Managing Pharmacogenomic Studies with Ingenuity Variant Analysis

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Recently, Ingenuity grant winner Dr. Vivien Sheehan, Assistant Professor of Pediatrics at Baylor College of Medicine, presented an overview of how she used Ingenuity Variant Analysis in her pharmacogenomics research of sickle cell disease (SCD). The webinar, which was hosted by The Scientist Magazine, has been archived online for viewing at your convenience.

Sheehan’s presentation focused on how she utilized whole exome data from 171 patients to investigate the genetic components of fetal hemoglobin response to the drug hydroxyurea. Hydroxyurea has been shown to increase fetal hemoglobin (HbF) production and concentration in the body. Because HbF can reduce the chance that red blood cells will sickle in a person who has SCD, it can reduce the occurrence of sickling-related complications such as pain and the need for blood transfusions.  As the only disease-modifying therapy approved for SCD, there is tremendous interest in understanding more about the effects of hydroxyurea use.

Some of the topical areas Sheehan covered in the webinar include:

  • How Ingenuity Variant Analysis can be used to analyze variants associated with high or low drug response or drug dosage.
  • How the exonically variable criteria found in the confidence filter can be helpful in eliminating genes with a high degree of variability that may result in false associations.
  • How burden analysis is a valuable addition to the analysis.
  • Feedback on the common-variants filter, which she found should be used with caution in phenotypes not subject to evolutionary pressure, such as drug response.

The genomic investigation of SCD is one of the success stories from the era of GWAS studies  and Sheehan’s research contributes to the body of work enhancing the ability to predict drug response and improve patient care by enabling better selection of individuals who will benefit most from hydroxyurea.

Some of the key benefits she found in using Ingenuity Variant Analysis include:

  • Capability to analyze samples for different phenotypes (She looked at three)
  • Ease to use; do not need to be a statistician
  • Ability to quickly share with findings with collaborators

To hear the full the webinar and Q&A session with Dr. Sheehan please visit The Scientist Magazine website.