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Bioinformatics, Genomics, and Functional Genomics: Overview

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Textbook of Pulmonary Vascular Disease

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Abstract

Recent advances in high-throughput genetic and genomic technologies, such as efficient DNA sequencers, multiplex genotyping platforms, microarrays, and proteomics and metabolomics assays, have provided researchers with an unprecedented ability to seek out and characterize the genetic determinants of diseases and clinical outcomes of all sorts. In fact, the application of these technologies has led to the identification of hundreds, if not thousands, of genomic loci that are associated with or even responsible for many different disease conditions, clinical outcomes, and responses to medications. As useful as these technologies are, however, their ability to generate data easily outpaces an ability to draw compelling inferences from those data. The field of bioinformatics evolved out of a need to manage, analyze, and interpret high-dimensional data of the type generated from the application of high-throughput genetic and genomic technologies. Necessary bioinformatics tools include those that enable one to test statistical associations between DNA sequence variations and phenotypes, find patterns in gene or protein expression data, understand how specific perturbations in a protein may affect the functioning of that protein, and determine which fundamental processes, pathways, or genetic networks may harbor the molecular “lesions” causing disease. In this chapter we provide an overview of available bioinformatics strategies and tools that have either been applied or are simply applicable to the genetic and genomic dissection of complex pulmonary vascular diseases (PVD) and other complex diseases. We start with a brief summary of the motivation for examining the genetic basis of PVD, consider various strategies for identifying genetic factors contributing to PVD, and then describe the bioinformatics tools and resources available to facilitate these analyses. We provide relevant Web resources in addition to references, and also provide example analyses and results.

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Authors and Affiliations

  1. Scripps Genomic Medicine, Scripps Translational Sciences Institute, 3344 North Torrey Pines Court, La Jolla, CA, 92037, USA

    Ali Torkamani

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  1. Ali Torkamani
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  2. Eric J. Topol
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  3. Nicholas J. Schork
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Correspondence to Ali Torkamani .

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Editors and Affiliations

  1. Departments of Medicine, COMRB Rm. 3131 (MC 719), University of Illinois at Chicago, 909 South Wolcott Avenue, Chicago, 60612, Illinois, USA

    Jason X. -J. Yuan

  2. 310 Admin.Office Building (MC 672), University of Illinois at Chicago, 1737 W. Polk Street, Suite 310, Chicago, 60612, Illinois, USA

    Joe G.N. Garcia

  3. Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0623, California, USA

    John B. West

  4. Dept. Pulmonary & Critical Care Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, 02114, Massachusetts, USA

    Charles A. Hales

  5. Department of Medicine, University of Chicago Medical Center, 5841 S. Maryland Ave., Chicago, 60637, Illinois, USA

    Stuart Rich

  6. Department of Medicine, University of Chicago School of Medicine, 5841 S. Maryland Ave., Chicago, 60637, Illinois, USA

    Stephen L. Archer

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Torkamani, A., Topol, E.J., Schork, N.J. (2011). Bioinformatics, Genomics, and Functional Genomics: Overview. In: Yuan, JJ., Garcia, J., West, J., Hales, C., Rich, S., Archer, S. (eds) Textbook of Pulmonary Vascular Disease. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-87429-6_39

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