L18 - GWAS and Bacterial Research Flashcards
What does GWAS stand for?
Genome-Wide Association Studies
What is the purpose of GWAS?
To analyze genetic variants across individuals to find correlations between genotype and phenotype.
What type of traits does GWAS identify?
Traits like disease susceptibility virulence
What are the key components of GWAS?
Genotype phenotype
How is GWAS data typically presented?
As a Manhattan plot.
What is shown on the x-axis of a Manhattan plot?
Genomic location.
What is shown on the y-axis of a Manhattan plot?
Significance (-log10 P-value) of genetic associations.
What human disease was linked to a mutation in complement factor H via GWAS?
Age-related macular degeneration.
What is required for an effective bacterial GWAS?
Large datasets of sequenced bacterial genomes and clear phenotypic data.
Why is phylogenetic analysis important in bacterial GWAS?
It assesses population structure and genetic variation.
What challenge does bacterial asexual reproduction pose for GWAS?
It leads to linkage disequilibrium making causal mutations harder to identify.
What is homoplasy in bacterial GWAS?
When mutations arise independently in different lineages.
How do mixed models help in bacterial GWAS?
They control for population structure improving accuracy in genetic associations.
What gene mutation in Staphylococcus aureus was linked to vancomycin resistance?
The orpB gene mutation.
How was the role of orpB in resistance validated?
Using transposon mutant libraries.
What pathogen was studied using GWAS to track antibiotic resistance mutations?
Mycobacterium tuberculosis.
What phenotypes were examined in Staphylococcus aureus GWAS?
Virulence determinants and infection severity.
How can bacterial GWAS predict patient outcomes?
By correlating genetic factors with clinical parameters.
Why is antimicrobial resistance (AMR) a major focus of bacterial GWAS?
It helps identify genetic markers linked to antibiotic resistance.
What major limitation affects bacterial GWAS?
High linkage disequilibrium in bacterial populations.
How does whole genome sequencing contribute to GWAS?
It provides comprehensive genetic data for analysis.
What statistical model is often used to account for population structure in GWAS?
Linear mixed models.
What is the role of SNPs in GWAS?
They are single nucleotide polymorphisms linked to phenotypic traits.
What are insertions and deletions in the context of GWAS?
Genetic variations that may affect bacterial traits.
How can GWAS aid in vaccine development?
By identifying genetic factors influencing bacterial pathogenicity.
Why is GWAS useful in tracking bacterial outbreaks?
It helps trace genetic changes and transmission patterns.
How does bacterial GWAS differ from human GWAS?
Bacterial GWAS deals with clonal reproduction and horizontal gene transfer.
What computational tool is used to analyze GWAS data?
Bioinformatics software for statistical genetic analysis.
How does GWAS help understand bacterial adaptation?
By identifying genetic mutations linked to survival in host environments.
What is a key advantage of GWAS over traditional genetic studies?
It examines the entire genome without prior assumptions about gene importance.
How can GWAS findings improve antibiotic stewardship?
By guiding targeted treatments based on resistance markers.
What does a high p-value in GWAS indicate?
Weak evidence of genetic association with the phenotype.
What does a low p-value in GWAS suggest?
Strong evidence of a genetic association with the phenotype.
How can GWAS impact public health?
By informing policies on bacterial resistance and infection control.
What is an epistatic interaction in GWAS?
When multiple genes interact to influence a trait.
What is the significance threshold in a Manhattan plot?
A p-value cutoff used to determine statistically significant associations.
What is horizontal gene transfer?
The movement of genetic material between bacteria affecting GWAS results.
Why do bacterial populations show high genetic diversity?
Due to mutations recombination
What is the role of reference genomes in GWAS?
They provide a baseline for identifying genetic variations.
How do environmental factors influence GWAS results?
They can affect bacterial gene expression and phenotypic traits.
What bioinformatics approach helps visualize GWAS results?
Manhattan plots and QQ plots.
How does GWAS contribute to precision medicine?
By linking genetic markers to disease susceptibility and treatment response.
What is a false positive in GWAS?
A genetic association that appears significant due to random variation.
How do researchers confirm GWAS findings?
Through replication studies and functional validation.
What is the relationship between GWAS and bacterial virulence?
GWAS identifies genes linked to bacterial pathogenicity.
What does a strong genetic association mean in GWAS?
A high likelihood that a variant influences the trait.
Why is sample size important in GWAS?
Larger datasets increase the reliability of genetic associations.
What are genome-wide significance thresholds?
Stringent p-value cutoffs to minimize false positives.
What is the ultimate goal of bacterial GWAS?
To understand bacterial genetics and improve treatment strategies.
How can GWAS improve diagnostic tools for infections?
By identifying genetic markers associated with antibiotic resistance and virulence.
What is the main goal of GWAS in bacterial research?
To identify genetic variations linked to bacterial traits such as pathogenicity and antimicrobial resistance.
What type of genetic variations does GWAS analyze?
Single nucleotide polymorphisms (SNPs), insertions, and deletions.
How does GWAS contribute to understanding antimicrobial resistance?
By identifying genetic mutations responsible for antibiotic resistance in bacterial populations.
What data sources are commonly used in bacterial GWAS?
Whole genome sequencing and DNA microarray analysis.
Why is population structure important in bacterial GWAS?
It helps distinguish true genetic associations from confounding effects due to relatedness.
How does linkage disequilibrium affect bacterial GWAS?
It makes it difficult to pinpoint causal mutations due to genetic variants being inherited together.
What statistical approach is often used to control for population structure in bacterial GWAS?
Linear mixed models.
What is the significance of a Manhattan plot in GWAS?
It visually represents genetic associations across the genome, highlighting significant loci.
Why is homoplasy a challenge in bacterial GWAS?
Mutations may appear independently in unrelated strains, complicating association studies.
How can GWAS findings in bacteria aid clinical treatment?
By informing targeted antibiotic therapies and resistance prediction.
What role does phylogenetics play in bacterial GWAS?
It helps understand evolutionary relationships and control for shared ancestry among bacterial strains.
How was vancomycin resistance identified in Staphylococcus aureus using GWAS?
By detecting a mutation in the orpB gene linked to resistance.
What experimental approach validated GWAS findings in bacterial research?
Transposon mutant libraries.
How has GWAS been used to study Mycobacterium tuberculosis?
By identifying genetic mutations linked to antibiotic resistance.
How does GWAS help in tracking bacterial virulence?
It identifies genetic factors contributing to toxicity, biofilm formation, and infection severity.
How can GWAS assist in predicting patient outcomes in infections?
By linking bacterial genetic markers to disease severity and treatment response.
What makes bacterial GWAS different from human GWAS?
Bacteria reproduce clonally and undergo horizontal gene transfer, affecting genetic linkage patterns.
Why is a large dataset necessary for bacterial GWAS?
To ensure statistical power and reduce false-positive associations.
What does a strong peak in a Manhattan plot indicate?
A significant genetic association with the studied trait.
What type of mutations were identified in Staphylococcus aureus that influence virulence?
Mutations affecting toxicity and biofilm formation.
What is one application of bacterial GWAS in public health?
Monitoring the emergence and spread of antibiotic-resistant strains.
How can GWAS findings support vaccine development?
By identifying conserved genetic targets involved in bacterial pathogenesis.
What challenge does horizontal gene transfer pose for bacterial GWAS?
It can introduce foreign DNA, making it harder to distinguish inherited mutations from acquired genes.
How does GWAS contribute to precision medicine in infectious diseases?
By tailoring treatment based on bacterial genetic markers linked to resistance and virulence.
