Association Analysis

Question 1

What is genetic association?

Answer 1

The presence of a variant allele at a higher frequency in unrelated subjects with a particular disease (cases), compared to those that do not have the disease (controls).

Question 2

What is an allele?

Answer 2

One form of a variant in the genome

Question 3

What is a locus?

Answer 3

A position in the genome

Question 4

What is a genotype?

Answer 4

Both alleles at a locus e.g. locus 1: 1,4 and Locus 2: 1,1

Question 5

What is a haplotype?

Answer 5

This is the order of alleles along a chromosome

Question 6

Why are case-control studies used?

Answer 6

• Cases are subjects with the disease of interest e.g. obesity, schizophrenia, hypertension.
• Defintion of the disease must be applied in a rigorous and consistent way
• Controsl must be as well-matched as possible for non-disease traits such as age, sex, ethnicity, location etc

Question 7

What is case-control association?

Answer 7

Cases: gene variant is associated with disease

versus controls

Question 8

Describe how the case control study works

Answer 8

There are two groups:

• Affected cases
• Unaffected controls

Then measure the genetic loci of interest

Statistical analysis to determine which genetic loci correlate with disease

Identify genomic region associated with disease

Question 9

What is needed in a case-control genetic study?

Answer 9

• Large number of well-defined cases
• Equal numbers of matched controls
• Reliable genotyping technology (SNP array)
• Standard statistical analysis (PLINK)
• Positive associations should be replaced

Question 10

What is the ideal genetic marker?

Answer 10

• Polymorphic
• Randomly distributed across the genome
• Fixed location in genome
• Frequent in genome
• Frequent in population
• Stable with time
• Easy to assay (genotype)

Question 11

What is a SNP?

Answer 11

• Generated by mismatch repair during mitosis
• Common in the genome which is about 1/300 nucleotides
• About 12 million common SNPs identified in human genome

Question 12

How do SNPs arise?

Answer 12

• DNA strands are split and they undergo mitosis.
• One DNA strand replicates
• The other DNA strand replicates but there is a mismatch.
• Usually it would be repaired by the mismatch repair system.
• Rather than the mismatch repair system replacing the mismatch, it replaces the other base on the original strand.
• This because the SNP; T/C SNP.

Question 13

Where are SNPs located?

Answer 13

In the Gene coding region:

• No amino acid change (synonymous)
• Amino acid change (non-synonymous)
• New stop codon (nonsense)

In the Gene non-coding region:

• Promoter - mRNA and protein level changed
• Terminator - mRNA and protein level changed
• Splice site - altered mRNA, altered protein

In the intergenic region

Question 14

What is the dbSNP?

Answer 14

It is an online database at NCBI of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants.

Question 15

What is the minor allele?

Answer 15

It is the less common alllele. Each allele has a frequency in the general population and the minor allele has a MAF.

Question 16

What does the Minor AF + Major AF add up to?

Answer 16

1

Question 17

What is a genome wide association study (GWAS)?

Answer 17

Use markers across the whole genome

Question 18

What do SNP microarrays do?

Answer 18

• Look for association between disease and each marker - chi-squared test
• This has resulted in the detection of large numbers of disease-associated genes

Question 19

How is GWAS data presented?

Answer 19

It is presented as a single graph called a Manhattan plot.

Question 20

What is the X-axis and Y-axis in a Manhattan plot?

Answer 20

• X-axis is position of the SNP on the chromosome

- Y-axis is -log10 (p-value) on the chromosome

Question 21

What is a Manhattan plot?

Answer 21

A simple way to visualise the markers across the genome associated with the disease.

Question 22

What is the WTCCC?

Answer 22

It is the Wellcome Trust Case Control Consortium

• Contains 1958 Birth Cohort and the UK blood service as the controls.
• Looks at cases of CAD, Type 1 and 2 diabetes, hypertension, rheumatoid arthritis, Crohn’s disease and bipolar disorder

Question 23

What do the peaks indicate in manhatten plots?

Answer 23

Significant p-values of p <5x10-5

Question 24

What are some misconceptions of the peaks in GWAS results?

Answer 24

• The peak does not identify the gene causing the disease

- The peak identifies the genomic region associated with the disease

Question 25

What is another graph that can be used to show GWAS results?

Answer 25

Regional Association plot

Question 26

Advantages and Disadvantages of meta-analysis

Answer 26

• Difficult to do very large studies (>10K cases)
• Easier to combine smaller studies
• Pre-experiment - consortium
• Post-experiment - meta-analysis
• Meta-analysis allows the statistical combination of results from multiple studies

Question 27

What are the medical complications of obesity?

Answer 27

• Pulmonary disease
• Idiopathic intracranial hypertension
• Stroke
• Cataracts
• Coronary heart disease
• Severe pancreatitis
• Diabetes
• Cancer
• Phlebitis
• Gout
• Osteoarthritits
• Gynecologic abnormaltiies
• Gall bladder disease
• Nonalcoholic fatty liver disease

Question 28

What studies are used to investigate the genetic components of common obestiy?

Answer 28

• Twin studies
• Adoption studies
• Family Studies

Question 29

What did an obestiy GWAS show?

Answer 29

There were genes associated with waist size, extremes, fat mass and BMI and they all overlapped.

Question 30

What is the problem with GWAS?

Answer 30

• It has identified associations that are statistically strong and reproducible but their contribution to the genetic component of disease is estimated to be low (less than 5%)
• For example disease may infact be caused by other things usch as:
  
  • Common SNPs of small effect
  • Rare SNPs
  • Copy Number Variation
  • Epigenetic variation
  • Heritability is overestimated