ArticleCommunications biology2022
PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.
Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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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
15 citing papers in PubMed.
- BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies.BMC microbiology · 2026Article
- Genomic and clinical determinants of extraintestinalmedRxiv : the preprint server for health sciences · 2026Article
- Beyond AMR and virulence databases: genome wide associations of closely relatedFrontiers in microbiology · 2026Article
- External factors influence intrinsic differences in Stx2e production by Porcine Shiga Toxin-producing Escherichia coli strains.PLoS pathogens · 2025Article
- Bacterial genome-wide association studies: exploring the genetic variation underlying bacterial phenotypes.Applied and environmental microbiology · 2025Review
- microGWAS: a computational pipeline to perform large-scale bacterial genome-wide association studies.Microbial genomics · 2025Article
- Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Deciphering vancomycin resistance inFrontiers in microbiology · 2025Article
- Species-wide inventory ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Analysis of clinicalAntimicrobial agents and chemotherapy · 2024Article
- Optimising machine learning prediction of minimum inhibitory concentrations inMicrobial genomics · 2024Article
- Use of whole genome sequencing for surveillance and control of foodborne diseases:Frontiers in microbiology · 2024Review
- Analysis of clinicalbioRxiv : the preprint server for biology · 2023Article
- Using random forest to predict antimicrobial minimum inhibitory concentrations of nontyphoidal Salmonella in Taiwan.Veterinary research · 2023Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Genome-wide association studies (GWAS) are increasingly being applied to investigate the genetic basis of bacterial traits. However, approaches to perform power calculations for bacterial GWAS are limited. Here we implemented two alternative approaches to conduct power calculations using existing collections of bacterial genomes. First, a sub-sampling approach was undertaken to reduce the allele frequency and effect size of a known and detectable genotype-phenotype relationship by modifying phenotype labels. Second, a phenotype-simulation approach was conducted to simulate phenotypes from existing genetic variants. We implemented both approaches into a computational pipeline (PowerBacGWAS) that supports power calculations for burden testing, pan-genome and variant GWAS; and applied it to collections of Enterococcus faecium, Klebsiella pneumoniae and Mycobacterium tuberculosis. We used this pipeline to determine sample sizes required to detect causal variants of different minor allele frequencies (MAF), effect sizes and phenotype heritability, and studied the effect of homoplasy and population diversity on the power to detect causal variants. Our pipeline and user documentation are made available and can be applied to other bacterial populations. PowerBacGWAS can be used to determine sample sizes required to find statistically significant associations, or the associations detectable with a given sample size. We recommend to perform power calculations using existing genomes of the bacterial species and population of study.
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Registered trials
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