A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens

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A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens

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Title: A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Author: Farhat, Maha R; Shapiro, B Jesse; Sheppard, Samuel K; Colijn, Caroline; Murray, Megan

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Citation: Farhat, Maha R, B Jesse Shapiro, Samuel K Sheppard, Caroline Colijn, and Megan Murray. 2014. “A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.” Genome Medicine 6 (11): 101. doi:10.1186/s13073-014-0101-7. http://dx.doi.org/10.1186/s13073-014-0101-7.
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Abstract: Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little has been published on how and how many pathogen strains should be selected for studies associating phenotype and genotype. There are specific challenges when identifying genetic associations in bacteria which often comprise highly structured populations. Here we consider general methodological questions related to sampling and analysis focusing on clonal to moderately recombining pathogens. We propose that a matched sampling scheme constitutes an efficient study design, and provide a power calculator based on phylogenetic convergence. We demonstrate this approach by applying it to genomic datasets for two microbial pathogens: Mycobacterium tuberculosis and Campylobacter species. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0101-7) contains supplementary material, which is available to authorized users.
Published Version: doi:10.1186/s13073-014-0101-7
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256898/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:13581042
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