Annotation

         March 30, 2021
genomeAsia

The GenomeAsia 100K Variant Frequency database is a pilot annotation source now available to our users. This valuable database offers a deep characterization of specific populations in Asia that can be used to drive genetic studies. GenomeAsia is comprised of whole-genome sequencing data of over 1,000 individuals from 219 populations across Asia. Using this as an annotation, users can analyze… Read more »

New Assessment Catalogs Improve Saving and Tracking Variant Interpretations

         March 23, 2021

In this blog, we will be covering new assessment catalogs and how they work to improve saving and tracking variant interpretations. VarSeq is a variant analysis tool that effectively analyzes single nucleotide (SNVs) and copy number variants (CNVs) in both cancer and germline workflows.  Because VarSeq enables such diverse variant analysis, there are many research labs and institutions that evaluate… Read more »

New Mendel Error Algorithm in VarSeq

         March 2, 2021
mendel algorithm

In many cases, VarSeq users typically run single trio projects or perhaps an extended family project. Not only are all the inheritance model algorithms available in the VarSeq software to capture de novo, dominant, or recessively inherited variants but there are a number of quality control fields to help ensure the pedigree was set up properly. The last thing any… Read more »

Lock in Annotation Source Versions to Increase Workflow Consistency

         February 25, 2021
Annoation Sources

Next-generation sequencing generates an immense amount of data which is then subject to a multi-step process to establish a validated bioinformatic pipeline. From processing raw sequence data to the detection of genetic mutations, establishing a validated and consistent bioinformatic pipeline makes a huge difference in the quality of patient care and accuracy of results. In this blog, we are focusing… Read more »

Customer Publications February 2021: The Heart Edition

         February 23, 2021
heart

Welcome to our Customer Publications for February 2021. As we commemorate the 57th American Heart Month, it is important to remember why we are wearing red and using #OurHearts. Heart disease is the leading cause of death worldwide. The National Heart, Lung, and Blood Institute urges Americans to do what they can to be heart-healthy and mitigate the risks of… Read more »

New CNV Tools with VarSeq 2.2.2 Update

         February 16, 2021
copy number variant algorithm

Our latest release of the VarSeq software has had a major upgrade with the addition of the new CNV ACMG guidelines! Here are some recent webcasts we’ve given covering the new guideline tool: Family-Based Workflows in VarSeq and VSClinical A User’s Perspective: ACMG Guidelines for CNVs in VSClinical Not only does VarSeq 2.2.2 come with the new guideline tool, but… Read more »

Webcast Recap: Family-Based Workflows in VarSeq and VSClinical

         February 13, 2021
screen shot from webcast

Thank you for attending the webinar focused on implementing VarSeq and VSClinical for family-based workflows. If you would like to use the webinar as a reference or were not able to attend, you can access it using the following link to view ‘Family-Based Workflows in VarSeq and VSClinical. Here is a brief recap of what we discussed: This webinar demonstrated… Read more »

Applying the Probability Segregation Algorithm for CNV Analysis

         February 4, 2021
Bioinformatics software

There is a multitude of interesting new features that have been incorporated into VarSeq 2.2.2. In this blog, I want to continue the discussion of these features and how each can be incorporated into your workflow, and also discuss the application of the Probability Segregation algorithm for copy number variation (CNV) analysis. The Probability Segregation algorithm is a new algorithm… Read more »

Updates on Splice Site Analysis

         February 2, 2021

Our latest VarSeq release is one of the largest we’ve ever had, boasting an extensive list of new features and improvements. As part of this release, we have dramatically expanded our support for splice site analysis. This includes improvements to our novel splice site algorithm and support for splice site effect prediction along with several other small improvements. Novel Splice… Read more »

January 2021 Publications

         January 28, 2021
Customer Publications

New discoveries using NGS data analysis are never-ending and are pushing precision medicine to the forefront. In this month’s customer publication blog, I am focusing on our VarSeq software as investigators harness its power to perform a variety of investigational study designs. From cancer to inherited rare disease research, VarSeq is the rising star in research and diagnostic tools. At… Read more »

New eBook Update: Precision Medicine – Third Edition

         January 27, 2021
Precision Medicine - Third Edition

I am pleased to share with you the official release of my updated eBook, “Precision Medicine“. Almost 2,500 years ago, Hippocrates captured one of the key principles underlying precision medicine. In the 21st century, we take an understanding of the individual characteristics of a person to a new level. By leveraging information about an individual’s genome, we are able to… Read more »