Tag Archives: Clinical Genetics

Webcast Recap: VarSeq, the Complete Tertiary Platform for Short and Long-Read NGS Data

         January 18, 2024

Many thanks to those who came to view our most recent webcast, From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short and Long-Read NGS Data. This was a great opportunity for us to showcase the breadth of our workflows, from short-read to long-read, panels to genomes, singleton analysis to families. In this blog, we would like to… Read more »

Customizing Your Clinical Reports: Reordering the Variant List

         June 7, 2022

Oftentimes, the endpoint of a clinical variant analysis is a standardized, clinical report. As such, we ship a number of default templates with VSClinical for users to report their findings. But these templates are just a starting point! Our platform allows users to fully customize their reports to adhere to lab-specific preferences. We have shared a plethora of how-to’s on… Read more »

Manage gene lists across projects with VarSeq and VSClinical

         August 18, 2021

Clinical labs often maintain gene panels, which are lists of genes with evidence of disease association. These panels are used to prioritize variants and limit interpretations to a predefined set of test-specific genes. In general, gene panels should be stored independently of any specific project or interpretation, as it is common for an individual gene panel to be generally applicable… Read more »

VarSeq NGS Workflow Design: Clinical vs. Research

         April 22, 2021
NGS Clinical Research

In many cases, VarSeq users design their next-gen sequencing workflows for a clinical application. One of the major values of using VarSeq is the standardization of sample analysis via project templates for filtering down to rare variants and isolate any clinically relevant variant. However, VarSeq also doubles as a robust research application as well. There are specific algorithms that can… 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 »

Adding Population Catalogs to VSClinical

         December 10, 2020
example population view

Our previous webcast demonstrated some of the new functionalities of VSClinical, including the ability to add ACMG frequency sources for the ACMG BA1, BS1, and PM2 criteria. This new feature was spurred by the feedback from our users, which requested supporting frequency tracks other than gnomAD Exomes and 1kG Phase3. Now, users can implement population catalogs to VSClinical such as… Read more »

WEBCAST: CNV Analysis with VarSeq

         November 22, 2016

December’s webcast will provide the Golden Helix community with a more in-depth look at CNV analysis in VarSeq. On December 7th, Dr. Nathan Fortier will discuss the challenges and metrics surrounding CNV detection and then demonstrate VarSeq’s new capability from VCF to clinical report.  Wednesday, December 7th @ 12:00 PM, EST Numerous studies have documented the role of Copy Number Variations (CNVs)… 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 »

Using Clinical Reports in a Gene Panel Pipeline

         June 30, 2016
Gene Panel

Upcoming Golden Helix Webcast: Using Clinical Reports as part of a Gene Panel Pipeline Wednesday, July 13th @ 12:00 pm EDT VarSeq Reports can be used as part of an automatic pipeline to quickly list variants with information that can be used to make actionable clinical decisions in a readable HTML format. Need to further filter the variants or add interpretation… Read more »

N-of-One Integration comes to VSReports

         April 28, 2016

Submit directly to N-of-One from VarSeq If you or your lab uses N-of-One solutions for clinical annotations, here’s some good news: You can now submit directly to N-of-One from VarSeq! N-of-One’s set of preferred transcripts may differ from those outputted by our algorithms in VarSeq, so our solution was built with that in mind. Our slick, easy to use, and… Read more »

Handling Singletons & Complex Pedigrees with Gene Count Algorithms

         December 3, 2015

As VarSeq’s adoption has grown among analysts using whole exome data to diagnose rare diseases, a couple of family designs outside of the common trio of an affected child and both parents have come up frequently. While having both parents provides the maximum power to discover de novo mutations and recessively inherited variants, it is not always possible to contact… Read more »

A New and Unexpectedly Powerful VarSeq Feature

         November 17, 2015

With the release of VSReports, we added the ability to “select” rows of your filtered output (often variants, but potentially things like coverage regions or genes) with a new feature dubbed “Record Sets”, but more often described as “colored checkboxes” for your tables. Although necessary for the important task of marking primary, secondary or other sets of variants for a… Read more »

Fulgent Diagnostics Implements VSPipeline to Speed Analysis & Interpretation

         July 22, 2015

Today, we are proud to announce our collaboration with Fulgent Diagnostics, a CLIA certified molecular diagnostics lab. Fulgent offers more than 4,000 single gene tests among others and will implement VSPipeline to help speed up their analysis and interpretation process. On our quest to enable precision medicine, we look forward to working with Fulgent and other diagnostics labs in the… Read more »

Baby Genes is raising the bar for Newborn Screening

         May 28, 2015

Today we wanted to share a recent client case study to demonstrate how VarSeq has been implemented in a CLIA certified clinical laboratory. Please feel free to contact us if you have questions or if you would like to discuss VarSeq further at info@goldenhelix.com. It is standard practice for newborns to be screened for genetic diseases before leaving the hospital to… Read more »

What’s in a Name: The Intricacies of Identifying Variants

         May 26, 2015

There’s a strong desire in the genetics community for a set of canonical transcripts. It’s a completely understandable and reasonable thing to want since it would simplify many aspects of analysis and especially the downstream communicating and reporting of variants. Unfortunately, biology isn’t so tidy as to provide a clear answer for which transcript is the important one. Consequently, there… Read more »

VarSeq as a Clinical NGS Platform Q&A

         April 21, 2015
CNV User

Our VarSeq as a Clinical Platform webcast last week highlighted some recent updates in VarSeq that support gene panel screenings and rare variant diagnostics. The webcast generated some good questions, and I wanted to share them with you. If the questions below spark new questions or need clarification, feel free to get in touch with us at info@goldenhelix.com. Question: Should… Read more »

Introducing Phenotype Gene Ranking in VarSeq

         March 3, 2015

Personal genome sequencing is rapidly changing the landscape of clinical genetics. With this development also comes a new set of challenges. For example, every sequenced exome presents the clinical geneticist with thousands of variants. The job at hand is to find out which one might be responsible for the person’s illness. In order to reduce the search space, clinicians use various methods… Read more »

PreventionGenetics to Use GoldenHelix’s VarSeq for Dx Test Offering

         February 9, 2015

Today, we at Golden Helix announced our collaboration with PreventionGenetics as they prepare to implement the VarSeq software into their exome sequencing pipeline. The VarSeq software will allow PreventionGenetics to offer an exome test by dramatically speeding up the analysis process. VarSeq will narrow down sequence data into gene(s) of interest based on inheritance patterns, facilitating the identification of clinically relevant… Read more »