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

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.

journal_name

Genome Med

journal_title

Genome medicine

authors

Farhat MR,Shapiro BJ,Sheppard SK,Colijn C,Murray M

doi

10.1186/s13073-014-0101-7

subject

Has Abstract

pub_date

2014-11-15 00:00:00

pages

101

issue

11

issn

1756-994X

pii

101

journal_volume

6

pub_type

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