Association Analysis Flashcards

1
Q

What is genetic association?

A

→ 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

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2
Q

What is a haplotype?

A

→ The order of alleles along a chromosome

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3
Q

What is an allele?

A

→ One form of a variant in the genome

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4
Q

What is a locus?

A

→ a position in the genome

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5
Q

What is a genotype?

A

→ both alleles at a locus

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6
Q

What is a case control study?

A

→ Case group who all have the disease

→ Controls that match the people with the disease for non-disease traits such as ; age, location, ethnicity

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7
Q

What are the requirements for a good case control study?

A

→ Large numbers of well defined cases
→ Equal numbers of matched controls
→ Reliable genotyping technology
→ Standard statistical analysis

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8
Q

What extra step do you need to do when you find a positive association?

A

→ Replicate

→ To prove that it is not by chance

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9
Q

What are characteristics of an ideal genetic marker?

A
→ Polymorphic 
→ Randomly distributed across the genome 
→ Fixed location in the genome 
→ Frequent in genome
→ Frequent in population 
→ Stable with time 
→ Easy to assay (genotype)
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10
Q

How often are SNPs found in the genome?

A

→ 1 in every 300 nucleotides

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11
Q

How many SNPs have been identified in the genome?

A

→ 12 million

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12
Q

How are SNPs formed?

A

→ The repair mechanism inserts a matching nucleotide to the wrong base so it is different from the original pair

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13
Q

What is the effect of SNPs found in the coding region?

A

→ Coding region
→ no amino acid change
→ amino acid change
→ new stop codon

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14
Q

Where can SNPs be found in the non coding region and what is the effect?

A

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

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15
Q

What do the major and minor allele frequency add up to?

A

→ 1

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16
Q

What is a GWAS?

A

→ genome wide association study

→ association between disease and alleles of each marker - chi squared test

17
Q

How is GWAS data represented?

A

→ a single graph called the Manhattan plot

18
Q

What are the axes on a Manhattan plot?

A

→ X axis is the position of the SNP on the chromosome

→ Y axis is the -log10 (P value) of the association - done by chi squared

19
Q

What does a peak on the Manhattan plot signify?

A

→ The peak does not identify the gene causing the disease

→ It identifies the genomic regions associated with disease and is smaller than 100kb

20
Q

Why is the scale -log10 on the manhattan plot?

A

→ The probability of a result being due to chance is very high because there are so many samples

21
Q

What is meta analysis?

A

→ Allows the statistical combination of results from multiple studies

22
Q

What % of body shape is genetically determined?

A

→ 70-80%

23
Q

What is the gene associated with obesity?

A

→ FTO