Illumina Arrays Software Update

By: Sophie Coon, Product Manager, Array Software (scoon@illumina.com)

Prescription drugs are not one-size-fits-all. Adverse Drug reaction is the 4th leading cause of death, and significant genetic differences affect drug response for 90% of the population [1]. Pharmacogenomics screening (PGx screening) is a type of genetic testing that is at the basis for customizing therapies, producing optimal outcomes, minimizing adverse reactions and improving health economics. CYP2D6 is a key pharmacogene involved in the metabolism of 25 to 40% of medications, and one whose function is frequently impacted by copy number variation.

We are excited to announce the upcoming release of a downloadable command line software, to analyze CYP2D6 CNV variation for GSAv3. GSAv3 is a commercially available genotyping microarray that enables clinical research applications including, but not limited to, pharmacogenomics. Copy number variant calling for CYP2D6 is currently not supported for our commercially available GSAv3 product. With this software, we are strengthening the utility of GSAv3 for use in clinical research applications which will help reduce the barrier to entry for PGx testing for current Infinium customers and customers intending to start PGx this year.

The CYP2D6 CNV Caller is a standalone command line software solution. With just one installation package to download from the Illumina support page and configure, customers will be able to:

  • Install and run this software on Windows, MacOS X or Unix.
  • Output genotype calls and CNV calls for key regions of CYP2D6 for their Infinium GSA v3 samples in VCF format.
  • Output auxiliary files to help assess the quality of the data generated.
  • Generate the necessary input file to process their GSA v3 with custom add-on product.

We are always interested in improving our software solution to better support your needs, so please submit any requests in via this blog or techsupport@illumina.com.

The Array Analysis Development Team.

For Research Use Only. Not for use in diagnostic procedures.

References

[1] Bank PCD, Swen JJ, Guchelaar HJ. Implementation of Pharmacogenomics in Everyday Clinical Settings. Adv Pharmacol. 2018;83:219-246.

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