SGA Tools

Question 1

Describe

The genotype to phenotype challenge

Answer 1

Genotype: the actual alleles present in an individual
Phenotype: observable characteristics of an individual
That translation is complicated due to genetic buffering

Question 2

Why use yeast as a genetic model organism?

Answer 2

• Conserved eukaryotic biology and gene function
• Non-pathogenic
• Rapid growth rate
• Amenable to genetic manipulation due to efficient transformation and homologous recombination

Question 3

Describe

Essential gene function of yeast

Answer 3

• Budding yeast contains 5.8k genes
• 20% genes essential for viability

Question 4

Describe

Synthetic viability

Answer 4

• If two genes act in parallel pathways and either one is disrupted, there is no effect on viability because the second gene buffers its loss

2 disruptions would be lethal

Question 5

Define

Genetic interaction

Answer 5

Unexpected outcome resulting from a combination of individual mutations

= Observed - Expected double mutant fitness

Question 6

Describe

Systematic chemical-genetic profiling

Answer 6

• Identifying the molecular targets of the drug, testing it in various genetic backgrounds
• Compare the drug effects to effects of genetic perturbation to infer the drug’s mechanism of action and potential targets.

Question 7

Describe

Complex genetic interactions

Answer 7

Phenotypes in metazoans and simple eukaryotes influenced by complex genetic interactions involving larger sets of genes

Question 8

Describe

Scoring genetic interactions

Answer 8

1. Grow an ordered array of strains on agar plates as individual colonies
2. Score the colonies’ size changes in response to perturbation

Statistical analyses and further processing required because of positional effects on colonies

Question 9

How is SGA Tools useful in scoring genetic interactions?

Answer 9

• Outlines a series of steps that allows the quantifying of colony sizes, correction of systematic biases and calculation of a fitness score
• Can also view distribution of scores, highlight genes w strongest signal and perform GO enrichment analysis

Question 10

Describe

The SGA analysis pipeline

Answer 10

1. Ordered array of colonies imaged
2. Colonies segmented to produce raw size measurements
3. Raw measurements normalized to correct systematic biases
4. Genetic interactions scored using multiplicative model

Scores can further be visualized and selected genes tested for enrichment in GO terms

Question 11

Describe

The correction of systematic biases

Answer 11

• Differences in growth conditions like duration of incubation
• Differences in nutrient availability, such as location of colony on plate, uneven preparation surfaces and neighboring mutant strain fitness