Author Archives: Jennifer Dankoff

About Jennifer Dankoff

Jennifer has been a FAS with Golden Helix since September 2021. She has a PhD in Microbiology and Immunology from Montana State University, and is passionate about working with customers to fulfill their NGS analysis needs. When she isn't working with customers or writing blogs, Jennifer can be found hiking in the mountains or playing softball.

Webcast Recap: Somatic Variant Analysis in VarSeq 2.3.0

         December 22, 2022
Webcast Recap: Somatic Variant Analysis in VarSeq 2.3.0

Our FAS team would like to thank everyone who attended our December 2022 webcast, A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0. This webcast allowed three members of our FAS team to give their unique insights concerning the improvements to our new VarSeq 2.3.0 release, which will be recapped here. Starting with template creation, our Technical Field Application Scientist,… Read more »

Women in STEM: Golden Helix Employees

         November 10, 2022

Here at Golden Helix, we would like to take a moment and highlight some of our amazing and talented women in STEM! Below are short excerpts from some of our own Golden Helix employees and their experiences both in STEM and here at Golden Helix.   Rana Smalling Field Application Scientist B.S. in Biological Sciences, Ph.D. in Biochemistry My experience in STEM started in… 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 »

FASTQ to Report: Streamlining the process with Golden Helix Software

         August 3, 2022

Manually converting FASTQs to VCFs, importing these into VarSeq, and building projects from scratch is adequate when you have only a handful of cases per week. But as you start ramping up production, the key to your lab’s success quickly becomes how quickly and efficiently you can get to the reporting of your analysis. This blog will explain how you… 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 »

Handling a Variety of CNV Caller Inputs with VarSeq – Webcast Recap

         July 19, 2022

First, thank you to everyone who joined us for our recent webcast, Handling a Variety of CNV Caller Inputs with VarSeq. Also, we would like to thank those that Tweeted #CNVsupport @GoldenHelix or emailed us (mmarks@goldenhelix.com) to throw in their questions. This was a successful trial run, and we would like to continue engaging with our users through these outlets…. 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 »

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 »

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 »

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 »

VarSeq Advanced Reporting Customizations: Part 1

         November 9, 2021
BLOG-11.9.21-VarSeq-Custom-Reports-Part-1

As we move towards the end of the year, our FAS Team is excited to announce our short blog series highlighting some of the Customization Features in our up-and-coming VarSeq release! The goal of this blog series is to show examples of how generating a clinical report can be customized to accommodate a wide range of functionality. Our December webcast,… Read more »