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

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.

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.

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 you to version the clinical analysis conducted by lab work including the annotation 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.