The Geogenomic Mutational Atlas of Pathogens (GoMAP) web system

• Published in: PloS one Vol. 9; no. 3; p. e92877
• Main Authors: Sargeant, David P, Hedden, Michael W, Deverasetty, Sandeep, Strong, Christy L, Alaniz, Izua J, Bartlett, Alexandria N, Brandon, Nicholas R, Brooks, Steven B, Brown, Frederick A, Bufi, Flaviona, Chakarova, Monika, David, Roxanne P, Dobritch, Karlyn M, Guerra, Horacio P, Levit, Kelvy S, Mathew, Kiran R, Matti, Ray, Maza, Dorothea Q, Mistry, Sabyasachy, Novakovic, Nemanja, Pomerantz, Austin, Rafalski, Timothy F, Rathnayake, Viraj, Rezapour, Noura, Ross, Christian A, Schooler, Steve G, Songao, Sarah, Tuggle, Sean L, Wing, Helen J, Yousif, Sandy, Schiller, Martin R
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 27.03.2014; Public Library of Science (PLoS)
• Subjects: Amino acid sequence; Antiretroviral agents; Biology and Life Sciences; Business travel; Communicable Diseases - etiology; Computer and Information Sciences; Data mining; Data processing; Databases, Genetic; Drug resistance; Drug therapy; Drugs; Earth Sciences; Genetic aspects; Genome, Microbial; Genomes; Genomics; Genomics - methods; Geographical distribution; Geography; Global Health; Highly active antiretroviral therapy; HIV; HIV Infections; Homesteading; Humans; Jet lag; Medicine and Health Sciences; Microbial drug resistance; Mutation; Nanoparticles; Pathogenic microorganisms; Pathogens; Population Surveillance - methods; Social Sciences; Viral proteins; Web Browser; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0092877

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/