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Human Genetics > Quantitative Traits > Flashcards

Quantitative Traits Flashcards

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1
Q

What are Qualitative traits? How do they differ from Quantitative traits?

A

Qualitative traits have clear, distinct differences, like Purple or White flowers
Qualitative traits usually have simple genetic causes (ex: P or p)

-Quantitative traits fall somewhere on large spectrum of possibilities
-Quantitative traits often have complex causes

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2
Q

what is the phenotype for Continuous traits ? Is it Quantitative or Qualitative ?

A

Continuous traits have a phenotype that could be *any REAL NUMBER *
(ex: measure the height of different people; get broad range of heights)
Continuous trait is a QUANTITATIVE trait

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3
Q

What is phenotype for Discontinuous traits?

A

Discontinuous trait: has a phenotype of an INTEGER
(counting number)
(discontinuous traits not studied a lot on people. useful for fruit fly studies)
ex; counting the number of bristles on fruit flies

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4
Q

What is the phenotype for a threshold trait?

A

The phenotype for a threshold trait is *PROBABILITY of an event *
ex: BRCA1 mutation causes an increased risk of cancer; hence this changes threshold of whether or not person has cancer
(Threshold traits are important medically)

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5
Q

What are the three different kinds of Quantitative traits?

A

Continuous, Discontinuous and threshold traits

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6
Q

What are the statistical measures of population? What are the equations for each?

A

Statistical Measures of population:
Mean= average (X bar) (add up values for everyone and divide by size of group you study)
Variance ; how much individuals differ from the mean
eqaution : summation of (one value- mean) ^2 /(n-1)
n= sample size units: ex. m^2
Standard Deviation; = square root of variance
units; ex. meters

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7
Q

Compare and contrast the differences with High vs low variance ?

A

Low variance= less variation
high variance = high variability (many differences from mean)

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8
Q

Why do we square the differences in variation equation

A

We square the differences (xi- mean) ^2 in variance equation:
1. To make all values positive and add up to something we can calculate
2. accentuates the impact of bigger differences

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9
Q

What are the values needed to determine normal distribution in a population ?

A

mean and standard deviation

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10
Q

What is the median?

A

Median: a value for which half of the data points are higher and half are lower
-Sort the data into ascending order(least to greatest)
- then look at the one in middle
(if population is normal distribution: the median is close to mean
if not, the population may not have normal distribution)

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11
Q

Why is variance important ? How does it contribute to genetics?

A

Variance
-our major interest is understanding DIFFERNCES within in a population:
-Comparing different phenotypes helps us understand each of them better
- Evolution requires differences in order to work
-These differences represent the variance, and the average phenotype is the mean

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12
Q

What does standard deviation provide a measure of?

A

Standard deviation = square root of the variance
*The standard deviation gives a measure of how much the population VARIES from the mean, in useful units.

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13
Q

What’s the normal distribution ?

A

Normal distribution : is graph that has values of mean and standard deviation
-the mean is in middle part of graph and there is +/- 1SD (standard deviation) that will be 68.2% of population that will occur if population is normally distributed

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14
Q

What creates the normal distribution?

A

The normal distribution is created by two things:
- A mean
-A set of random events that will make each individual larger or smaller than the mean
For example: watch a quincunx machine

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15
Q

What is a Binomial distribution ?

A

Binomial distribution: mathematical expansion of yes or no decisions
(usually gives normal distribution curve)

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16
Q

What are the causes of quantitative traits

A

if there are a bunch of genes involved

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17
Q

Describe the curve in population with one gene and two alleles? What are the phenotypic ratios?

A

One gene, two alleles
all alleles are co-dominant
(ex; color of flowers; RR- red, Rr is pink and rr- white)
-Heterozygous parents
-In the simplest case:
*THREE classes *
1:2:1 ratios
-Crude cuve
(not quite normal distribution ) (have twice as many heterozygotes (Rr) as homozygous RR or rr)

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18
Q

Describe the curve in population with two genes and two alleles? What are the phenotypic ratios?

A

Two genes, two alleles
All alleles are co-dominant
-heterozygous parents
-In the simplest case:
*FIVE classes *
-1:4:6:4:1 ratios
-Better curve
(start to look like normal distribution) (lot more choices than previous curve
(1/16 for homo recessive both genes; 1/16 for homozygous dominant; 4/16 3 recessive, 1 dominant (or vice versa) ; 6/16 for two big Dominant alleles and 2 recessive alleles

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19
Q

Describe the curve in population with three genes and two alleles? What are the phenotypic ratios ?

A

Three genes, two alleles
all alleles are co-dominant
Heterozygous parents
In the simplest case:
*SEVEN classes
1:6:15:20:15:6:1 ratios
-Good curve
(even closer proximation to normal distribution)

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20
Q

Explain how Variance can be caused by multiple alleles of many genes ? Provide info on Wheat kernel example.

A

Variance can be caused by multiple alleles of many genes
-The color of a kernel of wheat is controlled by Threee genes
-Dark colored kernels : homozygous dominant (AA BB CC) for three alleles
- Light colored Kernels- Homozygous dominant for three alleles
- intermediate colored kernels- mixture of dominant and recessive
Hence you have nice, normal distribution of colors of kernels in population (different possibilities)
Quantitative traits are likely to be caused by multiple genes that we study.

21
Q

What is the purpose of Pascal’s triangle ?

A

Pascal’s triangle is used to work with the binomial expansion
-The coefficients for the one, two and three gene models are found on Every other Row
each row gives you coefficient for one of gene cases (mentioned previously)
every other row because, each time add new gene, you add two different alleles of that gene
(you get all numbers in triangle by addition of numbers in previous row (lets you do a lot of calculations)

22
Q

How can you map genes that control quantitative traits ?

A

Mapping quantitative trait genes:
1. by crosses between strains
2. Genome Wide Association Studies

23
Q

What occurs when mapping genes by crosses between strains ?

A

Mapping genes by crosses between strains:
ex: two different mouse strains; find trait that is different between them; make heterozygous mice, and have children, each getting two or one of parents genome. Then look at which pieces of genome are associated with which traits

24
Q

What is ventricular septal defect in mice caused by?

A

the ventricular septal defect (in mice) are caused by alleles of several genes
gene on chromosomes 6 and another gene on chromosome 8, 10; they all have peaks on graph that show there is something contributing to risk of the heart disease)
QTL mapping was done using mice

25
Q

Can humans maps genes by crossing between strains? What other method do humans use to map genes?

A

NO, humans cannot map genes by crossing between strains (do not have different strains of humans)
- Humans Map genes by Genome Wide Association Studies (powerful, but less controlled)
- you determine DNA sequence of 10,000 individuals, and determine whether they have a trait (that is of interest) you will see if there is any DNA sequence that goes along with trait (that is highlighted)

(ex: if everyone with heart defect had a particular sequence, it could be a mutation in gene causing trait or mutation nearby chromosome linked to mutations that causes trait.
These studies help us find out what the genes are.

26
Q

What was found in Chinese study regarding a congenital heart malformations?

A

Identification of a genetic region (in chromosome 13) that poses risk for congenital heart malformations

27
Q

What are other factors that influence quantitative traits?

A

other factors that influence quantitative traits :
penetrance and expressivity

28
Q

What causes some variance? Provide example of this in fruit flies

A

Some variance is caused by random fluctuations in cell or the environment
ex; all fruit flies with identical genotypes can have huge variability.(this may be due to mutation that affects normal eye structure, causing some flies to have no eye, some to have normal eye)
-hence variability even though flies are genetically identical

29
Q

What is penetrance? What is Expressivity?

A

Variable Penetrance: Not everyone with the same genotype will have the same trait. (some will show trait, some will not show trait)
Variable Expressivity: Everyone with same genotype shows the trait, buts some may it show it more severely (strongly), while others show it less severely.

30
Q

What is Heritability?

A

Heritability: Measuring how important genes are

(both large number of genes and environmental factors can control aspects of quantitative trait)

31
Q

What is Broad heritability? What is an equation for it? How does this affect environment and population?

A

Broad Heritability: The fraction of the variance that is caused by All genetic variation in the population
(fraction of variance caused by genotypes and fraction caused by environment)
H^2= variance of genotype/Total variance
H^2 = Variance of genotype/(variance of genotype + variance of environment )
(for simplicity, these formulas ignore genetic/environmental covariance )
**broad heritability for a phenotype changes for each environment and population **

32
Q

What happens during inbreeding by self-fertilization ?

A

Inbreeding by self-fertilization rapidly ELIMINATES HETEROZYGOTES (seen in nematodes and plants)

33
Q

Explain what occurred in Johannsen’s experiments with Phaseolus vulgaris

A

Johannsen carried out experiment with beans . He took a parental population and may three inbred lines (each of the lines are genetically different)
Parental population average weight of 450 mg; SD of 110 mg
Each of his inbred lines (3) had different averages for weight, but they all had much smaller Standard deviations (sd; 75 mg) (than parental), and hence much smaller variance.
This occurs because since they are inbred, there is No genetically variability (only variability is caused by environment)

34
Q

How was the H2 (heritability) calculated for the Johannsen experiment ?

A

Calculating H2
parental population: mean = 450 mg; SD= 110 mg
in bred lines: all had SD (75 mg) (average weights : 420, 480, 450)
The variance of the total population is:
(SD) ^2= (110 mg)^2 = 12,100 mg^2
Within each inbred line, there is NO genetic variation (the inbred lines are all genetically identical ) :
(SD)^2= 0
Thus, the measured variance in each inbred line is due to random or environmental effects:
(SD)^2 - (75 mg)^2 = 5625 mg^2
*He assumes that if environmental variance is similar to parental population vs inbred subpopulation, he can use same environmental variance.
Hence: H^2 (inbred) = 0
H^2 (total) = (12100-5625)/12100= 0.53
(genetic variance- environmental variance) /(total variance)

half of differences in plants caused by genetic alleles and half caused by environment )

35
Q

What are the different types of genetic variation? Which one is easy to work with ?

A

Genetic Variation has several causes
-Addition Variation ( semi-dominant alleles, where each individual allele adds to the phenotype)
-Dominance variation (dominant or recessive alleles, which do not always influence the phenotype)
-Interaction variation (epistasis, where interactions stop some alleles from affecting the phenotype )
**ONLY ADDITIVE variation is easy to work with

36
Q

What is narrow heritability?

A

Narrow Heritability: the amount of variance that is caused by only Additive genetic variability
(this value is smaller than broad heritability)
*Narrow heritability= additive genetic variance /population total variance *
**Narrow Heritability = selective response/selective differential: **
(describes how different children are from their parents if we select for a particular trait)
ex: in population of different bean widths, we can choose parents with largest bean size to reproduce; the children will still have normal distribution for average size, but will move towards bigger size (due to selection of bigger ones)

37
Q

Can selection differential method (narrow heritability) be used for humans? What other animals used this method?

A

NO, humans cannot use selective differentiation in their studies.
Plants use this method to dramatically increase yield for crops (they breed by selective diffentation)

38
Q

What must be observed when looking at Heritability in humans ?

A

To study heritably in humans you need to understand COVARIANCE
Covariance for two things measured; x and y (ex: height and arm span)
Covariance= summation (x- x mean) (y- y mean)/N-1
if y is always Bigger than average when x is bigger than average, Covariance e will be POSITIVE
if y is always LESS than average when x is bigger than average, covariance will be NEGATIVE
if there is NO relationship between x and y, covariance will be zero
(trying to observe how much differences in one trait go with differences in another trait )

39
Q

What is the purpose of covariance ?

A

Covariance- used to see if two things go with each other (ex: if height and arm span are traits that go with each other)
Cov can be used in interpreting twin studies

40
Q

what is Correlation Coefficient? How is it calculated?

A

Correlation Coefficient:
covariance /SD for 1st trait x SD for 2nd trait
Cov (x,y) can be any number
-to evaluate the significance of equation we normalize the equation
r xy= Cov (x,y) /SDx x Sty
The denomiator uses standard deviation
r= summation of (x-x mean) (y- y mean) /SDx x Say
thus -1 < or equal to r x, y < or = to 1
(negative correlation–. -1; NO correlation –> 0 ; positive correction –> +1 )

41
Q

Discuss the Twins, sibling inheritance

A

Twins, siblings and inheritance
-Monozygotic twins (MZ)
-gentically identical
-Dizygotic twins (DZ) : share 50% of alleles
-Like other siblings
Siblings: share 50% of alleles
-parent/child share 50% alleles

Having identical twins give us two genetically identical individuals to determine whether twins are more like each other for traits than average people are for traits(tell us how much genotype plays a role in the study)

42
Q

Explain how we can control for environment in human studies. What is the genetic variance for identical twins ?

A

Controlling for environment in human studies:
-We can further subdivide variance:
variation of population = g variance+ ce variance + ue variance
-g variance= Genetic variance
ce variance= variance due to a common environment
(ex: two different twins in same household )
ue variance = variance due to a unique environment
(things that everyone is different from)
*For identical twins , the genetic variance = 0 *
(only unique evironment focused on in twins)

43
Q

How do you calculate the heritability from twin data. What is the problem?

A

Calculating H2 (heritability) from twin data
-problem : correlations in phenotype could be due to genetics or to a common environment
solution
H^2- CE- rMZ
H^2/2 - CE= r DZ
H^2 - H^2/2 = rMz - rDZ
** H^2= 2 (rMZ - rDZ) **
This equation should factor out the effects of the common environment (CE)
H^2—> Broad heritability
rMz = correlation for mono twins
DZ= dizygotic twins (only share half genes)
CE–> common environment

44
Q

What is the Dermal Ridge count ? is it heritable?

A

Dermal Ridge Count
-To quantify one aspect of fingerprint, count the number of ridges between two foci in the fingerprint .
-Total ridge count is the sum of values for all ten fingers
yes Dermal Ridge count is very HERITABLE
(ex; if H^2 (heritably) = 0.92, means its a highly heritable trait

45
Q

Explain what may change when looking at studies that discuss twins raised apart

A

Twins raised apart
-What if identical twins are not raised the same as fraternal twins>
if so, we would not be evaluating environmental effects properly
-some twin studies compare pairs of twins who were raised in the separate households.
In these studies, the Environment is NOT shared among each pair of twins.

46
Q

Explain the example of correlation of height measured in twins living together vs apart.

A

Height
-Monzygotic twins raised together = 0.93 (strong correlation)
Monozygotic twins raised apart = 0.86 (still high)
-However, since the monozygotic twins who are raised together have a HIGHER correlation than those twin apart, which means the environment also plays a role in determining
*so height is strongly affected by genetic makeup, but environment plays a small role too.
(also look at sample size (n) for twins in each situation . look out and be skeptical of twin studies that have low n values)

47
Q

Describe the correlation of IQ scores in twins living together vs apart.

A

WAIS IQ scores
monozygotic twins raised together: 0.98 (very good correlation)
Monozygotic twins raised apart = 0.69 (lower correlation)
-So IQ (whatever it is) is strongly affected by genetic makeup, but environment plays a MAJOR role.
(since twins raised together had a higher correlation value than those living apart)

48
Q

What happens when the environment changes? Describe an example regarding the PKU diet that relates to this.

A

Changing the environment also changes H^2 (heritability)
-In areas where the diet is RICH in phenylalanine, being homozygous for PKU is Strongly correlated with mental retardation
-But if the diet is LOW in phenylalanine, then being homozygous for PKU does not usually lead to mental retardation
changing the environment changes heritability

Human Genetics (13 decks)

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