March Newsletter

Reporting Secondary Germline Variants in VSClinical AMP 

Reporting Secondary Germline Variants in VSClinical AMP

By Dr. Rana Smalling
Field Application Scientist

Tumor profiling via next-generation sequencing (NGS) often reveals secondary germline variants that may constitute important incidental findings. In May 2021, the American College of Medical Genetics and Genomics (ACMG) released an updated policy statement for reporting incidental findings in exome and genome sequencing data along with a corresponding list of genes. These recommendations state that laboratories should report pathogenic and likely pathogenic mutations occurring in genes on the secondary findings list, because these genes are linked to “actionable disorders”. In our Gene Panel library (Figure 1), VarSeq houses both versions of this list, namely version 2.0 with 59 genes and the more recent version 3.0 with 73 genes. Any user doing clinical variant analysis in a cancer setting can take advantage of these gene panels to keep track of notable secondary germline variants that may be present in a cancer patient. A common challenge for users doing somatic variant analysis...Read More

New Annotations Product Page

New Annotations Product Page

By Julia Love
Genomic Curator & Product Quality Manager

Golden Helix is always trying to add new helpful resources to aid in using Golden Helix products for NGS analysis. In today’s blog, I am very excited to introduce a new resource for Golden Helix users! A new resource that is now available in our Golden Helix Annotations product page available on the Golden Helix Learning Hub! The goal for this page is to inform Golden Helix customers of news or updates regarding the annotations sources that we curate. Currently, the annotations product page serves a dual purpose of 1) tracking updates to popular annotation sources and 2) informing users of any known issues that exist for an annotations...Read More

Review of VarSeq Export Options

Review of VarSeq Export Options

By Dr. Rana Smalling
Field Application Scientist

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 1). These options include converting your data into Text Files, VCF Files, Annotation Files, and Excel Spreadsheets. First, we can take a look at exporting a data set into a Text File. The first screen will let you select which tables in the project you would like to export. Here there is a Variant table, a Coverage Regions table, and a CNV table (Figure 2)...Read More

 

 

CEO Corner
New eBook: Clinical Variant Analysis for Cancer

This year's ACMG conference in Nashville, TN, marked a positive turning point after two years of virtual meetings in our community. The conference was well attended and we found an outstanding balance between on-site meetings and virtual talks. From our perspective, it was wonderful to connect again with customers and partners at the event. We were humbled by the great interest in our NGS software and its clinical applications. From our discussions, we have outlined our impressions in a recent blog that you can read here. Thank you to our customers and partners for making this a memorable conference. We are grateful to the ACMG 2022 organizers for their dedication and perseverance. I look forward to seeing you all at ESHG 2022.

Recent Webcast

Automating Clinical Workflows with the VarSeq Suite

Presented by Dr. Nathan Fortier, Director of Research

The automation of clinical NGS workflows provides a number of important benefits. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In this webcast, we discuss how the VarSeq Suite can be leveraged to automate the full analysis workflow from sequencer to clinical report. Watch as we demonstrate how VarSeq’s automation capabilities can enable your laboratory to:  

  • Automatically perform secondary analysis when a new sequence run is complete
  • Go from FASTQ to BAM and high-quality variants in VCFs using Sentieon
  • Automatically start VSPipeline to go from raw VCFs to candidate variants
  • Compute coverage and call CNVs alongside small variants with VS-CNV
  • Efficiently interpret a small set of annotated candidate variants and CNVs
  • Draft reports with VarSeq and VSClinical

In this webcast, we discussed the automation of the clinical analysis process for NGS genetic tests from FASTQ to Clinical Reports using the VarSeq Suite and discover how your laboratory’s NGS workflows may benefit from these automation capabilities.  

Watch Now
Customer Success

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

Whole genome sequencing identifies rare genetic variants in familial pancreatic cancer patients - Ming Tan & colleagues, Odense University Hospital / Published in Annals of Human Genetics

USP13 Genetics and Expression in a Family With Thyroid Cancer- Nikolaos Settas & colleagues, NICHD / 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.