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 Medjournal_title
Genome medicineauthors
Farhat MR,Shapiro BJ,Sheppard SK,Colijn C,Murray Mdoi
10.1186/s13073-014-0101-7subject
Has Abstractpub_date
2014-11-15 00:00:00pages
101issue
11issn
1756-994Xpii
101journal_volume
6pub_type
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