April Newsletter

VarSeq Template Design Recommendations: Single Sample Variant Filtering 

VarSeq Template Design Recommendations: Single Sample Variant Filtering

By Dr. Rana Smalling
Field Application Scientist

When doing next-generation sequencing (NGS) analysis in VarSeq, the fundamental goal is to develop efficient ways to filter through your NGS data. If you are just getting started with Varseq, a pre-designed project template can really come in handy for variant filtering! This blog series will cover a number of template design recommendations for variant filtering on data types ranging from single samples to large cohorts of whole exomes or whole genomes. To get started, let’s review one of our templates suitable for variant filtering on a single clinical or research sample...Read More

Annotation Updates: RefSeq and Ensemble gene tracks for GRCh38

Annotation Updates: RefSeq and Ensembl gene tracks for GRCh38

By Julia Love
Genomic Curator & Product Quality Manager

I’d like to take a moment to announce the release of updated gene tracks for the GRCh38 genome assembly! Gene annotation tracks are essential to all VarSeq projects and workflows. Whether your favorite gene track is Ensembl or RefSeq, both sources have been updated and released and can be used for variant annotation. These gene tracks are used to annotate the variant table displaying details about the known transcripts for a gene, the effect of a variant on a given transcript, splice site predictions, and sequence ontology. In addition, much of this data is applied to algorithms used in VSClinical. Of note, the algorithm considers the selection of the clinically relevant transcript for variants of...Read More

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

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

By Dr. Jennifer Dankoff
Field Application Scientist

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 literature. In Figure 1, I have a simple field of view in GenomeBrowse, where I am examining the Reference Sequence, the Ref/Alt designations of the current variant in my sample, along with the gene my variant falls in from the RefSeq Genes track. Other information in this field of view...Read More

 

 

CEO Corner
New eBook: Clinical Variant Analysis for Cancer

We are continuing to strive and provide the best resources and customer support, and with that, we have revamped our learning hub. Within our learning hub, you will find monthly updates to our annotations as well as tutorials, manuals, and other resources to assist. Our team is also beginning to prepare for ESHG 2022 in Vienna, Austria. The conference will again be another positive turning point after many virtual meetings and I am personally excited to talk with many of you there. This continued progression of our learning resources is a clear indicator of our dedication to being the best. Without the support of our customers and partners this would not be possible, so thank you and I look forward to speaking with some of you in Austria.

Recent Webcast

VarSeq Custom Database Curation Capabilities

Presented by Darby Kammeraad, Director of Field Application Services

As our users have come to know, VarSeq serves as a hub for variant annotation and the full interpretation/classification of germline (ACMG) and somatic (AMP) variants. Whether direct annotation or backend variant evidence is being presented to the user via VSClinical for the interpretation process, users greatly benefit from the hosted variant databases being available directly from VarSeq. Our team has automated much of the curation process and hosts the ongoing updates to these tracks so that users no longer suffer manual review of each database via the web or manual curation efforts. Useful databases include ClinVar and ClinGen for classification submissions, gnomAD exomes/genomes for filtering out common variants in the population, RefSeq for gene impact and sequence ontology assessment, and OMIM for phenotypic information. Obviously, there is a large collection of databases out there, and not all of them make it into our automated queue. However, GHI supports the utilization of custom databases in our software. During the presentation, we discuss many different approaches with custom annotations, including:

  • Interval Tracks: Bed files defining target regions for coverage calculations and CNV detection.
  • Assessment catalogs: record-keeping of variant classification/interpretations in VSClinical.
  • Frequency catalogs: approaches to capture all variant allele frequencies at a project level and cohort level with VSWarehouse.
Watch Now
Customer Success

Congratulations to all of our customers who have published this month! To highlight just a few:

Genome-wide Sequencing and the Clinical Diagnosis of Genetic Disease: The CAUSES Study- Alison Elliott & colleagues, University of British Columbia / Published in ScienceDirect

Genome-Wide Signature of Positive Selection and Linkage Disequilibrium in Ethiopian Indigenous and European Beef Cattle Breeds- Kwan-Suk Kim & colleagues, Chungbuk National University / Published in Research Square

About Golden Helix

Golden Helix has been delivering industry-leading bioinformatics solutions for the advancement of life science research and translational medicine for over 20 years with 1,000s of users around the world. Their innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from NGS sequencers and microarrays. With their solutions, hundreds of the world's top hospitals, testing labs, pharmaceutical, biotech, and academic research organizations can harness the full potential of genomics to identify the cause of disease, improve the efficacy and safety of drugs, develop genomic diagnostics, and advance the quest for personalized medicine.