Golden Helix Blog

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

Aug 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…

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Building Gene Panels in VarSeq: Missense Variant in TP53

Aug 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…

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Kaviar and Allele Frequency Aggregator (ALFA): The Databases You Didn’t Know Existed in VarSeq

Aug 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…

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Customer Publications Throughout July 2020

Jul 30, 2020

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…

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

Jul 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…

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Coming to SVS: LiftOver Capability

Jul 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…

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Webcast Recap: Whole Genome Trait Association in SVS

Jul 21, 2020

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…

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Using the AMP Guidelines for Rhabdoid Tumor Analysis in VSClinical

Jul 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…

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Featured in The European Journal of Clinical and Biomedical Sciences: Investigating COVID-19 Infections Leveraging Next-Gen Sequencing

Jul 8, 2020

It is an honor to be published in the European Journal of Clinical and Biomedical Sciences (Volume 6, Issue 4) in an article co-authored by Dr. Christiane Scherer and myself, “Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis.” This study highlights how genomic surveillance of COVID-19…

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Golden Helix Featured in Various Publications

Jul 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…

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Customer Publications Throughout June 2020

Jun 25, 2020

As I prepared to write the Customer Publication blog for June 2020, 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…

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

Jun 22, 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: Clinical OMICs Article: What has been Golden Helix’s most significant success or contribution to the industry over the…

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

Jun 18, 2020

The University of Washington’s Combined Annotation Dependent Depletion (CADD) algorithm, now available in CADD v1.4 and CADD v1.5, 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…

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Exporting Genes as Exon Regions in VS-CNV

Jun 16, 2020

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…

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Recent Webcast: Evaluating Oncogenicity in VSClinical

Jun 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…

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Updates to Default Transcripts and Gene Preferences in VarSeq

Jun 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…

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Coping Mechanisms in the COVID-19 World

Jun 4, 2020

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…

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An Open Letter to Our Community

Jun 3, 2020

Dear All, Going back in time to the beginning of this year, it would have been difficult to imagine what our world would look like as of June 2020. Things changed quickly. While we are still in the midst of the COVID-19 pandemic, the senseless killing of George Floyd triggered…

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Customer Publications Throughout May 2020

May 29, 2020

Writing the 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…

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Golden Helix Named as Top 10 Genetic Diagnostics Companies of 2020

May 28, 2020

Today, we’re thrilled to announce that Healthcare Tech Outlook has named Golden Helix among the Top 10 Genetic Diagnostics Companies of 2020. This recognition places us alongside a remarkable group of companies that are leading innovation in genomics, diagnostics, and precision medicine. We are honored to receive this distinction and…

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