May Newsletter

Sentieon Updates: Now Supporting Long-Read Alignment and Calling 

Sentieon Updates: Now Supporting Long-Read Alignment and Calling

By Darby Kammeraad
Director of Field Application Services

Here at Golden Helix, we’ve sought to develop top-quality bioinformatic software to handle not only high-throughput clinical next-gen sequencing pipelines but also cater to research groups exploring their cohorts. Our tools fit in this NGS pipeline by importing the VCF and BAM files for downstream filtration, annotation, and classification/interpretation as well as clinical reporting. It was obvious early on and even more so now that our users had a need to bring all the established secondary and tertiary tools in-house and do away with the hurdles of customized pipelines constructed from public tools on the web. These public tools are driven by innovation and global need but the reality is that these tools need optimization and ongoing support/development...Read More

Expanding Clinical Trial Search in VSClinical

Expanding Clinical Trial Search in VSClinical

By Dr. Nathan Fortier
Director of Research

While the interpretation of germline variants generally focuses on the pathogenicity of a variant for a specific disease, the interpretation of somatic variants is centered around each variant’s impact on clinical care. As a result, clinical trials play an important role in assessing the clinical significance of somatic biomarkers, with the AMP Guidelines assigning a higher level of evidence to biomarkers that serve as inclusion criteria for clinical trials. Furthermore, clinical trials can provide additional treatment options to the oncologist, including treatments that are not yet approved or are approved for a different tumor type. Until recently, VarSeq’s Clinical Trials annotation was based on the database of clinical trials provided by the National Cancer Institute...Read More

Mining Curated Databases for Literature in VSClinical

Mining Curated Databases for Literature in VSClinical

By Dr. Rana Smalling
Field Application Scientist

Curated databases are a real-time saver when compiling published evidence to support your variant evaluations and classifications. Leveraging the curated databases at your fingertips in our VSClinical variant interpretation hub is even more efficient. Not only does VSClinical provides users with automated variant classification for germline variants according to the ACMG guidelines and somatic variants according to the AMP guidelines, but we also give users immediate access to the curated databases and literature sources that are relevant for their evaluation. This blog is meant to highlight the curated databases such as ClinVar, dbSNP, PMKB, COSMIC, and others that users have access to and describe how to leverage them in VSClinical. When evaluating a germline variant in VSClinical ACMG, we often focus on the...Read More

 

 

CEO Corner
New eBook: Clinical Variant Analysis for Cancer

We are excited to be traveling again and attending ESHG 2022 in just one week! For anyone who is attending this year's conference, I would like to extend an invitation to our Corporate Satellite Talk, Maximizing Profitability in Your NGS Testing Lab, on Monday, June 13, 12:00 – 13:00 hrs. This talk will address how our customers can provide the full spectrum of all relevant NGS services such as cancer and germline tests based on gene panels, whole exomes, and whole genomes while maximizing profitability. This topic becomes increasingly important in times of economic uncertainty and high-interest rates that put a premium on deployed capital. We look forward to discussing this topic at the appropriate level of detail and look forward to seeing you there.

Recent Webcast

Evaluating Cloud vs On-Premises for NGS Clinical Workflows

Presented by Gabe Rudy, Vice President of Product & Engineering

In the era where cloud-based solutions are the default for the modern office, it may not be obvious why many laboratories and testing centers choose to host their data and analysis pipelines on-premises or on self-managed cloud services. Next-generation sequencing enables a precision medicine approach to rare disease diagnostic and cancer therapeutics through its power to detect unique variants in individuals. This data is generated quickly and cheaply but requires a lot of disk space and processing power to arrive at clinically useful insights. When providing a clinical lab service under a regulated environment: data security, long-term affordable storage, and versioning through locked-down pipelines are all factors that must go into the choice of whether to choose a hosted analytics platform versus on-premises solutions or self-managed cloud infrastructure.  

Watch in this webinar as we covered:

  • The validation and regulatory requirements that inform infrastructure and hosting decisions for NGS labs
  • The cost structure of scaling NGS labs to exomes and genomes
  • Deployment and security architecture for on-premises and self-managed cloud infrastructure
  • Validating and versioning analysis pipelines with clinical tests through self-managed software lifecycles and versioned annotation sources
Watch Now
Customer Success

Congratulations to all of our customers who have published this month! To highlight just a few:

Clinical whole exome sequencing revealed de novo Heterozygous Stop-Gain and Missense variants in the STXBP1 gene associated with Epilepsy in Saudi Families- Peter Pushparaj & colleagues, University of British Columbia / Published in ScienceDirect

Innovative in Silico Approaches for Characterization of Genes and Proteins- Rakesh Kumar Mishra & colleagues, Centre for Cellular and Molecular Biology India / Published in Frontiers in Genetics

About Golden Helix

Golden Helix has been delivering industry-leading bioinformatics solutions for the advancement of life science research and translational medicine for over 20 years with 1,000s of users around the world. Their innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from NGS sequencers and microarrays. With their solutions, hundreds of the world's top hospitals, testing labs, pharmaceutical, biotech, and academic research organizations can harness the full potential of genomics to identify the cause of disease, improve the efficacy and safety of drugs, develop genomic diagnostics, and advance the quest for personalized medicine.