Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology

• Type of Material: Article
• Authors: Timothy Read, Emory University; Ruth C. Massey, University of Bath
• Language: English
• Date: 2014-11-22
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © 2014 Read and Massey; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1186/s13073-014-0109-z
• Title of Journal or Parent Work: Genome Medicine
• ISSN: 1756-994X
• Volume: 6
• Issue: 11
• Start Page: 109
• End Page: 109
• Grant/Funding Information: The manuscript resulted from a visit by TDR to RCM’s laboratory that was funded by the Raymond Schinazi International Scientific Exchange Program (SIEP).
• Keywords: MYCOBACTERIUM-TUBERCULOSIS; NEISSERIA-GONORRHOEAE; Science & Technology; PAN-GENOME; POPULATION GENOMICS; RECOMBINATION; STATISTICAL POWER; Life Sciences & Biomedicine; STAPHYLOCOCCUS-AUREUS; SEQUENCE; MACULAR DEGENERATION; CHLAMYDIA-TRACHOMATIS; Genetics & Heredity
• Research Categories: Biology, Genetics; Chemistry, Biochemistry

Abstract

Genome-wide association studies (GWASs) have become an increasingly important approach for eukaryotic geneticists, facilitating the identification of hundreds of genetic polymorphisms that are responsible for inherited diseases. Despite the relative simplicity of bacterial genomes, the application of GWASs to identify polymorphisms responsible for important bacterial phenotypes has only recently been made possible through advances in genome sequencing technologies. Bacterial GWASs are now about to come of age thanks to the availability of massive datasets, and because of the potential to bridge genomics and traditional genetic approaches that is provided by improving validation strategies. A small number of pioneering GWASs in bacteria have been published in the past 2 years, examining from 75 to more than 3,000 strains. The experimental designs have been diverse, taking advantage of different processes in bacteria for generating variation. Analysis of data from bacterial GWASs can, to some extent, be performed using software developed for eukaryotic systems, but there are important differences in genome evolution that must be considered. The greatest experimental advantage of bacterial GWASs is the potential to perform downstream validation of causality and dissection of mechanism. We review the recent advances and remaining challenges in this field and propose strategies to improve the validation of bacterial GWASs.