Search Results for: annotation

VSClinical Updates & a Tour of Cancer Annotations – Webcast Q&A

         November 8, 2018

This webcast generated a lot of great questions about the content covered in the video above. I have summarized our Q&A session below and included some questions I didn’t have time to answer during the live event. If you have any further questions, reach out to us at info@goldenhelix.com! Q: Can I upload my existing classifications into a consortium source?… Read more »

New & Improved ClinVar Annotations

         March 13, 2018
ClinVar

ClinVar is the NCBI variant database that focuses on the categorizing of variant alleles and their interpretation from a clinical standpoint. This has made it a great resource, especially for those seeking variant allele disease correlations and pathogenicity. And this all worked fairly well, but it was changed… Previously, the ClinVar variant track annotation took some time to curate due… Read more »

New and Updated Annotations

         December 7, 2017
Genotype Imputation

Golden Helix is excited to announce a new round of novel and updated annotations; including a frequency track, a region track, and a gene track. All three of these tracks were created with the use of VarSeq and its Convert Wizard functionality. First, the expansive 1000 genomes track (1kG) has been updated to include sub-population allele frequencies and heterozygous and… Read more »

Annotation Education Series: CNV Annotations

         November 9, 2017
CNV Annotations

With the recent upgrade to VarSeq 1.4.7, users gain access to some new great features. Among the additions are new CNV annotations (Figure 1). In this final chapter of the annotation blog series, we are going to provide descriptions of the new CNV annotations and how they can be used. The types of CNV annotations vary and include frequency, clinical… Read more »

Annotation Education Series: Frequency, Functional Prediction, and Gene Annotations

         October 26, 2017
VarSeq annotations

In our final chapter of this variant annotation blog series, we will discuss additional annotations that provide powerful variant filtering and analysis capability. Golden Helix curates many annotations in a way that allows for simple analysis and saves the users the hassle of all this data management. Whether you are trying to capture rare variants known across multiple subpopulations in… Read more »

VarSeq Updated with CNV Annotations, CNV PhoRank and Region Assessment Catalogs

         October 19, 2017
VarSeq Updated

VarSeq Updated with CNV Annotations, CNV PhoRank, and Region Assessment Catalogs This year we have released multiple advances to support CNV analysis in VarSeq, expanding our target region based VS-CNV caller to handle exomes and low-depth genomes as well as additional supporting algorithms like calling Loss of Heterozygosity regions. To top this off, VarSeq 1.4.7 has been shipped with many… Read more »

All of your VS-CNV annotation questions answered

         October 12, 2017
VS-CNV Annotations

This month we hosted two, incredible webcasts officially announcing the latest CNV annotation capabilities our Software Engineering Team has been hard at work on for the past couple of months. Our first webcast, Comprehensive Clinical Workflows for Copy Number Variants in VarSeq, was presented by Golden Helix’s VP of Product & Engineering, Gabe Rudy, who reviewed the expanded capabilities of… Read more »

Annotation Education Series: Cancer Annotations

         October 5, 2017

CIViC The Clinical Interpretations of Variants in Cancer, better known as CIViC, is an open access open source, community-driven web resource available to all VarSeq users. Nature Genetics published an article that states, “CIViC accepts public knowledge contributions but requires that experts review these submissions”. Fundamentally, the focus behind CIViC is to make sure the variants contained in the database… Read more »

CNV Annotation Clinical Workflows Webcast: Q&A

         September 28, 2017
VS-CNV Annotations

  Gabe Rudy gave a fantastic presentation yesterday on the latest additions to VS-CNV annotations. If you weren’t able to join us for the live event, you can access the recording and webcast slides here: Comprehensive Clinical Workflows for Copy Number Variants in VarSeq. Additionally, there were many great questions asked that we wanted to share with the community. Question: Can I… Read more »

Annotation Education Series: Clinical Assessment Tracks

         September 21, 2017

Clinical Assessment Tracks Golden Helix provides a large catalog of annotation sources for our research and clinical clientele. Making these public data repositories available to all our users is no easy task. As Cody Sarrazin mentioned in his blog post, annotation curation is a complex data science pipeline. This process aggregates data from many disparate sources and normalizes it into… Read more »

Upcoming Webcast: Advantages of VarSeq’s Annotation Capabilities

         August 31, 2017
genetic variants

September 13, 2017 12:00 PM, EST This month we’re branching out and covering a topic we’ve never explored before – annotation capabilities! Darby Kammeraad, Field Application Scientist at Golden Helix, will be giving us some insight into the advantages of VarSeq’s capability with annotations. The number of annotation topics to cover are seemingly limitless. In this webcast, we will focus… Read more »

Top 10 Posts for Understanding Clinical Annotation of Genomic Variants

         August 24, 2017
Top 10

The VarSeq clinical platform is built on a strong foundation of data curation and annotation algorithms to ensure the variants identified have all the information required to make the correct clinical assessments.  It’s easy to make light of “variant annotation”, but the details run very deep into the roots of how we represent genomic data, how public data is aggregated, stored… Read more »

Golden Helix, Inc. – Your Annotation Curation Station

         June 15, 2017

The current reduced cost and increase availability of genome sequencing has been making academics, clinicians and individuals alike excited with the possibility of increased research depth, diagnosing capability and personal curiosity. And although a freshly sequenced genome is chock-full of tasty letter snippets, the real revelation and education occurs when comparing to an annotation foundation. In this post, I’ll review… Read more »

Updating VarSeq’s Transcript Annotation along with NCBI RefSeq Genes Interim Release

         March 30, 2017
transcription annotation

It may be possible to say that annotating a variant correctly and accurately against gene transcripts is the most important job of a variant annotation and interpretation tool. We take it very seriously at Golden Helix as we support VarSeq and its use by our customers in both research and clinical contexts. It has been a source of frustration that… Read more »

Custom Filtering using ClinVar Annotations

         July 19, 2016
ClinVar

ClinVar is one of our most used annotations sources for a variety of workflows. It is also the public annotation source that is updated most frequently of all the sources currently supported in VarSeq. ClinVar provides new versions of their database once a month in several formats (XML, VCF, TXT). We use custom Python scripts to convert the provided VCF… Read more »

Updates to dbNSFP – The Universal Remote of Annotation Sources

         December 8, 2015

Probably one our most popular public annotation sources we curate and update is the database of Non-Synonymous Functional Predictions (dbNSFP). In it’s recent update, it has expanded the predictions to include FATHMM-MKL and VarSeq now incorporates this new prediction into its voting algorithm of now 6 different discrete predictions per variant. You can update to dbNSFP 3.0 using the built-in… Read more »

New and Updated Annotation Tracks Now Available!

         June 11, 2015

In recent months we have been updating our public annotation library to include the most recent versions of existing sources as well as include new sources. Each of these annotation sources are compatible with our three major products (SVS, GenomeBrowse and VarSeq) and can be used for visualization, annotation and filtering. NHLBI ESP6500SI-V2-SSA137 Exomes Variant Frequencies 0.0.30, GHI Annotations are… Read more »

Accurate Annotations: Updates to the NHLBI Exome Sequencing Project Variant Catalog

         May 19, 2015

Since its early release in early 2012, the population frequencies from the GO Exome Sequencing Project (ESP) – from the National Heart, Lung and Blood Institute (NHLBI) have been a staple of the genomic community. With the recent release of ExAC exome variant frequencies, the ESP has been surpassed as the largest cohort of publicly available variant frequencies (by nearly… Read more »

Supercentenarian Variant Annotation: Complex to Primitive

         March 19, 2015

In a previous blog post, I demonstrated using VarSeq to directly analyze the whole genomes of 17 supercentenarians. Since then, I have been working with the variant set from these long-lived genomes to prepare a public data track useful for annotation and filtering. Well, we just published the track last week, and I’m excited to share some of the details… Read more »