PLoS ONE (Jan 2014)

The Geogenomic Mutational Atlas of Pathogens (GoMAP) web system.

  • David P Sargeant,
  • Michael W Hedden,
  • Sandeep Deverasetty,
  • Christy L Strong,
  • Izua J Alaniz,
  • Alexandria N Bartlett,
  • Nicholas R Brandon,
  • Steven B Brooks,
  • Frederick A Brown,
  • Flaviona Bufi,
  • Monika Chakarova,
  • Roxanne P David,
  • Karlyn M Dobritch,
  • Horacio P Guerra,
  • Kelvy S Levit,
  • Kiran R Mathew,
  • Ray Matti,
  • Dorothea Q Maza,
  • Sabyasachy Mistry,
  • Nemanja Novakovic,
  • Austin Pomerantz,
  • Timothy F Rafalski,
  • Viraj Rathnayake,
  • Noura Rezapour,
  • Christian A Ross,
  • Steve G Schooler,
  • Sarah Songao,
  • Sean L Tuggle,
  • Helen J Wing,
  • Sandy Yousif,
  • Martin R Schiller

DOI
https://doi.org/10.1371/journal.pone.0092877
Journal volume & issue
Vol. 9, no. 3
p. e92877

Abstract

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We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼ 502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/