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 »

Streamlining Variant Analysis for Large Genetic Cohorts: Part 2

         November 29, 2022
Streamlining Variant Analysis for Large Genetic Cohorts: Part 2

The last blog in this series covered streamlining variant analysis for large genetic cohorts, namely case-control studies, on a single-project basis. The reality when dealing with big data is that you often do not handle a high volume project all at once. Therefore, we will follow up on the topic of cohort analysis by discussing Golden Helix’s solution for streamlining… Read more »

Webcast Recap: VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation

         November 22, 2022

Thank you to everyone who joined us for our webcast on the upcoming VarSeq features supporting the full spectrum of genomic variation! Traditionally, NGS cancer testing started with small gene panels that looked at a small set of the most common genes to identify small mutations, such as BRAF V600E. However, there are many classes of mutation that cannot be… Read more »

Heading to Phoenix, AZ for AMP 2022

         November 1, 2022

The Golden Helix team is headed off to Phoenix, AZ for the Association for Molecular Pathology Annual Meeting & Expo (AMP) 2022. We are enthusiastically awaiting a week of genetics discussions with new and familiar faces. If you are attending, please stop by our booth and say hello! We will be exhibiting at booth 1432. Golden Helix President & CEO,… Read more »

Customer Publications – October 2022

         October 31, 2022

The month of VarSeq must be October. This month we saw incredible research and clinical application being utilized with the VarSeq suite. Whole exome sequencing and variant filtering and annotation, CNV calling for oncology research, and pathogenicity classification using the ACMG guidelines. VarSeq was able to be a front-runner this month, showing the full range of capabilities. Germline RB1 Mutation… Read more »

Using rsID lookup in a VarSeq Workflow

         October 4, 2022

There are many reasons a user may wish to focus in on specific variants as part of variant annotation and filtration workflow. You may be looking for the occurrence of specific SNPs in a cohort or perhaps looking for variants known to be associated with specific forms of cancer. For both of these use cases, VarSeq provides a Match String… Read more »

Predicting the Functional Impact of Genetic Variants Using VarSeq

         August 9, 2022
Predicting the Functional Impact of Genetic Variants Using VarSeq

Large-scale next-generation sequencing studies are becoming increasingly popular clinical and research tools. One enduring challenge for interpretion of these large amounts of data has been predicting the functional impact of genetic variants. Access to efficient computational tools for predicting the functional impact of variants is crucial to prioritizing the most potentially relevant variants in a dataset in a time-efficient manner…. Read more »

Locking down clinically validated workflows for routine analysis

         July 20, 2022

Let’s say you are the director of a large lab, which is running tens or hundreds of standard NGS sample analyses per week. You have a number of employees with varying levels of analysis background, and you want to be sure everyone is running the analysis the same way. You are also concerned about updating catalogs that could create differences… 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 »