Protocol

Pharmacogenomics

Volume 1015 of the series Methods in Molecular Biology pp 213-224

Date:

SCAN: A Systems Biology Approach to Pharmacogenomic Discovery

  • Eric R. GamazonAffiliated withSection of Genetic Medicine, Department of Medicine, The University of Chicago
  • , R. Stephanie HuangAffiliated withSection of Hematology/Oncology, Department of Medicine, The University of Chicago
  • , Nancy J. CoxAffiliated withSection of Genetic Medicine, Department of Medicine, The University of Chicago

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Abstract

Genome-wide association (GWA) studies have identified thousands of genetic variants that contribute to disease and pharmacologic traits. More recently, high-throughput sequencing studies promise to provide a more complete catalog of genetic variants with roles in human phenotypic variation. Yet, characterizing the influence of functional variants on genes, RNAs, proteins, and ultimately disease or pharmacologic traits is a critical challenge for a vast majority of the implicated susceptibility loci. Here we describe SCAN, a bioinformatics resource we have developed to elucidate the functional consequences of genetic variants identified by genome-wide scans. In particular, this public resource implements a systems biology approach to pharmacogenomic discovery.

Key words

eQTLs Pharmacogenomics Expression profiling Transcriptome SNP function Genetic variation