SCAN: A Systems Biology Approach to Pharmacogenomic Discovery

  • Eric R. Gamazon
  • R. Stephanie Huang
  • Nancy J. Cox
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1015)

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 

Notes

Acknowledgments

This work was funded through Pharmacogenomics of Anticancer Agents Research (PAAR; U01 GM61393), ENDGAMe (ENhancing Development of Genome-wide Association Methods) initiative (U01 HL084715), the Genotype-Tissue Expression project (GTeX) (R01 MH090937), Rare Variants and Complex Human Phenotypes (U01HG005773), and the University of Chicago DRTC (Diabetes Research and Training Center; P60 DK20595).

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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Eric R. Gamazon
    • 1
  • R. Stephanie Huang
    • 2
  • Nancy J. Cox
    • 1
  1. 1.Section of Genetic Medicine, Department of MedicineThe University of ChicagoChicagoUSA
  2. 2.Section of Hematology/Oncology, Department of MedicineThe University of ChicagoChicagoUSA

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