Tag Archives: Golden Helix

Golden Helix’s NGS-Solutions for Clinical Variant Analysis: VarSeq’s CNV Frequency Assessment Catalogs

         August 20, 2020

Our software solutions and partners have brought dramatic improvements to the secondary and tertiary analysis stages of variant evaluation. Regarding secondary analysis, we’ve discussed increased efficiencies in speed and overall accuracy in the variant calling process with Sentieon. On the tertiary side, we have explored numerous workflows in VarSeq highlighting filtration to clinically relevant variants, as well as the automated… Read more »

Golden Helix Announces New Workflow for the Interpretation and Reporting of Copy Number Variants in Concordance with the Recently Updated ACMG Guidelines

         August 18, 2020

The detection and interpretation of Copy Number Variants (CNVs) is vital for the clinical evaluation of individuals with a wide range of disorders. Golden Helix has remained at the forefront of CNVs in Next-Gen Sequencing (NGS) data since 2016 with the release of VS-CNV, our solution that allows you to both detect and analyze CNVs directly from NGS data. Earlier… Read more »

Golden Helix’s NGS-Solutions for Clinical Variant Analysis: VSClinical’s Assessment Catalog

         August 14, 2020

It doesn’t take much effort to find articles discussing the value of Next-Generation Sequencing (NGS). There is a consistent tone amongst authors that implementing NGS pipelines are critical for clinical efficiency in both hereditary disorders and somatic. However, NGS strategies do not come without their own challenges. Challenges include not only the detection and calling of high quality/probability variants from… Read more »

Golden Helix Named on Inc 5000 List of Fastest-Growing Private Companies for 2nd Consecutive Year

         August 12, 2020

Golden Helix has secured its reputation as a global leader in Next-Generation Sequencing solutions for over two decades. Today, we have been included in the esteemed Inc. 5000 list of rapidly growing American companies. Out of the 6 million business in the United States, Golden Helix has been honored with a spot in the annual list for the 2nd consecutive… Read more »

Case Study with the Rutgers Cancer Institute of New Jersey: Researching the Impact of HLA on COVID-19 Patients with SNP & Variation Suite

         August 8, 2020

The COVID-19 Pandemic ferociously spread across the globe bringing our daily lives to a quick halt – desks, streets, and towns nearly empty as our world united together to help “flatten the curve”. While most of us were introduced to remote work, medical workers from all different specialties were called upon to help treat and test COVID-19 patients. One long… Read more »

Building Gene Panels in VarSeq: Missense Variant in TP53

         August 6, 2020

Golden Helix software provides huge analytic gain in handling large-scale genomic data. For example, a number of VarSeq users run cohort projects of whole genome level data processing hundreds of millions of variants at a time. However, many of our users are running gene panel level data for custom panels related to cancer (both hereditary and somatic), autism, cardiac, and… Read more »

Kaviar and Allele Frequency Aggregator (ALFA): the databases you didn’t know existed in VarSeq.

         August 4, 2020

In the search for disease causing mutations it is important to determine if the variant has been previously observed in humans and at what frequency. With the advent of increasing genomic information, there is now a variety of different databases and annotation sources that can be utilized. For some, this could be a tedious task that leads only to implementing… Read more »

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 »

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 »

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 »

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 »

Webcast Recap: Next-Gen Sequencing of the SARS-CoV-2 Virus with Golden Helix

         May 13, 2020

Thank you to everyone who joined me for our latest webcast, “Next-Gen Sequencing of the SARS-CoV-2 Virus with Golden Helix.” 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… Read more »

Featured in Clinical Lab Manager: Leveraging Next-Generation Sequencing Technology in the Fight Against COVID-19

         May 5, 2020

It is an honor to be featured by Clinical Lab Manager where I discuss how Next-Gen Sequencing can be leveraged in the fight against COVID-19. You can access this article directly by visiting https://www.clinicallabmanager.com/thought-leadership/leveraging-next-generation-sequencing-technology-in-the-fight-against-covid-19-22584. If this is an area of interest for your organization, please reach out to our team and we would be happy to discuss this in more detail.

Recent Customer Publications – April 2020

         April 30, 2020
customer

Scientific investigations and genetic discoveries continue to happen in several diverse areas even while our world is currently consumed by the greatest health challenge of our era. Below are a few examples of some of the great work being done in the fields of human medicine, ecology, and breed conservation of animal species. As always, we are so very proud… Read more »

Genetic Analysis of the COVID-19 Virus and Other Pathogens: Part IV

         April 28, 2020

Next-Generation Sequencing (NGS) technology has decreased the price of nucleotide sequencing exponentially in the last 10 years. The clinical applications are broad, from diagnosis of rare diseases, to carrier screening and hereditary disease risk, and finally, for the personalized treatment of cancer with molecular profiling of tumors for therapeutic, diagnostic, and prognostic genomic biomarkers.  Discovery and Sharing of the Reference Genome for SARS-CoV-2  With… Read more »