Tag Archives: Golden Helix

Controlling Your Preferred Transcripts for Clinical Interpretation

         September 24, 2020

Did you know you can control your preferred transcript settings for clinical interpretation in VSClinical? Your lab is analyzing the DNA of a tissue sample from a patient with small cell lung cancer. The lab technician has imported the patient data into VSClinical to detect clinically relevant variants and evaluate and score these according to the AMP Guidelines, as well… Read more »

Advanced Plotting Capabilities with GenomeBrowse

         September 22, 2020

The strategy with any next-gen sequencing analysis is to filter down to interesting variants for either research or clinical conclusion. Golden Helix produces powerful software specifically tailored for this efficient and comprehensive search for interesting and clinically relevant variants. One additional advantage of our software is the ability to visualize the results. Visualizing the genomic data answers multiple questions; for… Read more »

Variant Analysis of Bechet Disease Using VSClinical

         September 15, 2020

VSClinical is a feature to evaluate clinically relevant variants according to the ACMG or AMP guidelines. This feature can also be used to identify if a variant has been observed previously or evaluate a manually inserted variant. Take, for example, the scenario where a colleague is interested to see if you have seen any variants associated with Bechet syndrome, which… Read more »

Webcast Recap: VSClinical: First Commercial Product to Integrate the Updated ACMG Guidelines for CNVs

         September 15, 2020

In our recent webcast announcing the upcoming release of VarSeq VSClinical and the implementation of the ACMG guidelines for NGS CNVs, we had a number of live questions we didn’t get a chance to cover at the end of the presentation. I will follow up on those questions in this blog post. But first, if you didn’t get a chance to join us for… Read more »

Updates to dbSNP 154 v2

         September 3, 2020

In the 1990s the genetic industry voiced a request for a variant catalog that incorporates associated variant information such as phenotypic and metabolic pathways. The call was answered by NCBI, which created dbSNP; dbSNP became publicly available in 1998 and around 1.5 million variants. Fast forward to the present and dbSNP now contains over 2 billion SNPs spanning human, rat,… Read more »

Golden Helix’s NGS-Solutions for Clinical Variant Analysis: VSWarehouse

         August 27, 2020
VSWarehouse Updates

We have now reached the final blog of the NGS-Solutions for Clinical Variant Analysis series. Part I of this series explored the capture of variant classifications in the VSClinical environment when following the ACMG and AMP guidelines. Part II was similar in content but for the capture of clinically relevant copy number variants as well as using a CNV catalog… Read more »

Golden Helix gets full marks in ClinGen’s list of Genomic Analysis Software Platforms

         August 26, 2020
Clinical Genome Resource

The potential of genetic testing to impact a patient’s life has been greatly accelerated by the sharing of variant interpretations done by clinical labs in public repositories such as ClinVar. This is not an inevitable outcome, but the persistent work and advocacy of people like Dr. Heidi Rehm and organizations like ClinGen. We recently participated in a survey and vetting… Read more »

SVS 8.9.0 Release Notes

         August 24, 2020
Eigenvalue Decomposition

SVS 8.9.0 was released on August 19th and features a new GBLUP by Bin feature and a new utility to find the LD scores of markers and categorize them into bins, along with several mixed-model upgrades and many other upgrades, fixes, and polishes. The two new features LD Score Computation and Binning and Compute GBLUP Using Bins, while they can… Read more »

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 »