Next-generation sequencing (NGS) embodies the process of elucidating the signal from the noise. Given the genetic data of a patient, ranging from a targeted gene panel to a whole genome, a healthcare provider’s onus is to glean as much actionable information from the detected variants. As the field of NGS has grown and improved, the scope of available genomic markers and clinically relevant findings has increased in volume and precision. One such augmentation is the ability to include pharmacogenomics (PGx) analysis in existing NGS pipelines. Pharmacogenomics, broadly the process of determining personalized gene-drug interactions for patients, has a proven history of empowering clinicians and patients alike. Hence, it ties in naturally to the information-rich landscape of Golden Helix, Inc.’s VarSeq Suite. Our users can use VarSeq’s PGx module in tandem with existing somatic or germline analysis, or as a standalone product, either way enabling more precise outcomes.

Seamless handling of historical methods

While the ability to include PGx analysis in NGS workflows is the most comprehensive solution for precision medicine, the VarSeq Suite’s reputation for versatility shines in allowing users to import PGx array data just as easily as derive PGx diplotypes from NGS data. With the near limitless scope of bioinformatic freedom afforded to VarSeq users, the conversion of array data in VCF format, import into VarSeq, and the generation of a PGx report can all be achieved in a few steps or automated with VSPipeline, VarSeq’s command line interface. This ability is highly beneficial to users with existing array pipelines, and will produce results concordant with the panels being used according to CPIC and FDA guidelines.

Next-generation sequencing and pharmacogenomics

In tandem with VarSeq PGx’s support for array data, we have developed a comprehensive suite of tools to handle NGS data, allowing users to extract fast, reliable PGx reports from their existing NGS data. On the secondary analysis side, through our partnership with Sentieon, we provide pipelines for users to perform forced-calling of CPIC variants for input into the PGx algorithm. Alternatively, we have developed tools to call PGx-relevant variants on import using either a BAM/CRAM file or a gVCF as input. Hence, virtually any user with NGS data can get started seamlessly with VarSeq PGx.

In summary, whether you have existing NGS pipelines that you would like to integrate PGx into, array data that you would like to use as the input for PGx calls, or some combination of the two, VarSeq PGx includes the tools you need to make it happen. VarSeq PGx has quite a bit more to offer than flexibility, though, so please check out some of our previous blogs, request a demo or evaluation of the software, and stay tuned for more content regarding the breadth of our pharmacogenomics offerings.