GWAS

Question 1

Define Genetic Epidemiology

Answer 1

Study of the role of genetic factors regulating physiological traits (e.g. LFT) and modifying disease risk

Either alone or through interaction with environmental factors

Question 2

What 4 study designs are used in genetic epidemiology? Indicate which uses DNA and which does not.

Answer 2

No DNA

• Familial Aggregation
• Seggregation Analysis

DNA

• Linkage
• Association

Question 3

Explain what familial aggregation investigates

Answer 3

Looks at whether there is a genetic component to a study

• Are relatives of diseased indiviuals more likely to be diseased than the general population?*
• Is the clustering of disease in families different from what you’d expect based on the prevelance in the general population?*

Question 4

Explain what Seggregation analysis investigates

Answer 4

Looks at the mode of inheritence of the trait

Dominant, recessive, additive, X-linked

Question 5

Explain what Linkage studies investigates

Answer 5

Identifies the chromosomal region where the causal gene is located

Question 6

Explain what Association studies investigates

Answer 6

Identifies which genetic variant of which gene is asociated with the trait

Question 7

What is the difference between a variant and a mutation

Answer 7

Varient is a ‘common’ change in the DNA

Mutations are rare variations (<1%)

Question 8

Which mutation or varitation occurs frequently and is commonly studied and explain what it means

Answer 8

Single Nucleotide Polymorphism (SNP)

Single base-pair change

Question 9

With regards to Gene Association Studies, what are the two main approaches to study design?

Answer 9

• Hypothesis-driven
  
  • Candidate-gene Association Studies
• Hypothesis-free
  
  • Genome-wide Assosication Studies (GWAS)

Question 10

Explain the features of a hypothesis-driven approach.

Answer 10

• Investigation of a known variant in genes and whether is is related to a trait
• Priori hypothesis
• Gene variant chosen based on
  
  • Biological knowledge (in vitro or animal models)
  • Previous knowledge of association

Question 11

What is a limitation of a candidate-gene association study (hypothesis-driven)

Answer 11

Can only investigate the chosen gene variant

Question 12

Explain the features of a hypothesis-free approach.

Answer 12

• Investigates genetic variation across the whole genome
• No priori hypothesis

Question 13

What is a benefit of conducting a GWAS (hypothesis-free)

Answer 13

• Can identify gene variatns that are no suspected to be associated with trait
  
  • New genes could be associated to trait
• More power to detect genetic associations

Question 14

Whats are the limitations for GWAS (hypothesis-free)

Answer 14

• Requires multiple testing (hypothesis testing in the same data set)
  
  • Needs huge sample size to reach low significance levels
• Can only detect common variatns that has small effects
  
  • Natural selection selects to decrease disadvantageous alleles
• Only investigates SNP variants
  
  • CNV: Copy number variation
• SNP assessed are tags and not causal
  
  • Variants near each other are often inherited together
  • SNP acts a a surrogate for the causal gene variant using correlation knowdlege between SNP and causal variant
  • Loss of power if this correlation is not strong
• Difficult to evaluate gene-environment interactions

Question 15

What can be done to increase the power to identify new genes in GWA studies (3)

Answer 15

• Increase coverage of genotyping
  
  • Next Generation Sequencing
  • No jumps from SNP to another
  • Too expensive for large smaple size
• Improve phenotyipng and increase its specificty
  
  • Asthma phenotypes
• Incorporate prior knowledge about SNPs and genes

Question 16

What is the significance of multiple testing, it’s implication and how can it be corrected?

Answer 16

Significance

• Normal p-value of significance (5%) has a 1 in 20 chance of false positives
• Therefore, need a lower p-value to reduce false positives

Implication

• To reach significance on low p-value, you need a huge sample size (↑↑n)

Correction

• Bonferroni Correction
  
  • Divide p-value by numver of tests you perform
• Significance threshold set at n=1,000,000 (i.e. p < 5 x10^-8)
  
  • Found no difference over 1,000,000
• Also addtressed through meta-analysis (international consortia)

Question 17

How have GWAS improved knowledge on chronic disease

Answer 17

• Identification of new biological pathways to disease
  
  • ORMDL3 - childhood asthma - Moffat et al Nature 2007
  • ATGI61 - Crohn’s Disease - Rioux et al
• Discovery of links between diseases thought of as unrelated
  
  • ORMDL3 - childhood asthma and Crohn’s disease

Question 18

Describe a study that found a new gene variant associated with Severe childhood asthma, by looking at a specific phenotype in the GWAS

Answer 18

Bonnelykke et al Nat Genet 2014

Identified CDHR3 as an asscoiated gene variant

Only possible because they looked through a specific asthma phenotype

Question 19

Define penetrance in the context of GWAS

Answer 19

Proportion of subjects with variant who have the disease

Question 20

With regards to penetrance and allele frequency, describe:

1. Mendelian disease
2. Hard to identify genetically
3. Highly unusal for common disease
4. Variants identified by GWAS
5. Intermediate

Answer 20

1. Mendelian disease
   
   1. ↑Penetrance
   2. ↓Frequency
2. Hard to identify genetically
   
   1. ↓Penetrance
   2. ↓Frequency
3. Highly unusal for common disease
   
   1. ↑Penetrance
   2. ↑Frequency
4. Variants identified by GWAS
   
   1. ↓Penetrance
   2. ↑Frequency
5. Intermediate
   
   1. ↔Penetrance
   2. ↔Frequency

Question 21

What is the main difference with classical and genetic epidemiology

Answer 21

Classical = observatrional

Genetic = Genetic association

Question 22

What is the main limitation of classical epiddemiology

Answer 22

Difficult to establish causality due to:

• Confounding
• Reverse Causation
  
  • Presence of diseaseoutcome that modified the exposrues not vv

Question 23

What is the (only) source of confounding in Genetic epidemiology studies

Answer 23

Population stratification

Selecting for specific subjects