GWAS in prokaryotes

Question 1

GWAS

- define

Answer 1

association analysis performed w/ panel of polymorphic markers adequately spaced to capture most of linkage disequilibrium info in entire genome

Question 2

Study designs

Answer 2

Family based
OR
Case control

Question 3

Linkage disequilibrium

Answer 3

Genes close together in genome
- closer they are = higher the linkage
= more likely to be inherited together

Question 4

Study design

• cases
• controls

Answer 4

> those with the phenotype of interest e.g. disease
presumed to have high prevalence of susceptibility alleles

> those w/out phenotype
presumed to have lower prevalence of such susceptibility alleles

case + controls ideally similar in majority of other factors

Question 5

Misclassification bias

Answer 5

study participant categorised into incorrect category

-> alters the observed association or research outcome

Question 6

what can identification of susceptibility variants lead to?

Answer 6

*novel biological insights
-> clinical advances
-> therapeutic targets
OR
biomarkers
OR prevention

*improved measure of individual aetiological processes
-> personalised medicine
–> diagnostics
OR
prognostics
OR
therapeutic optimisation

Question 7

Genotyping

- what is it?

Answer 7

Looking for a nt variation associated w/ a given phenotype

e.g. GC change associated with a disease
AT means you don’t have disease

Question 8

Genotyping

- process

Answer 8

1. Extract, amplify + fragment DNA
2. Either:
   Microarray
   OR
   Sequencer
3. Genotype calling
4. SNP genotype

Question 9

Genotype calling

Answer 9

Determining genotype for each individual

- typically only done for positions in which a SNP or a ‘variant’ has already been called (=estimated)

Question 10

Significance of hits

- Contigency tables (Fisher’s Exact Test)

Answer 10

Gives a p values for the significance of the SNP being associated w/ disease

Sum all probabilities for observed + all more extreme values with same marginal totals to compute probability of null hypothesis

Question 11

Does the affected or control group exhibit Population Stratification?

• what is this?
• what can it cause?
• how is this controlled?

Answer 11

When subpopulations exhibit allelic variation because of ancestry

Can cause false +ves if there are SNP differences in the case + control population structures

Control for this by testing control SNPs for general elevation in X^2 distribution between cases + controls

Question 12

Associated haploblocks

Answer 12

Linkage disequilibrium organises genome into haplotype blocks

Question 13

Haplotype block

Answer 13

region of genome where there’s little evidence of a history of genetic recombination

contain only a small number of distinct haplotypes (group of alleles inherited together from 1 parent)

Question 14

Bottom-up approach

Answer 14

Starts w/ DNA sequence

-> tests effect on phenotype

Question 15

Top-down approach

Answer 15

Starts w/ phenotype + associates it w/ particular genomic elements

(by 2010 had large bacterial collections)

Question 16

Campylobacter

- causes

Answer 16

most common cause of bacterial food poisoning in developing countries

meat gets contaminated

• > people eat meat
• > get ill

Question 17

Campylobacter

- who carries it?

Answer 17

humans don’t
- get ill and then bacteria goes away

chickens, sheep, cows + birds carry the bacteria

Question 18

Old signals vs New signals of adaptation

Answer 18

Old
= host-associated clonal complexes

New
= host-associated mobile elements

Question 19

GWAS study method

Answer 19

1. sample lots of isolates from cows + chickens
2. sequence genomes
3. divide into 30bp fragments
   ( have 1 for every position in genome)
4. sort by cow or chicken origin by:
   looking for fragments overrepresented in 1 org

Question 20

Difference in overrepresentation of a gene fragment in 1 species

• compare to…?
• shows…?

Answer 20

compare observed vs expected by descent

which bit of DNA might be adaptive

Question 21

ST-45 complex

- how many host-associated words?

Answer 21

9034

Question 22

Vitamin B5 synthesis gene

Answer 22

Present in cow campylobacter

NOT in chicken campylobacter

B5 found in grain not grass
Cows eat grass
-> need to synthesise own B5

Question 23

Campylobacter survival through the food chain

Answer 23

ST-45 most prevalent in chicken carcass or meat

ST-21 increasing prevalence from farm -> meat -> clinical

ST-45 meat + ST-21 clinical have same prevalence of 8%

Question 24

Campylobacter survival through the food chain

- deletion mutants have altered functions

Answer 24

nuoK
(associated in ST-21)
- involved in NADH activity
+ switching from anaerobic to O2 enviro

mutants grow better in enhanced O2

Question 25

Staphylococcus epidermidis

Answer 25

Coagulase-negative staphylococci
= commensal on human skin

major cause of nosocomial infection associated with surgery

Question 26

Evolutionary models of infection

Answer 26

Pathogenic clones
- only pathogenic sub-population can cause disease

True opportunistic pathogenicity
- all strains can cause disease if they get into blood
(same virulence elements in both strains)

Divided genome
- any clone can cause disease (pathogenicity elements can move between strains)

Question 27

Evolutionary models of infection

- associated variation in genomic data

Answer 27

Pathogenic clones
- all clones related

True opportunistic pathogenicity
+ divided genome
- identical evolutionary tree

Question 28

GWAS method 1 = matching isolate pairs

- findings

Answer 28

61 genes
containing infection-associated genetic elements that correlate with in vitro variation in known pathogenicity traits
e.g. biofilm formation

Question 29

pan genome

Answer 29

set of all strains of a species

Question 30

GWAS method 2 = correlating with in vitro phenotype

- what is it?

Answer 30

Infection associated SNP prevalence correlated w/ pathogenicity phenotypes