ArticleGenome medicine2014
A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens.
Article in Genome medicine, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 35 citations in OpenAlex.
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- Population genomics of Streptococcus mitis in UK and Ireland bloodstream infection and infective endocarditis cases.Nature communications · 2024Article
- Prophage-encoded immune evasion factors are critical forCell genomics · 2022Article
- Mutations in theMicrobial genomics · 2021Article
- Bacterial evolution during human infection: Adapt and live or adapt and die.PLoS pathogens · 2021Review
- Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics.The Plant cell · 2021Article
- Sample size calculation for phylogenetic case linkage.PLoS computational biology · 2021Article
- Exact mapping of Illumina blind spots in theMicrobial genomics · 2021Article
- In-host population dynamics ofeLife · 2021Article
- Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance inFrontiers in microbiology · 2021Article
- Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes.Microbial genomics · 2020Article
- Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges.Genome medicine · 2019Review
- Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni.Microbial genomics · 2019Article
- Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis.BMC genomics · 2018Article
- A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination.PLoS computational biology · 2018Article
- Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes.American journal of respiratory and critical care medicine · 2017Article
- The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens.Frontiers in microbiology · 2017Review
- Identifying lineage effects when controlling for population structure improves power in bacterial association studies.Nature microbiology · 2016Article
- Microbial Speciation.Cold Spring Harbor perspectives in biology · 2015Review
Corrections and comments
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Authors and funding
5 authors at 5 institutions in 3 countries.
Funding
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.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.