Customer Publications Throughout July 2020

         July 30, 2020
customer

In this month’s Customer Publications blog post, our VarSeq software is taking center stage! From whole exome sequencing to copy number variant calling, VarSeq can be used for a range of scientific investigations. Although this blog features several examples of cancer investigations in human patients, it’s interesting to see how this platform can be utilized in a variety of investigational… Read more »

WT1 Mutations: Side-by-Side Germline and Somatic Variant Evaluation in VSClinical

         July 28, 2020

It is common knowledge that variants can be germline or somatic depending on whether the variant was inherited or acquired after birth. A well-known example is cancer-causing mutations in the BRCA genes, wherein the mutation may or may not have been inherited. Understanding the origin of the cancer-causing mutation is important when assessing potential treatment options as well as identifying… Read more »

Coming to SVS: LiftOver Capability

         July 23, 2020

The world has been making a shift to use GRCh38 human genome reference coordinates, but the transition has not been fast. Many of the mainstay human catalog projects are changing to use native GRCh38 catalogs, or are remapping their current data to GRCh38 coordinates. While this seems to be the advancing goal, it is leaving researchers and analysts with the… Read more »

Webcast Recap: Whole Genome Trait Association in SVS

         July 21, 2020
VS-CNV Annotations

Thank you to everyone who joined our webcast, “Whole Genome Trait Association in SVS.” If you missed the live event and are interested in knowing what we talked about, you may access the recorded event below: Our Live Q&A generated a lot of great questions. Unfortunately, we were unable to answer them all, but we have compiled some of the… Read more »

Using the AMP Guidelines for Rhabdoid Tumor Analysis in VSClinical

         July 15, 2020

Introduction: Malignant Rhabdoid tumors (MRT) are among the most aggressive and lethal forms of infant and child cancer (1). These tumors are characterized by an unusual combination of mixed cellular elements similar to but not typical of teratomas and can originate at any anatomic location. When MRTs are present in the brain, they are called atypical teratoid/rhabdoid tumors (AT/RT), which… Read more »

Featured in The Journal of Precision Medicine: Diagnosing and Tracking COVID-19 Infections Leveraging Next-Gen Sequencing

         July 8, 2020

It is an honor to be published in The Journal of Precision Medicine’s June/July 2020 issue in an article co-authored by Dr. Christiane Scherer and myself, “Diagnosing and Tracking COVID-19 Infections Leveraging Next-Gen Sequencing.” In this article, I detail: The key facts about COVID-19, reviewing the epidemiology, reservoir hosts, transmission routes, and clinical manifestation. Answering the question of how Next-Generation Sequencing can… Read more »

Golden Helix Featured in Various Publications

         July 8, 2020

Golden Helix has been incredibly fortunate to have been featured in a variety of publications over these last six months. Topics span from the history and future of our company to several new use cases for our solutions that extend into the infectious disease space, recently coming to fruition with the COVID-19 pandemic. We are so grateful to have received… Read more »

Customer Publications Throughout June 2020

         June 25, 2020
customer

As I prepared to write the Customer Publication blog this month, I was excited by the number of recently published papers that stood as examples of how both VarSeq and SVS software are employed to advance diagnostics and treatments in human medicine. We often think of SVS as the go-to platform for Agrigenomics, however both of our platforms have broad… Read more »

Golden Helix’s Virtual 2020 Conference Booth

         June 24, 2020

In lieu of conferences making the absolutely necessary decision to cancel this year’s conference, we created our Virtual 2020 Conference Booth! Even though it will never compare to the real deal, we hope you enjoy this blog post containing a few events we had planned this year. To start, let us paint the picture with some of our favorite conference… Read more »

Golden Helix’s 2020 T-Shirt Competition Begins

         June 23, 2020

It’s everyone’s favorite time of the year; Golden Helix’s Annual T-Shirt Design Competition is starting! If you’d like to participate, simply send a sketch of your design to marketing@goldenhelix.com. Don’t forget about the sweet prizes we’re handing out for the top three designs: First Place: $300 Second Place: $200 Third Place: $100 Deadline: August 25, 2020 How It Works Draw it… Read more »

Featured in Clinical OMICs: Enabling Precision Medicine with Cutting-Edge NGS Technologies

         June 22, 2020
Clinical OMICs May/June 2020

It is an honor to be featured in the Clinical OMICs May/June 2020 issue in a Q&A with the Editor discussing the past, present, and future of Golden Helix. In this article, I detail: Our most significant success throughout the past five years How our products differentiate Golden Helix in the market Our most significant opportunities in the next five years. If… Read more »

CADD Scores: New and Improved v1.4 and v1.5

         June 18, 2020

The University of Washington’s Combined Annotation Dependent Depletion (CADD) algorithm measures the deleteriousness of genetic variants. This includes single nucleotide polymorphisms (SNVs) and short insertions and deletions (indels) throughout the human reference genome assembly. This algorithm was introduced in 2014 and has since become one of the most widely used tools to assess human genetic variation. Since 2014, the algorithm has been… Read more »

Exporting Genes as Exon Regions in VS-CNV

         June 16, 2020
CNV Het Deletion

We have had many customers come to us over the years with a simple problem: they have BAM files for whole exome or gene panel data and would like to call CNVs using VarSeq’s powerful CNV calling capabilities, but they don’t have a bed file defining the target regions for their samples. To address this problem, we have developed a… Read more »

Recent Webcast: Evaluating Oncogenicity in VSClinical

         June 11, 2020

Abstract Before assessing the clinical significance of a somatic mutation, one must determine if the mutation is likely to be a driver mutation (i.e. a mutation that provides a selective growth advantage, thereby promoting cancer development). To aid clinicians in this process, VSClinical provides an oncogenicity scoring system, which uses a variety of metrics to classify a given somatic mutation… Read more »

Updates to Default Transcripts and Gene Preferences in VarSeq

         June 9, 2020

An under-appreciated area of complexity when looking into the field of genetics from the outside can be found in genes and transcripts. Alternative splicing allows eukaryotic species to have a wonderfully powerful genetic code, resulting in multiple protein isoforms being encoded in a single section of DNA. But when it comes to variant interpretation, different transcripts can result in widely different predicted… Read more »

Coping Mechanisms in the COVID-19 World

         June 4, 2020
Working from home

Like many of you, I was supposed to attend the 2020 ACMG Meeting in San Antonio this March with a few colleagues. In addition to attending the conference, my first blog post for Golden Helix was going to be about our time at the conference. Thanks to the world-wide COVID-19 pandemic, none of us got to attend the conference. (We… Read more »

Customer Publications Throughout May 2020

         May 29, 2020
customer

Writing this blog post to summarize and highlight our customer’s publications is undoubtedly one of my favorite things to do! The wide variety of topics is always surprising and inspiring, and I am humbled by the efforts of dedicated scientists who are helping to protect and enrich our lives in so many ways. Our SNP & Variation Suite (SVS) software… Read more »

Golden Helix Named as Top 10 Genetic Diagnostics Companies of 2020

         May 28, 2020

Today, Healthcare Tech Outlook announced its collection of the Top 10 Genetic Diagnostics Companies of 2020. We are incredibly honored to have received this award and being recognized amongst the top biotech companies! If you are interested in reading our story, and why we were selected for this award, you can access the publication here: https://genetic.healthcaretechoutlook.com/vendor/golden-helix-bioinformatics-for-advanced-life-science-research-cid-1369-mid-128.html. As always, we would not be… Read more »

Auto-Updating Template Sources

         May 21, 2020
ClinVar

In VarSeq 2.2.1, you can set template annotation sources to automatically update to the latest version. Previously, VarSeq templates were frozen in time. Now, each new project created from a template would use the same source that was used when the template was created. When you save a template, you can have the sources automatically update to the latest version…. Read more »