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genetics > Complex Traits > Flashcards

Complex Traits Flashcards

1
Q

What are complex traits?

A

Coupling genetic factors along with environmental influences

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2
Q

What do association studies include?

A

transmission disequilibrium testing
case-control association studies

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3
Q

Characteristics of complex diseases

A

incomplete penetrance
phenocopies
high frequency of disease-causing allele

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4
Q

Relative risk calculation

A

λ= frequency in relative of affected person/ population frequency

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5
Q

What does a higher λ mean?

A

The higher the contribution of the genetic component in determining the disease risk

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6
Q

What does an λ of 15 mean?

A

If you have a sibling that is affected, your risk of being affected is 15x higher

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7
Q

What happens when there is a genetic component involved in disease manifestation?

A

The liability distribution among siblings of affected individuals shift to the right, signifying an elevated risk for them to develop the disease

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8
Q

Affected sib-pairs method

A

If the marker locus is linked to trait locus, an excess of shared alleles among affected sib-pairs will be expected

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9
Q

State what affected sib-pair might share and the probabilities

A

may share 0,1,2 alleles identical by descent with probabilities 0.25, 0.5, 0.25 respectively

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10
Q

What happens if we perform this test for many markers in the genome?

A

We can identify those that present a distortion in the expected ratio. If the distortion favours the 1 and 2 shared alleles while lowering the % of 0 shared alleles then there might be a linkage between the marker and risk factor

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11
Q

Advantages of affected sib-pairs method

A
  1. non parametric analysis eliminates the need for specifying allele frequencies or inheritance patterns
  2. provides a precise location of the disease gene
  3. initial insight into the localisation of risk factors on the chromosome
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12
Q

Disadvantages of affected sib-pairs method

A
  • limited power compared to parametric methods
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13
Q

Linkage disequilibrium

A

The non-random association in a population of alleles at closely linked loci: tendency of alleles that are close on the same chromosome to be co-inherited throughout generations

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14
Q

Why do markers near a risk factor tend to be inherited together?

A

Because the same chromosome block is maintained across generations due to limited recombination in chromosomal regions

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15
Q

Where does recombination frequency take place?

A

At specific positions

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16
Q

How is the genome organised?

A

In specific haplotype blocks conserved throughout generations

17
Q

What do the red squares show in a linkage disequilibrium map of a chromosome?

A

1:1 relationship in terms of linkage disequilibrium

The redder the squares the higher the LOD score

18
Q

What does maximum linkage disequilibrium mean?

A

2 loci are always segregating

19
Q

What does it mean when we see a triangle in a linkage disequilibrium map of a chromosome?

A

All the loci that are underneath are in linkage disequilibrium

20
Q

What does the transition from one triangle to the next in a linkage disequilibrium map of a chromosome mean?

A

A hotspot for crossing over event

21
Q

How many SNPs are required for genome wide association studies?

A

500,000 non-African SNPs
1,000,000 African SNPs

22
Q

Why are more African SNPs required?

A

The African genome is heterogenous: it is more ancient and therefore there was more time to create new recombinations and new haplotype blocks

23
Q

What is the difference between linkage and association?

A

Association is a relation between alleles while linkage is a relation between loci.

24
Q

What is case-control study?

A

2 populations: one is the case, individuals affected by a specific disease and the other one is control, healthy individuals

25
Q

Odds ration

A

ad/bc= OR

26
Q

What are the best samples for linkage disequilibrium mapping?

A

Genetically isolated populations
younger populations

27
Q

What does a positive associate imply?

A

A direct causal effect
Linkage disequilibrium
Population stratifaction

28
Q

Describe the importance of the ApoL1 gene

A

Mutations in this gene causes African Americans to be more susceptible to kidney disease [characterised by the presence of G1 and G2 haplotypes]. However, ApoL1 has been positively selected as it gives resistance to a trypanosoma infection.

29
Q

Furosemide

A

A sodium transport blocker to reduce the transport of sodium due to uromodulin mutation

30
Q

Why did Homo sapiens have a selection of keeping the risk variant of uromodulin?

A

The pressure that has kept this SNP variant associated with high expression level in nowadays population is selection against UTIs

31
Q

What is used to calculate the polygenic risk score PRS?

A

Different genome-wide association studies

32
Q

What is polygenic risk score?

A

If we have a number of loci, each of them with a risk allele, they can be combined using genome-wide polygenic risk scores

33
Q

What happens if the polygenic risk score is clinically relevant?

A

We have a tool that associates a genetic risk for a specific disease that can be calculated for each individual

34
Q

Transmission Disequilibrium Test study

A

to examine the transmission of a particular allele at a locus from heterozygous parents to their affected offspring: depends on alleles being transmitted in trios

35
Q

What should we see if a marker is not close to a risk factor?

A

We should see that the transmission to the affected individual should be the same for the alleles of both parents

36
Q

What is the aim of the Transmission Disequilibrium Test study?

A

To find the frequency of the transmitted allele relative to the non-transmitted allele

37
Q

What does it mean if the numbers are comparable to each other in a Transmission Disequilibrium Test study?

A

It is probably not a risk factor

38
Q

What does it mean if the numbers are skewing to each other in a Transmission Disequilibrium Test study?

A

The allele more frequently transmitted is a risk factor

genetics (29 decks)

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