Genetic research methods

the Hardy-Weinberg equilibrium

from alleles to genotypes

  • A - is the normal allele (wild type),

  • a - is the mutant allele

possible genotypes:

  • AA is the homozygous wild genotype

  • aa is the homozygous mutant genotype

  • Aa is the heterozygous genotype

Allele & genotype frequencies

  • if frequency of A allele is 50% = 0.5 (hypothetical. not always 50%)

  • if frequency of a allele is 50% = 0.5 (hypothetical. not always 50%)

  • what is the frequency of the following genotypes?

    • AA = 0.5 × 0.5 = 0.25

    • Aa = (both Aa and aA) = 2 × 0.5 × 0.5

    • aa = 0.5 × 0.5 = 0.25

monogenic example

R – a rolling tongue dominant allele
NR – a non-rolling tongue recessive allele

R = 60% allele frequency – 0.6 - all alleles in a population = 100%

NR = 40% allele frequency – 0.4

  • Can roll: RR, RNR, NRR
    =RR + 2xRNR=
    (0.6*0.6) + (2* 0.6*0.4) = 0.36 + 0.48 = 0.84 = 84%.     - all genotypes in a population = 100%

  • Cannot roll: NR homozygotes = NRNR = 0.4 x 0.4 = 0.16 = 16%

The hardy-weinberg equilibrium

  • The frequencies of alleles and genotypes DO NOT CHANGE across generations unless forces such as natural selection or migration change them (implied by the Mendelian laws).

  • A – allele1

  • a – allele2

  • A allele frequency = p

  • allele frequency = q

  • Genotypes: AA Aa aA aa

  • (p+q)2 =p2 +2pq+q2 =1

  • p+q=1

Based on this equation we will able to calculate the proportion of alleles, genotypes, carriers, affected and non-carriers!

how do we know that every 50 person is a PKU carrier?

  • prevalence: 1/10000 (people with the aa genotype)

  • (p+q)2 = p2 + 2pq + q2 = 1

  • p+q = 1

  • what is to be calculated?

    • PKU carriers Aa (2pq)

  • what do we know?

    • aa (affected) = 1/10000, q2 = 0,0001

  • by taking the square root of q2

    • q=0,01

  • based on the equation above

    • p=1-0,01 = 0,99

  • 2pq = 2 × 0,99 × 0,01 = 0,0198 = about 2% = 1/50

twin & adoption studies

Adoption studies I. Parent-child dyads

  • adoptive parent-offspring resemblance reflects - environmental factors

  • bio parent-offspring resemblance reflects - genetic factors

adoption studies II. Siblings

  • adopted siblings - environmental siblings → share only environment

    • environmental siblings’ resemblance reflects environmental factors

  • separated siblings - genetic siblings → share only genes

    • genetic siblings’ resemblance reflects genetic factors

  • environmental siblings: pairs of genetically unrelated children adopted early in life into the same adoptive home

  • genetic siblings: full siblings adopted APART early in life and reared in different homes

History of adoption studies

  • 1920s-1940s use of adoption studies to study IQ

    • most studies found that adoptees correlated more highly with their biological parents than their adoptive parents

  • no adoption studies of psychopathology yet

    • 40s, 50s, thought that environmental factors explained psychopathology:

    • “The schizophrenic is ... due to the severe early warp he encountered in important people in his infancy and childhood, as a rule, mainly in a schizophrenogenic mother.” Fredia Fromm-Reichmann (1948)14

The first adoption study of Schizophrenia: Leonard Heston, 1966

  • 47 children born to SZ mothers between 1915-1945 in Oregon State hospitals.

  • separated from mothers within first few days of life and adopted by non-SZ parents

  • followed-up at 26, compared to foster children whose mothers had no history of SZ, matched on sex & type of placement

  • over 10% of adopted children of SZ mothers developed SZ (similar ratio is found when children are raised by their SZ mother)

  • none of the compare control children developed SZ.

Twin studies

  • monozygotic (MZ; “identical“)

  • Dizygotic (DZ, “fraternal“ or “non-identical“)

types of twins

  • monozygotic (MZ; “identical“):

    • result from the fertilization of a single egg by a single sperm; share 100% of their genetic material.

  • Dizygotic (DZ, “fraternal“ or “non-identical“):

    • result from the independent fertilization of two eggs by two sperms; share on average 50% of their genes, can be same sex or opposite sex

Zygosity determination

  • DNA based

  • Physical similarity

    • eye color, hair color and texture (if pairs differ on one of these traits: fraternal pair)

  • questionnaire methods

    • e.g. is it hard for others, family members to differentiate them?

equal environment assumption EEA

  • if the twins are raised in the same family, the env. effects for the MZ and DZ twins are close to identical.

  • (although MZ twins are sometimes raised more similar, as compared to DZ twins. e.g. dressed similarly)

What is heritability?

  • Heritability is the proportion of phenotype variance that can be accounted for by genetic effects.

  • calculated based on twin studies

logic of classical twin studies

  • MZs share 100% genes, DZs share (on avg) 50%

  • both twin types share 100% env.

  • r (the correlation coefficient) represents similarity of pairs

  • similarity = r correlation coefficient

  • if rMZ = rDZ, then genetic factors are NOT important.

  • if rMZ > rDZ, then genetic factors ARE important.

  • heritability index = twice the difference between rMZ and rDZ

  • heritability the proportion of phenotypic variance that can be accounted for by genetic factors

  • if rMZ < 1, (usually this is the case) then non-shared env factors are also important

P = G + E

Total Phenotype Variance = Genetic effects + Environmental effects

G = A + D

A = Additive genetic effects

D = Dominance genetic effects

E = C + U

C = Common (shared) env effects make siblings similar e.g. shared parenting

U = Unique (unshared) env effects make sibilings different, e.g. car accidents

P = A + D + C + U

Total Phenotypic Variance = Genetic Effects + Environmental Effects

A = additive genetic effects,
D = dominance genetic effects
C = common (shared) environmental effects (make siblings similar, e.g. shared parenting)

E = unique (unshared) environmental effects (make siblings different, e.g. car accident)

Interpreting Heritability

  • heritability refers to the genetic contribution to individual differences (variances), not to the phenotype of a single individual, both genotype and env are indispensable — a person would not exist without genes and env.

  • for example, the heritability of height is about 90%, but this does not mean that you grew to 90% of your height for reasons of heredity and that the other inches were added by the env.

  • what it means is that most of the height differences among individuals are due to the gentic differences among them.

summary

• The Hardy-Weinberg equilibrium and related calculations

• Adoption Studies

  • Adoptee & Biological Parent → genetic influence

  • Adoptee & Adoptive Parent → environmental influence

• Twin Studies

  • rMZ > rDZ → genetic influence (the difference twice = heritability)

  • rMZ < 1 → also environmental influence

  • total Phenotypic Variance (P) = A+D+C+U

• heritability index (h2) and it’s interpretation