The global NGS market is expected to grow exponentially in the coming years. This is contributed to the increased amount of treatment options. Moreover, more practitioners are utilizing precision medicine and molecular diagnostics now than ever before. There have been advancements in NGS platforms as well. Sequencers can now provide increased throughput and better data quality. Concurrently, capital requirements have decreased, making the technology more accessible. Additionally, payers are now compensating for tests due to reimbursement changes.
Though these are positive and crucial steps forward, they have created a dilemma for those in the industry. The diagnostic process is both labor-intensive and requires specific expertise. With clinical labs effectively doubling their workforce in the next few years, the problem of managing the inevitable shortage of clinical experts is expected to appear. Analysts must give a ruling upon multiple lines of evidence, following complex decision trees and leveraging evidence weighing systems. Automation is the only solution to this problem as it eliminates human error and subjectivity. By providing guided workflows the time and labor of molecular geneticists will be cut to a fraction of what was previously presented.
Golden Helix is a company that has been extensively collaborating with its customers to illuminate what processes, workflows, and other challenges need to be addressed. Founded in 1998, the Bozeman, Montana-based company has hundreds of customers around the world with thousands of users that are provided with innovative bioinformatics solutions for both clinical and research spaces analyzing NGS data.
All-in-One Software Solutions
The software provided by Golden Helix accomplishes several things. It enables a clinician to deliver consistent, high-quality interpretations. It provides a framework for newer, less experienced clinicians.
What truly sets golden Helix in the market is its simple business model with no per-sample costs. Its products are available through an annual license fee, which allows their users to retain all the efficiencies they generate in their lab, reducing the cost per samples.
As a company, Golden Helix stays abreast of new developments. Its software is consistently updated so that customers can rest assured that they have the most current information. Moreover, experts can make sound, clinical decisions leveraging a constantly growing kit of specialty databases, publications, and algorithms that are designed to predict the impact of specific variants in the resulting protein.
- VarSeq
VarSeq is an intuitive, integrated software solution for tertiary analysis. It can automate workflows and analyze variants for gene panels, exomes, and whole genomes. It boasts intuitive and repeatable workflows, industry-leading automation sources, two forms of coverage metrics, clinical-grade variant annotations, great visualization, and no learning curve. VarSeq is used in many spaces including—cancer diagnostics, hereditary testing and diagnosis, research, and trio analysis. This single-testing paradigm also includes an additional CNV interpretation framework. Given full marks by ClinGen, this solution is truly one-of-a kind in the marketplace.
- VS-CNV
VS-CNV is a powerful detection tool that uses an industry-leading algorithm to call CNVs directly from gene panels, exomes, or whole-genome NGS data. Coupled with VarSeq, this robust solution allows CNVs to be considered alongside the annotated and filtered NGS small variants, all within one workflow. This integration has been found to be in concordance with other methods such as MLPA or CMA, at a fraction of the cost, while meeting the thresholds for clinical validation and adoption. Additionally, by using NGS data already generated to call small SNPs and InDels variants to call CNVs, one can integrate LOH with CNV calling to distinguish Copy-Neutral LOHs from LOH events that support Heterozygous Deletion CNV Calls.
- VSClinical
VSClinical is a guided workflow that enables following the American College of Medical Genetics (ACMG) guidelines used to identify and classify casual variants for inherited disease risk, cancer predisposition, and the diagnosis of rare diseases. VSClinical includes integrated ACMG guidelines, a variant knowledge base, a standardized workflow, accelerated interpretation, automated classification, and the bonus of learning as you go. Moreover, as an optional add-on, VSClinical can follow the Association for Molecular Pathology (AMP) guidelines used for performing targeted cancer gene panel tests popular in molecular pathology labs to report significant biomarkers of clinical utility.
VSClinical had a major update at the end of 2020, boasting an additional CNV interpretation framework based on the ACMG guidelines for CNVs. The ACGS guidelines are also now available in VSClinical, which was recently announced in the Journal of Precision Medicine.
- VSPipeline
VSPipeline provides repeatable clinical workflows essential for CLIA and CAP certified analysis, creation of high-throughput pipelines, and access to curated annotation sources that are regularly updated. It is a convenient way for users in CLIA and CAP certified labs to lock down a workflow that has been designed in VarSeq. This can then be automated, mitigating the risk of human error. The creation of high throughput pipelines will benefit by automating the entire tertiary analysis process. Along with fully computed VarSeq projects, VSPipeline can also be used to generate other deliverables such as annotated text or VCF files as well as multi-tab Excel reports of filtered variants, sample, and coverage region statistics.
- VSReports
VSReports allows the conversion of the output of tertiary analysis into a fully-customizable clinical report. The report includes identifiers from various catalogs, descriptions of gene function from OMIM, pathogenicity, exon numbers, coverage information, and much more. The reports are modeled off the ACMG guidelines, the de-facto gold standard for clinical reporting. These brandable reports have templates for both gene panels and trio analysis and can be used for both hereditary and cancer analysis.
- VSWarehouse
As precision medicine continues to grow into more and more labs, the number of samples and subsequent data is ever-expanding. An organized system of storing this data is not only imperative but can also create a wealth of knowledge for ongoing research and future analysis. VSWarehouse is Golden Helix’s scalable, multi-project warehouse for NGS variant calls, catalogs for variant assessments, and clinical reports that are built on algorithms and high-powered storage technology.
Expanding the Footprint
In the years to come, Golden Helix will continue to expand its global customer base, will innovate, stay at the forefront of technology, and maintain its high standards for quality and support through which it has managed to consistently thrive in the increasing competition.
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