Flashcards in Population Genetics Deck (65):

1

## Only 10% of human DNA codes for genes, and only 1% are

### Exons

2

## The promoter upstream of the 5' terminus regulates the initiation of DNA transcription into single stranded

### mRNA

3

## How many codons specify translation into the 20 amino acids of the protein?

### 64 (three are stop codons)

4

## Non-corrected transcription errors make

### Mutant (abnormal) proteins

5

## Humans have 2 sets of homologous chromosomes (diploid). Thus, there are 2 copies of each

### Gene (allele)

6

## If both alleles are the same, the individual is said to be a

### Homozygote

7

## If the two alleles are different, the individual is a

### Heterozygote

8

## At a population level, there may be multiple alleles at each locus. These allelic variations can be expressed in different proportions in the

### Population

9

## A single nucleotide change (SNP) or insertion/deletion (Indel) of a nucleotide that has been transmitted throughout generations

### Polymorphisms

10

## Polymorphisms are a single nucleotide change (SNP) or insertion/deletion (Indel) of a nucleotide that has been transmitted throughout generations reaching a frequency of

### 1 in 100 in the population

11

## The frequency of “Phenotypic Traits” caused by an allele within a loci can vary among

### Populations

12

## Remember that many phenotypic manifestations defy a simple Phenotype-Genotype Mendelian categorization and must be modeled using

### Gene interactions together with environmental exposures

13

## What are the assumptions needed for assuming we have a population in Hardy-Weinburg (H-W) equilibrium?

###
1.) Random mating

2.) No changes due to migration

3.) No large fluctuations in allele frequency (i.e. genetic drift)

4.) No positive or negative selection

14

## Means that all genotypes reproduce equally well

### No positive or negative selection

15

## In H-W equilibrium, we can have no large fluctuations in allele frequency caused by the effects of: natural selection, genetic drift, founder effect, bottleneck, or

### Inbreeding

16

##
Selection against homozygous individuals and advantage for heterozygotes in a given environment

Ex: the ability of sickle cell heterozygotes to fight off malaria

### Natural selection

17

## Variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce

### Genetic Drift

18

## The frequency of Ellis-van Creveld syndrome in PA is greater than expected from random distribution of alleles, this is due to

### Genetic drift

19

## Characterized by short stature, polydactyly, and heart disease

### Ellis-van Creveld syndrome

20

##
A deleterious rare allele seen at a relatively high frequency in a small/isolated population derived from 1 ancestor

Ex: Huntington’s Disease in Maracaibo

### Founder effect

21

##
High frequency of an allele in a population that underwent historical population constrictions

-Ex: the frequency of Gaucher, Tay-Sachs, Torsion dystonia in the Ashkenazi Jewish population

### Bottleneck effect

22

## Consanguinous mating (between relatives) that increases the amount of homoxygotes

### Inbreeding

23

## Subpopulation stratification by selective mating (marriage arrangements) increases the rate of homozygotes and the probability of distinct phenotypic traits in some

### Populations

24

## Occurs in up to 60% of people in some geographic regions

### Endogamy (marrying only within limits of tribe/community)

25

## What leads to genetic variations among populations?

### Natural selection, Genetic Drift, Founder effect, Bottleneck effect, and Inbreeding

26

## Says that the chance that a genetic disorder will occur depends on the observed frequency of the disease in the population

### Hardy-Weinberg principle

27

##
Allows us to calculate the frequencies for 2 alleles (A and B) in a population in equilibrium (p + q = 1)

-Where p = frequency of A and q = frequency of B

### H-W calculation

28

## In the H-W calculation, what are the types of people in the population?

###
AA = p^2

BB= q^2

AB = 2pq

29

## What is the H-W equation?

### p^2 + 2pq + q^2 = 1

30

## In the H-W equation, the total number of allele A in the population is

### #A = p^2 + 2p

31

## In the H-W equation, the total number of allele B in the population is

### #B = q^2 + 2q

32

## For X-linked recessive traits, males are

### Hemizygous for A or B (i.e AY or BY)

33

## For X-linked recessive traits, females can still be

### AA, BB, or AB

34

##
When talking about H-W and a disease, what is the:

1.) frequency of the normal allele?

2.) Frequency of the disease producing allele?

###
1.) p

2.) q

35

## If the disease frequency is 1/2500, what is q^2? what about q?

###
q^2 = 1/2500

q = 1/50

36

## What portion of alleles are shared by 1st cousins?

### 1/8

37

## What is the coefficient of inbreeding (f) for 1st cousins?

### (1/8) x (1/8) x 4 possible alleles for that loci = 1/16

38

## When 1st degree relatives mate (father-daughter, brother-sister), what is the risk for a significant phenotypic abnormality?

### 40%

39

##
When dealing with incest, what is the percentage of children born with

1.) AR disorders

2.) malformations/sudden infant death syndrome

3.) severe intellectual impairment

4.) mild intellectual impairment

###
1.) 12%

2.) 18%

3.) 12%

4.) 14%

40

## When second degree relatives (i.e. uncle and niece or half siblings) have children, the overall risk for congenital anomalies lies between the risk for 1st cousins and incest. It is about

### 6%-18%

41

##
When 1st cousins procreate, since they are sharing 1/8 of their genes, what is the risk for

1.) mental retardation

2.) infant mortality

###
1.) 3-6%

2.) 4.4%

42

##
What is the empiric risk in the general population for

1.) AD disorders

2.) AR disorders

3.) X-Linked disorders

4.) Chromosomal disorders

5.) Congenital malformations

###
1.) 1%

2.) 0.25%

3.) 0.2%

4.) 1%

5.) 3-5%

43

## Increases the risk for multi-factorial and recessive diseases

### Consanguinity

44

## Autosomal dominant disorder affecting 1 in 20,000 individuals in the general population. Classical example of age dependent penetrance of a devastating neurologic deterioration disorder.

### Huntington's disease

45

## Very few individuals manifest signs of huntingtons in childhood, while 100% have symptoms by age

### 80

46

## Huntington's inevitably leads to death with loss of the basal ganglia of the brain, specifically the

### Caudate Nucleus

47

## One of the first disorders subjected to “ large family genome polymorphic markers scan and positional cloning ” making in 1981 for linkage-based diagnosis by haplotype analysis in pre-symptomatic patients.

### Huntington's

48

## An X-linked recessive disease caused by an F-VIII gene pathogenic mutation (most common in intron 22-A and intron-1 inversion)

### Hemophilia A

49

##
What is the incidence of hemophilia A in

1.) Males

2.) Females

###
1.) 1/4000

2.) rare

50

## 10-15% of hemophilia A occurs

### De novo

51

##
What is the penetrance of hemophilia A in

1.) Males

2.) Females

###
1.) 100%

2.) 10%

52

## Severe deficiency in the factor-VIII clotting activity assay is associated with spontaneous joint or deep tissue

### Bleeding

53

## Associated with prolonged bleeding after tooth extractions, surgery, or injuries

### Moderate/mild deficiency of factor V-III clotting activity

54

## What are the four Bayesian Terminologies?

###
1.) Prior probability

2.) Conditional probability

3.) Joint probability

4. Posterior probability

55

## Mendelian probabilities that the parent is or is not a carrier

### Prior probability

56

## Information gathered based on whether siblings are or are not affected

### Conditional probability

57

## The product of prior and conditional probabilities

### Joint probability

58

## The ratio of the joint probability of one outcome to the sum of all joint probabilities

### Posterior probability

59

## When 2 events are independent, p1 and p2, the probability for both occuring together is

### p1 x p2

60

## When one event can happen in 3-ways with individual probabilities of p1, p2, and p3, then the overall probability is

### p1 + p2 + p3

61

## The probability that in this scenario the event will happen by way of #1 is then

### p1 / (p1 + p2 + p3)

62

## Relates to the quantitative study of the distribution of genetic variation in populations and how they are maintained or changed over time

### Population genetics

63

## Disease frequencies often vary based on

### Ethnicity

64

## When we need to use H-W, knowing the disease frequency will give us

### q^2

65