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

Farhat, Maha R; Shapiro, B Jesse; Sheppard, Samuel K; Colijn, Caroline; Murray, Megan

doi:10.1186/s13073-014-0101-7

Table 2 Literature search results

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

Author	Reference	Year	Strains sequenced (n)	Stated study purpose^a	Clinical strains?	Time series?	Method	Report specific genotypic association?
Zhang et al.	[26]	2013	161	Identify drug resistance genes	Yes	No	Phylogenetics and comparison of rates with poisson distribution	Yes; list of genes provided
Farhat et al.	[15]	2013	124	Identify drug resistance genes	Yes	No	Phylogenetics and convergence analysis	Yes; list of genes provided
Lin et al.	[27]	2013	2	Identify drug resistance genes	Yes	No	Comparison with reference mycobacterial strains	No
Wu et al.	[28]	2013	4	Identify Beijing associated pathways	Yes	No	COG enrichment of genes with snps	General pathways rather than individual genes
Das et al.	[29]	2013	5	Identify genes related to extrapulmonary TB	Yes	No	COG enrichment of genes with snps	General pathways rather than individual genes
Ilina et al.	[30]	2013	4	Identify drug resistance genes	Yes	No	Comparison with reference mycobacterial strains	No
Abrahams et al.	[31]	2013	-	Identify resistance targets(s) for novel imidazole	No	Yes: spontaneous mutants resistant to drug and their sensitive ancestor	Identification of all mutations	Yes qcrb
Supply et al.	[32]	2013	5	Identify genes associated with smooth TB phenotype	Yes	No	Comparison with reference mycobacterial strains	General pathways rather than individual genes
Hartkoorn et al.	[33]	2012	-	Identify resistance targets(s) for pyridomycin	No	Yes: spontaneous mutants resistant to drug and their sensitive ancestor	Identification of all mutations	Yes acyl-carrier-protein inha
G. Sun et al.	[34]	2012	7	Identify drug resistance genes	Yes	Yes: serial samples from same patient	Identification of all mutations	No; but list of potential candidates with new fixed mutations provided
Grzegorzewicz et al.	[35]	2012	-	Identify resistance targets(s) for novel compound Adamantyl Urea	Yes	Yes: serial samples from the same patient	Identification of all mutations	Yes mmpl3
Casali et al.	[36]	2012	59	Identify drug resistance genes	Yes	No	Phylogenetic tree and parallel evolution and convergence	Yes rpoc
Tahlan et al.	[37]	2012	-	Identify resistance targets(s) for novel compound SQ109	No	Yes: spontaneous mutants resistant to drug and their sensitive ancestor	Identification of all mutations	Yes mmpl3
La Rosa et al.	[38]	2012	-	Identify resistance target(s) for 1,5-diarylpyrrole derivative BM212	No	Yes: spontaneous mutants resistant to drug and their sensitive ancestor	Identification of all mutations	Yes mmpl3
Comas et al.	[39]	2011	10	Identify drug resistance genes	Yes	Yes: serial samples from the same patient	Identification of all mutations in rpoc. Assessment of convergence across different strain pairs	Yes confirmed rpoc
Manjunatha et al.	[40]	2006	-	Identify resistance targets(s) for PA-824	No	Yes: spontaneous mutants resistant to drug and their sensitive ancestor	Identification of all mutations	Yes Rv3547

^aThe term `phenotype related genes is used loosely here to describe genes that are associated with but not necessarily causative of the phenotype.

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ISSN: 1756-994X

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