Golden Helix’s End-to-End Architecture for Clinical Testing Labs

Precision Medicine and the usage of Next-Gen Sequencing to conduct genetic tests is rapidly growing. NGS based tests are increasingly used in therapeutic areas such as:

  • Oncology
  • Pediatrics and Newborn Screening
  • Rare diseases

There is also strong potential in areas such as diabetes and cardiac disorders, as well as in pharmacogenomics to determine safety, efficacy and cost of care. New applications of genetic testing will result in changes to current care, teams and processes. This trend reshapes how pathologists, clinicians, geneticists, genetic counselors, biostatisticians and bioinformaticians work together.

The genetic testing technology and infrastructure has evolved quickly. Hospitals and healthcare organizations around the globe are building the infrastructure necessary to handle the increasing testing volume. Golden Helix has built a complete end-to-end bioinformatics pipeline that is designed to receive the data from the sequencer and take it all the way to clinical reporting. Along side, we have created automation capability for high throughput labs, as well as an extensive data warehousing capability that allows the capture and querying of the entire lab output (see Fig 1).

Fig 1: Golden Helix End-to-End Architecture for Clinical Testing Labs (click to enlarge)

This complete end-to-end architecture sets Golden Helix apart in the market place. It allows our clients to conduct a thorough analysis of its sample data coming out of the sequencer. It supports the entire clinical interpretation and report generation. Lastly, it is able to store all data, make it retrievable and allows other hospital systems to connect to the data repository via APIs and standard protocols.

Secondary Analysis: Here we provide the unique ability to analyze genomic data in regards to Single Nucleotide Variations and Structural Variations. Via our partnership with Sentieon, we provide a highly performant secondary pipeline that includes alignment and variant calling on par with GATK and MuTect2 at much improved speed levels.  Our product VS-CNV is capable to detect CNV events starting at the exon level and all the way to aberrations of an entire chromosome.

Tertiary Analysis: VarSeq and VSReports are covering all clinically relevant workflows for the filtering and annotating of genomic data. For example, it supports gene panels, trios, single exome and whole genome workflows. With a single click, users can generate a clinical report that integrates the specific findings with annotation sources. There are powerful customization options available to make the reports exactly how your organization requires them to be. Moreover, with VSPipeline we have developed the ability to automate the entire pipeline to increase throughput. Our clients are able to automate the process from FASTQ to Clinical Report, including the computation of CNVs. This allows a highly efficient review of the resulting data. This not only saves time, but it also minimizes the potential for human error.

Data Warehousing: This products captures the artifacts of the bioinformatics pipeline. Via powerful APIs the product connects to other lab and hospital systems such as EPIC or Cerner’s Millennium. Moreover, it allows you to efficiently answer the following questions:

  • Have I seen this variant before in my clinical practice? If so, was it included in any clinical report?
  • Has the categorization of any variant that I reported on changed (e.g. from ‘unknown’ to ‘pathogenic’)?
  • It allows to version the clinical analysis conducted by a lab work including the annotations sources that have been used during the tertiary analysis. This is a key capability during discovery should your lab or hospital be involved in legal disputes.

Our software stack is deeply integrated. This is a major advantage over any software architecture consisting of different point solutions of other commercial vendors or homegrown applications. Labs would have to carry the burden to integrate the various components via so called ‘glue ware’, test the integration and maintain a detailed versioning log to stay in compliance with applicable regulatory requirements. In some cases, we are not even aware of any viable commercially available alternatives in areas such as our powerful CNV analysis product or our data warehousing solution. The high degree of integration brings enormous speed and performance advantages since we have been able to optimize data formats and leverage multi-threaded code components across the various products.

Golden Helix is pleased with its global market adoption, with references in the clinical NGS based market across the globe. Our work has been recognized by multiple media outlets, such as CIO Review and others, over the last view months. Please get in touch with us if you would like to learn more about how we can help your lab take Next Gen Sequencing to the next level.

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