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W9LECT - Complex inheritance Population genetics Flashcards

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1
Q

What is The role of genes and environmental factors in the development of diseases?

A
  • a polygenic trait reflects the activities of more than one gene.
  • Both single-gene and polygenic traits can also be multifactorial, which means they are influenced by the environment
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2
Q

What are the differences between early onset and late onset Alzheimer’s disease?

A
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3
Q

Frequency of diseases with genetic background
-> Identify

A
  1. Polygenic
  2. Oligogenic
  3. Monogenic
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4
Q

Which are the most frequent diseases?

A
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5
Q

What are the 2 types of Multifactorial diseases?

A
  1. Congenital malformations
  2. Chronic adult diseases:
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6
Q

What are the examples of Congenital malformations?

A

dislocation of hip, neural tube defects, cleft lip and/or palate, microcephaly

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7
Q

What are the examples of Chronic adult disease?

A

Cancer, Diabetes type II, Hypertension, asthma, atherosclerosis (coronary), rheumatoid arthritis, multiple sclerosis, epilepsy, schizophrenia, Parkinson disease, manic depression

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8
Q

Can traits be continuous?

A

YES! TRAITS can be CONTINUOUS
= quantitative trait
= varies along a continuum

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9
Q

What are the 5 predictions of the multifactorial threshold model?

A
  1. Recurrence risks represent average risks and will vary among different families.
  2. The risk increases with the number of affected relatives.
  3. The risk increases with the severity of the malformation or disease.
  4. The differential risk to relatives of an affected proband increases as the frequency of the disease or malformation in the general population decreases.
  5. When the sex ratio of affected probands deviates
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10
Q

I. Methods to determine Complex inheritance
1. What are the method to determine Complex inheritance?

A
  1. Family study
  2. Family-based association studies
  3. Accumulation within a family
  4. Concordance and disconcordance
  5. Twin studies
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11
Q

I. Methods to determine Complex inheritance
2. How do we use family study to determine complex inheritance?

A
  1. Provides estimates of the degree of family aggregation
  2. Risks to siblings, parents, offspring as well as to other relatives can be estimated
  3. Similarity of different types of relatives can permit modelling of genetic versus non-genetic familial influences
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12
Q

I. Methods to determine Complex inheritance
3. How can heritability be studied?

A

Comparing frequency within the family with that of the entire population

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13
Q

I. Methods to determine Complex inheritance
4. Give examples of Risk Ratios for Siblings of Probands with Complex Diseases with Familial Aggregation

A
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14
Q

I. Methods to determine Complex inheritance
5. How is diabetes inherited?

A

MODY (autosomal dominant)
(GCK, HNF-4 alpha and HNF-1 alpha mutations)

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15
Q

I. Methods to determine Complex inheritance
6. Describe Family-based association studies

A
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16
Q

I. Methods to determine Complex inheritance
7. How do we determine Accumulation within a family?

A

frequency of the disease among siblings/ frequency of the disease in the entire

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17
Q

I. Methods to determine Complex inheritance
8. How do we give Estimation of heretability by Twin studies?

A
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18
Q

I. Methods to determine Complex inheritance
9. What are Concordance and disconcordance?

A

The degree of concordance is the degree of similarity between two individuals
– If both twins carry the disease, they are concordant
– If only one twin carries it, they are disconcordant

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19
Q

I. Methods to determine Complex inheritance
10A. How do we calculate Concordance?

A
  • Calculated as the number of twin-pairs with disease amongst those twin-pairs with at least one affected twin (Gordis):
    #twins with both affected
    (# twins with both affected + # twins with only one affected)
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20
Q

I. Methods to determine Complex inheritance
10B. What happen if Concordance < 100% in MZ twins?

A

Concordance < 100% in MZ twins is evidence for nongenetic etiological factors.

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21
Q

I. Methods to determine Complex inheritance
10C. What happen if Concordance in MZ twins > DZ twins?

A

Concordance in MZ twins > DZ twins is evidence for genetic etiological factors.

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22
Q

I. Methods to determine Complex inheritance
10D. What are Concordance Rates in MZ and DZ Twins in case of DIABETES?

A
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23
Q

I. Methods to determine Complex inheritance
11. What are differences between monozygotic and dizygotic twins?

A
  • To form identical or monozygotic twins, one fertilised egg (ovum) splits and develops into two babies with exactly the same genetic information.
  • To form fraternal or dizygotic twins, two eggs (ova) are fertilised by two sperm and produce two genetically unique children.
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24
Q

I. Methods to determine Complex inheritance
12. Genes or shared family experiences?

A
  1. To disentangle genes and experience, we study special family groups
  2. Either family members sharing experiences but differing in shared genes, e.g. twin studies or
  3. family members sharing genes, but differing in their shared experience, e.g. adoption studies
25
Q

I. Methods to determine Complex inheritance
13. How can we investigate environmental factors based on studies on adopted children?

A
  1. Strong concordance with the biological parents
    -> the disease has strong genetic background
  2. Strong concordance with
    adopting parents
    -> environment is decisive
26
Q

I. Methods to determine Complex inheritance
14. Describe Worldwide prevalence of obesity

A
  • prevalence of obesity nearly tripled between 1975 and 2020
  • in 2020, more than 2 billion adults were overweight , over 600 million were obese
  • In Europe, more than half the population is overweight
    => This makes it the first generation predicted to have a shorter lifespan than their parents
27
Q

I. Methods to determine Complex inheritance
15. Why is it important to research the genomic background of multifactorial diseases?

A
  1. Molecular pathomechanimus
  2. Personalized treatment
  3. Screening people , genetic predisposition
28
Q

I. Methods to determine Complex inheritance - Difficulties in phenotyping
16. What are Difficulties in phenotyping?

A

– Many times there is no standard diagnosis.
– The clinical picture may change with age
– Symptoms may occur in episodes
– Otherillnesswithsimilarsymptoms
– Different diseases often occur together ( comorbidity ).

29
Q

I. Methods to determine Complex inheritance - Difficulties in phenotyping
17. What is QT: quantitative trait?

A
  • A characteristic that can be defined by a number.
  • Eg: LDL-C, blood pressure, IgE level, BMI
30
Q

I. Methods to determine Complex inheritance - Difficulties in phenotyping
18. What is QTL: quantitative trait locus?

A

a locus that segregates with a given feature .

31
Q

I. Methods to determine Complex inheritance
19. What are Hypotheses for obesity?

A

There are genetic variants, which gave earlier a selection advantage, but in our days they make us susceptible to certain diseases.

32
Q

I. Methods to determine Complex inheritance
20. What is Thrifty gene hypothesis?

A
  1. Thrifty genes enable individuals to efficiently collect and process food to deposit fat during periods of food abundance.
  2. Fatter individuals carrying the thrifty genes would thus better survive times of food scarcity.
  3. In modern societies with a constant abundance of food, this genotype efficiently prepares individuals for a famine that never comes.
  4. an absence of selection, combined with genetic drift
33
Q

I. Methods to determine Complex inheritance
21. What is Hypotheses for cariovascular diseases?

A

There are genetic variants, which gave earlier a selection advantage, but in our days they make us susceptible to certain diseases.

34
Q

I. Methods to determine Complex inheritance
22. What are the features of Salt-conserving phenotype?

A
  1. Earlier it was advantageous, if the salt-loosing was kept minimal especially for populations living in warm climate.
  2. In our days when salt is abundant this genetic background leads to a higher susceptibility to salt sensitive hypertension.
35
Q

I. Methods to determine Complex inheritance
23. State Antagonistic pleiotropy hypothesis

A
  • Variants, which are advantageous in younger age, but harmful in older
  • It is called antagonistic pleiotropy
    => The stronger inflammatory response can be advantageous in younger age, but harmful in older, because chronic diseases in old age are often inflammatory, like atherosclerosis, rheumatoid arthritis or Alzheimer disease.
36
Q

II. Population genetics
1. What is population?

A

A population is a group of individuals of the same species who share a geographic area and usually mate within the group

37
Q

II. Population genetics
2. What is gene pool?

A

The total genetic variation of that population is the gene pool

38
Q

II. Population genetics
3. What is frequency?

A

The total genetic variation of that population is the gene pool

39
Q

II. Population genetics
4. What is evolution?

A

evolution is the change in allele frequency over generations

40
Q

II. Population genetics
5. How do we give Evaluation of population genetic studies?

A
  • SNVs: binary: usually two nucleotides in one locus (eg A / G; p and q )
  • Genotype: 3 (eg AA; AG; GG)
  • MAF: minor allele frequency
41
Q

II. Population genetics - Hardy-Weiberg
6A. Give the equations of Hardy-Weiberg

A
42
Q

II. Population genetics - Hardy-Weiberg
6B. What are Major Allele Frequency (p) and Major Allele Frequency (q)?

A
  • The most common allele would be known as the major allele and its frequency would be the Major Allele Frequency (p)
  • Minor Allele Frequency (q) refers to the frequency of the second most common of the two alleles present.
43
Q

II. Population genetics - Hardy-Weiberg
7. For a given autosomal recessive disease, q = 0.01 (where q is the allele frequency of the mutant allele). Approximately what percentage of the population has two copies of the normal allele?

A
44
Q

II. Population genetics - Hardy-Weiberg
8. Describe Association studies (heart disease)

A
45
Q

II. Population genetics
9. What are the 2 types of sample collection?

A
  1. Retrospective study
  2. Prospective study
46
Q

II. Population genetics
10. What are the features of Retrospective study?

A

A retrospective study looks backwards and examines exposures to suspected risk or protection factors in relation to an outcome that is established at the start of the study

47
Q

II. Population genetics
11. Explain p value

A
  1. Def: What is the probability of a false association?
  2. The significance limit is usually p = 0.05: chance of error (type I error):
    – We can be wrong once in 20
  3. If many tests are performed (eg GWAS) the probability of a false association increases: it must be corrected by the number of tests: Bonferroni correction:
    – p = 0.05 / number of tests
48
Q

II. Population genetics
12. How do we use Risk calculation?

A
  1. OR=oddsratio.Use:retrospective studies.
  2. RR = relative risk : use: prospective studies.
  3. If the OR or RR > 1, the allele increases the risk of the disease
  4. <1reduces
49
Q

II. Population genetics
13. Give an example of Retrospective study

A
50
Q

II. Population genetics
14. What are Problems with retrospective studies?

A
  1. Relationship between environmental effects and disease: difficult to find relationship
  2. Those who have died and mild patients may be eliminated
51
Q

II. Population genetics
15. What are features of Prospective study?

A
  • A prospective study watches for outcomes, such as the development of a disease, during the study period and relates this to other factors such as suspected risk or protection factor(s).
  • where participants are enrolled before any of them have the disease or outcome being investigated.
52
Q

II. Population genetics
16. What are Results of Genetic Approaches to the Common Diseases?

A
  • Genetic variants associations (eg: ApoE4 in Alzheimer disease)
  • New pathomechanism (reduced insulin secretion: MTNR1B, TCF7L2, KCNJ11in T2DM
  • Personal predisposing gene set (BRCA1, BRCA2)
53
Q

III. Polygenic Risk Score
1. How do we calculate polygenic risk score?

A
  • The enormous amount of genomic data now available enables researchers to calculate which variants tend to be found more frequently in groups of people with a given disease. There can be hundreds or even thousands of variants per disease.
  • Researchers put this information into a computer and use statistics to estimate how the collection of a person’s variants affect their risk for a certain disease.
    => This yields polygenic risk scores.
    => All of this can be done without knowing the specific genes involved in the complex disease. While we may someday know all the genes involved, researchers can estimate risk now without this link.
54
Q

III. Polygenic Risk Score
2. What are the characteristics of The potential genetic variants?

A
  1. must be truly associated with the health condition or its measure, so that it can be used as a proxy for exposure of interest
  2. it should not be associated with measured/unmeasured confounders of the exposure-outcome relation,
  3. Exclusion restriction criteria, i.e., the instrument/genetic variant should not be directly associated with the outcome and its effect must be mediated only through the exposure
    => implying that no alternative causal pathway exists between instrument and outcome except via exposure
    => Mendelian randomization
55
Q

III. Polygenic Risk Score
3. What is the role of mendelian randomization?

A

assessing causal association of genetic variant which acts as a proxy for modifiable biological traits, with outcomes related to health economics.

56
Q

III. Polygenic Risk Score
4. There is One study examined causal association between child’s/adolescent’s height and
- cognitive
- mental health
- behavioral outcomes like academic carrier IQ
- self-esteem
- depression symptoms behavioral problems
By using genetic determinants of height
=> What can we conclude from mendelian randomization?

A

Height presents disadvantage rather than advantage as it was fund to increase hyperactive behaviour among girls and emotional and peer problems among boys.

57
Q

Give examples of Genomewide investigations

A

Genomewide GWAS, CGH, NGS investigations

58
Q

How do we Investigat3 of susceptibility genes

A

in linkage and target gene association studies

59
Q

. Environmental effects can be investigated by ___ (3 things)

A

adoption, migration and epidemiology studies

Genetics and genomes (19 decks)

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