Search Results for: annotation

The New Human Genome Reference and Clinical Grade Annotations: It’s All About the Coordinates

         February 17, 2014

On my flight back from this year’s Molecular Tri-Conference in San Francisco, I couldn’t help but ruminate over the intriguing talks, engaging round table discussions, and fabulous dinners with fellow speakers. And I kept returning to the topic of how we aggregate, share, and update data in the interest of understanding our genomes. Of course, there were many examples of… Read more »

New 1kG, dbNSFP, and ESP6500 Annotation Tracks and Associated Filters

         July 16, 2012

SVS 7.6.7 features new tools for filtering sequencing data based on functional predictions and allele frequencies. To complement these new features, new annotations tracks have been uploaded to our data server and are now available for our customers! Below you will find descriptions of the new tools and the related annotations track(s).

New Plant/Animal Genomes and Annotation Tracks Now Available

         December 8, 2011

Recently we have expanded our annotation track offerings with new human variant frequency catalogs such as the 1000 Genomes Phase 1 Data. Of course, we also curate data for plant and animal genomes – some of which are currently available in our software and some of which will be available in our next release. In this blog post, I will… Read more »

Getting the most out of variant visualizations in GenomeBrowse

         June 29, 2022

Genomic data visualization is an extremely powerful means to help users comprehend massive amounts of sequencing data and is valuable for communicating genomic information and findings. Genome browser tools allow users to visualize aligned sequence data in BAM format, map the data to a reference assembly, view annotation tracks, genomic region tracks, export graphics for sharing, and much more. Genome… Read more »

Customer Publications May 2022

         May 31, 2022

As we look back on May, I wanted to highlight a range of applications that our VarSeq suite is capable of and show the success of our partners. In these publications, our VarSeq suite is utilized for the analysis of whole-exome, clinical variant classification and association, and assisting in an NGS panel for clinical oncology use. VarSeq’s range and capability… Read more »

Import CNVs from any secondary caller using VarSeq

         May 25, 2022

Advances in high-throughput sequencing have allowed us to be able to detect structural variants such as copy number variants in addition to small variants such as SNVs and indels. We provide users with an industry-leading CNV calling algorithm to detect CNVs directly from their next-generation sequencing data including whole genome, whole exome, and gene panel datasets, and also import CNVs… Read more »

CNV Probability and Inheritance Based on Coverage with VarSeq

         May 17, 2022

The overall objective of Trio Analysis is to leverage inheritance data to determine the ancestry of variants in the proband, whether that be through transmission from the mother and father, or of de novo origin. We have previously covered family based analysis in this blog post and this webcast, but both of these sources have been based on variants brought… Read more »

What’s Coming to VSClinical: Expanded Clinical Trial Search Results

         May 17, 2022
Expanding-Clinical-Trial-Search-in-VSClinical

While the interpretation of germline variants generally focuses on the pathogenicity of a variant for a specific disease, the interpretation of somatic variants is centered around each variant’s impact on clinical care. As a result, clinical trials play an important role in assessing the clinical significance of somatic biomarkers, with the AMP Guidelines assigning a higher level of evidence to… Read more »

Sentieon Updates: Now Supporting Long-Read Alignment and Calling

         May 9, 2022

Here at Golden Helix, we’ve sought to develop top-quality bioinformatic software to handle not only high-throughput clinical next-gen sequencing pipelines but also cater to research groups exploring their cohorts. Our tools fit in this NGS pipeline by importing the VCF and BAM files for downstream filtration, annotation, and classification/interpretation as well as clinical reporting. It was obvious early on and… Read more »

Mining Curated Databases for Literature in VSClinical

         April 29, 2022

Curated databases are a real time saver when compiling published evidence to support your variant evaluations and classifications. Leveraging the curated databases at your fingertips in our VSClinical variant interpretation hub is even more efficient. Not only does VSClinical provides users with automated variant classification for germline variants according to the ACMG guidelines and somatic variants according to the AMP… Read more »

Mining VarSeq Curated Databases for Literature – Raw Data Search in Variant Table or GenomeBrowse

         April 21, 2022

An under-utilized use of VarSeq is the ability of mining raw variant data in GenomeBrowse for relevant literature. By bringing in various public and private annotation sources, GenomeBrowse allows the user to interface with raw variant data in a compressed and manageable view. This blog will show you how to leverage these sources to power up your search for variant… Read more »

Review of VarSeq Export Options

         March 10, 2022
varseq export options

Although best known for its auto-generation of custom reports, VarSeq comes with a slew of options for exporting your data. In this blog, we will review some of the lesser-known methods for exporting your data into usable formats. These four export options can all be found under the Export tab at the upper left corner of your VarSeq interface (Figure… Read more »

How to Create Your Own CNV Frequency Catalog

         January 20, 2022
cnv frequency catalog

Global population frequency catalogs like 1kG Phase 3, gnomAD, DGV, and others are excellent resources for identifying rare variants in your copy number variant (CNV) analysis. However, they are not exhaustive, and the reality is a lot of variants that are missing from global population frequency catalogs are still common variants. At the same time, CNVs that are identified by… Read more »

Using ACMG Secondary Findings v3.0 List in VarSeq and VSClinical

         December 21, 2021

As the number of genes on a gene panel increases, there is the possibility of picking up variants of medical significance that are not related to the primary indication for the test. Especially with large gene panels, exomes, and genomes, it is medically and ethically important to report variants that may be actionable to the patient. These include variants implicating… Read more »

Highlights from Advanced Report Customization in VSClinical Webcast: Germline Reports

         December 14, 2021
germline clinical report blog

When it comes to clinical variant analysis for germline variants using ACMG guidelines, we understand that the clinical report is essentially the receipt for your services for the patient. In our recent webcast, Advanced Report Customization in VSClinical, we displayed several examples of report templates to show off the range of possibilities our users have to format their clinical report…. Read more »

VarSeq 2.2.4 Release

         November 30, 2021
varseq2.2.4

We are very excited to announce that just last week, we released VarSeq 2.2.4! In the past few months, we have been building the excitement for the 2.2.4 version of VarSeq with several webcasts in which we describe some of the headlining features in detail such as the new support for Gene Panels and Gene Lists, PhoRank Clinical, and Customized… Read more »

Highlights From Our CancerKB Webcast

         November 24, 2021

Thank you to everyone who attended Using Golden Helix CancerKB to Accelerate NGS Cancer Testing! I had a great time showing off CancerKB and how it can enhance NGS analysis in cancer, I certainly hope you enjoyed it! If you were unable to make the live session, we have added the on-demand recording to our site, or we would be… Read more »

Top FAS Tricks You Wish You Knew When Getting Started with VSClinical

         November 18, 2021
vsclinical top things to know

As a newer member of the Golden Helix FAS Team I, like many of our customers, went through a phase of learning the ins, outs, and shortcuts of clicking around the program. In an effort to expedite new users coming up to speed, or to teach some tricks to experienced users, I’ve compiled a list of the top things I… Read more »