AUG 21, 2013 04:00 PM PDT

Development of Targeted Next Generation Sequencing for Pharmacogenomics

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  • Clinical Chemistry Postdoctoral Fellow, University of Chicago
      Born and raised in Vancouver, British Columbia, Canada. I received my Bachelor of Science and my Doctor of Philosophy from the Department of Molecular Biology and Biochemistry at Simon Fraser University. I studied the photochemistry and reduction-oxidation chemistry of nucleic acids with Dr. Dipankar Sen. I was a postdoctoral fellow for three years with Dr. Joseph Piccirilli from the Department of Biochemistry and Molecular Biology at the University of Chicago and studied RNA structural biology using phage-display technology and crystallography. For the past two years, I am in the clinical chemistry postdoctoral fellow at the University of Chicago Medicine, a ComACC certified training program under the directorship of Dr. Jerry Yeo. My research interest is in personalized medicine. My research interest is in personalized medicine. I am interested in developing and using mass spectrometry to study an observed phenotype (ie. protein levels, protein post-translational modifications, and active drugs and/or its metabolites) and next-generation sequencing to study the corresponding genotype. By combining genetic and phenotypic data, a more well-rounded and complete understanding of personalized medicine can be achieved.


    The goal of personalized medicine is to customize healthcare to the individual patient. Pharmacogenomics, the analysis of how a patient's genetic makeup affects the individual's response to certain drugs, plays a major role in the realization of personalized medicine. Pharmacogenomics studies the influence of genetic variation on the patient's drug response by correlating single-nucleotide polymorphisms (SNPs) with the drug's efficacy and/or toxicity, and therefore with the hope of optimizing drug therapy with respect to the patent's genotype, to ensure maximum efficacy with minimal adverse effects. Currently, most pharmacogenomic studies have been done using DNA chip arrays. A large amount of genetic information is generated in a cost effective way when using DNA chip arrays. However, one limitation of using this technology is that only a subset of mutations are analyzed and different manufacturers may use different SNPs to identify the same haplotype. Recent technological developments with next-generation sequencing (NGS) have enabled pharmacogenomics analysis at costs approaching to the cost of using DNA chip arrays. The advantage of using NGS is that all the SNPs corresponding to a haplotype can be analyzed. Currently, there are only a few targeting-sequencing kits for pharmacogenomics are commercially available. Because these kits may not cover some SNPs of interest, custom sequencing panels are needed to ensure that all interested SNPs are covered. This presentation will go over some of the important features of some commonly used targeted-enrichment technologies for NGS that are desirable for pharmacogenomic studies. This presentation will also highlight some of the challenges of developing and implementing pharmacogenomic NGS in a clinical laboratory for routine patient sample analysis.

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