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Genomics > Genetics of Common Disease > Flashcards

Genetics of Common Disease Flashcards

1
Q

What is mutated in cystic fibrosis?

A

→ F delta 508

→ phenylalanine codon is removed

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2
Q

What is the inheritance pattern like in mendelian disease?

A

→ Recessive loss of function
→ Autosomal dominant

→ X linked

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3
Q

How can you measure intermediate phenotype?

A

→ Electrocardiogram

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4
Q

What is the intermediate phenotype in people with sudden cardiac death?

A

→ Heart rate might be slower than it is supposed to be

→ heart is larger than usual - cardiomyopathy

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5
Q

What is the relationship between conduction and heart size?

A

→ The larger the heart muscle the longer it takes for conduction because the surface area is larger

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6
Q

What does a quivering signal on an ECG look like and why?

A

→ Ventricular fibrillation

→ Heart muscle gets tired and there is no electrical output

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7
Q

What do the P wave and QRS wave mean?

A

→ P wave - going across the atria

→ QRS - going across the ventricle

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8
Q

What is the QT interval associated with?

A

→ Highly associated with risk of sudden cardiac arrest

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9
Q

What does it mean if the QT interval is longer?

A

→ Increased susceptibility of a heart attack

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10
Q

Why are twin studies used?

A

→ twins are genetically identical
→ non identical twins are not genetically identical but the environment is the same

→ this enables you to eliminate the environment as a confounding factor

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11
Q

What percentage is the variation in heart rate due to genetics?

A

→ 58%

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12
Q

What percentage is the variation in QRS down to genetics?

A

→ 54%

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13
Q

What does high heritability imply?

A

→ Strong resemblance

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14
Q

What is concordance?

A

→ How similar a phenotype is

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15
Q

What does it mean if there are big differences between MZ twins and DZ twins?

A

→ Trait is more genetic than environmental

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16
Q

What are SNPs?

A

→ Variations in a single nucleotide

→ DNA sequence variations that occur when a single nucleotide is altered

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17
Q

What is the most common form of variation in the genome?

A

→ SNPs

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18
Q

What is a genotype?

A

→ A pair of alleles at a locus

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19
Q

What is a haplotype?

A

→ Sequence of alleles along a single chromosome

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20
Q

What is a qualitative measure example?

A

→ Disease status

→ Presence or absence of congenital defect

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21
Q

What is a quantitative measure example?

A

→ Blood glucose levels
→ % body fat

→ heart rate

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22
Q

What is the short term goal of genetic association studies?

A

→ Identifying genetic variants that explain differences in phenotype among individuals

23
Q

What is the long term goal of genetic association?

A

→ Inform the process of identifying and delivering better prevention and treatment strategies

24
Q

Why can the SNPs for cardiovascular disease not be in essential parts of the genome?

A

→ They do not manifest from birth

25
Q

What is the relationship between linkage disequilibrium and SNP distance?

A

→ Linkage disequilibrium between two SNPs decreases with physical distance

26
Q

When do you need fewer SNPs to capture variation?

A

→ When LD is strong

27
Q

Why are some variants not recombined?

A

→ The regions are physically together

28
Q

How many SNPs does an SNP chip have?

A

→ 317,000 SNPs

29
Q

Describe how an SNP microarray works

A

→ Run 12 samples
→ Each of the wells has tags for 300,000 variants

→ they are stuck to the base of the chip
→ DNA is run across the chip
→If the DNA has the variant it binds to it
→ fluorescent dye binds

30
Q

What are the axes of the graph for testing genetic association?

A

→ X axis is genotype

→ Y axis is phenotype

31
Q

What do the dots on the manhattan plot represent?

A

→ A variant

32
Q

What do the peaks on the manhattan plot show?

A

→ statistical test has a significant effect

33
Q

Why do you need a lot of people in a GWAS study?

A

→ If the genes are numerous and small in effect

34
Q

What are the 3 possibilities when finding a SNP associated with a disease?

A

→ Causal relationship between SNP and disease
→ Marker is in linkage disequilibrium with a causal locus

→ false positive

35
Q

How is the P value set?

A

→ 0.05/n

→ n is the number of tests

36
Q

What is linkage disequilibrium?

A

→linkage disequilibrium is the non-random association of alleles at different loci in a given population.

37
Q

Define heritability

A

→a measure of how well differences in people’s genes account for differences in their traits.

38
Q

What does a heritability close to one indicate?

A

→that almost all of the variability in a trait comes from genetic differences, with very little contribution from environmental factors.

39
Q

What percentage of shared genetic variation for MZ, DZ, full siblings and half siblings?

A

MZ= 100
DZ=50
Full siblings= 50
Half siblings= 25

40
Q

Equation for heritability(h2)

A

h2 = 2 x (MZ correlation – DZ correlation)

41
Q

What does it mean for h2<0.5?

A

Environmental influences are more important than genetic component

42
Q

What does h2>0.8 suggest?

A

→A trait highly influenced by genes

43
Q

On genetic susceptibility graph, what does the right side suggest?

A

→there are more environmental influences involved

→GWAS

44
Q

What does the left side suggest on a genetic susceptibility graph?

A

Linkage

45
Q

How else can you define linkage disequilibrium?

A

→the difference between the observed frequency of a particular combination of alleles at two loci and the frequency expected for random association.

46
Q

What happens to linkage disequilibrium between two NPS as physical distance increases?

A

→decreases with physical distance as more likely to have a recombination event between them.

47
Q

What other factor affects LD?

A

region of genome i.e. recombination hot spots.

48
Q

What are the advantages of strong LD?

A

→need fewer SNPs to capture variation in a region

→cheaper and easier/quicker to analyse.

49
Q

What is Bonferroni correction?

A

If the number of tests (SNPs genotyped) is n, we set the threshold to be 0.05/n so that we can avoid including false positives in our findings.

50
Q

What are the three possibilities if a SNP is identified as significantly associated with disease?

A

→a causal relationship between SNP and disease
→marker is in linkage disequilibrium with a causal locus
→False positive

51
Q

What is the standard p-value for GWAS?

A

5 × 10−8

52
Q

Dizygotic twins, as with siblings in general, share on average 50% of their genome with each other. However dizygotic twins usually share a little bit more of their genetic variation than other types of siblings – why?

A

they also have the same shared in utero environment

53
Q

How do you measure genetic susceptibility?

A

Measure heritability

54
Q

What are the goals of GWAS?

A

→Identify genetic regions that explain differences in phenotype among individuals in a study population
→To identify genetic variants that can be measured to determine whether an individual is at higher risk of disease​
→To identify potential drug targets to treat the disease

Genomics (21 decks)

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