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Genetics > Exam 3: Quantitative Genetics and Complex Disease II > Flashcards

Exam 3: Quantitative Genetics and Complex Disease II Flashcards

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1
Q

definition of heritability

A

the proportion of the total phenotypic variation that is due to genetic difference

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2
Q

the components of phenotypic variance (Vp): (3)

A
  1. genetic variance (Vg)
  2. environmental variance (Ve)
  3. genetic x environmental interaction (Vge)
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3
Q

components of genetic variance (Vg): (3)

A
  1. additive genetic variance (Va)
  2. dominance genetic variance (Vd)
  3. genic interaction variance (Vi)
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4
Q

Vp=

A

Va + Vd + Vi + Ve + Vge
additive genetic variance + dominance genetic variance + genic interaction variance + environmental variance + genetic x environmental interaction

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5
Q

types of heritability (3)

A
  1. broad-sense heritability
  2. narrow-sense heritability
  3. calculating heritability
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6
Q

broad-sense heritability

A

the ratio of total genetic variance to total phenotypic variance (all genetic modifiers)

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7
Q

narrow-sense heritability

A

ratio of additive genetic variance to the total phenotypic variance (additive effects only)

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8
Q

calculating heritability

A
  • heritability by elimination of variance components
  • heritability by parent-offspring regression
  • heritability and degrees of relatedness (mono vs dizygotic twins)
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9
Q

the narrow-sense heritability, h^2, equals the

A

regression coefficient, b, in a regression of the mean phenotype of the offspring against the mean phenotype of the parents

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10
Q

b=h^2=0

A

(horizontal line) no relationship btwn parental mean phenotype and offspring mean phenotype

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11
Q

b=h^2=1

A

(45 degree angle) perfect correlation btwn mean parental and offspring phenotype

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12
Q

b=h^2=0.5

A

genes and environment interact to determine phenotype

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13
Q

genetic-environmental interaction variance

A

gene effect is conditioned by the environment (ex a genotype affects plant weight, but the environmental conditions determine which genotype produces the heavier plant)

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14
Q

important points about heritability #1 (the heritability estimate is specific to…)

A

the heritability estimate is specific to the population and environment you are analyzing

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15
Q

important points about heritability #2 (the estimate is for a…)

A

the estimate is for a population, not for an individual and therefore is specific to that population

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16
Q

important points about heritability #3 (heritability does not indicate the…)

A

heritability does not indicate the degree to which a trait is genetic, it measures the proportion of the phenotypic variance that is the result of genetic factors for a population in a given environment

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17
Q

the limitations of heritability (3)

A
  1. heritability does not indicate the degree to which a characteristic is genetically determined
  2. an individual does not have heritability
  3. heritability indicates NOTHING about the nature of population differences in a characteristic
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18
Q

t/f: different environments=different population=different heritability

A

true

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19
Q

t/f: heritability varies by population and environment

A

true

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20
Q

quantitative traits are

A

phenotypes (characteristics) that vary in degree and can be attributed to polygenic effects )ie the product of 2 or more genes, and their environment)

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21
Q

a quantitative trait locus (QTL) is a

A

section of DNA that correlates with variation in a quantitative trait. (genetic tool to search for underlying contributions that make a contribution to a quantitative trait)

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22
Q

the QTL is typically is linked

A

to genes that control that phenotype

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23
Q

QTLs are mapped by identifying

A

which molecular markers (such as SNPs or microsatellites) that correlate (segregate with) with an observed trait

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24
Q

QTLs mapping is often an early step in

A

THIS IS OFTEN AN EARLY STEP IN IDENTIFYING AND SEQUENCING THE ACTUAL GENES THAT CAUSE THE TRAIT VARIATION (eg oil content in corn or muscle mass in pigs)

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25
Q

natural selection arises through

A

the differential reproduction of individuals with different genotypes (environment)

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26
Q

artificial selection is selection by

A

by promoting the reproduction of organisms with traits perceived as desirable (human)

27
Q

natural selection and artificial selection both are consequences of

A

successful reproduction that increases the frequency of certain alleles

28
Q

predicting the response to selection

A

= the extent to which a characteristic, subject to selection, changes in one generation

29
Q

factors influencing response to selection

A

S= selection differential

30
Q

selection for oil content in corn, can percentage of oil content through many generations continue increasing indefinitely?

A

no; exists a physiological limit for corn to have kernels that contain pure oil. expensive for plant to make that much oil and there is a limit in how much oil can be in that kernel; physiological limit. Cannot go to 0 either bc kernel needs to have some oil to be living. the seeds will not be fertile if selecting for high/low oil content bc they are going towards extreme physiological limits

31
Q

limits to selection response

A

response may level off after many generations (cannot continue forever)

32
Q

the 2 types of correlated responses

A
  1. phenotypic correlation

2. genetic correlation

33
Q

phenotypic correlation

A

eg larger size and larger/more offspring

34
Q

genetic correlation

A

eg pleiotropy, one gene affecting more than one characteristic; genes that regulate growth hormone impact the size of multiple structures

35
Q

the response of a population to selection often levels off bc

A

because of physiological limits

36
Q

why might butterfat and milk yield be inversely correlated?

genetic correlation = -0.38

A

high amount of fat in milk requires a lot of energy and thus do not produce as much milk, not a good yield, and thus a negative correlation. ie butterfat goes up and yield goes down

37
Q

complex disease caused by

A
  • multiple genes, each with a small contribution

- single gene plus significant environmental effects

38
Q

examples of currently studies complex diseases

A

diabetes (IDDM and NIDDM), alzheimer’s, asthma, rheumatoid arthritis, hypertension, schizophrenia

39
Q

GWAS identifies

A 
identify association (correlation) btwn sequence variants and phenotypes of interest (eg disease)
*reducing the # of variants requires complex tools to get a manageable set of candidate variants*
40
Q

phase 1 of GWAS

A

full set of SNPs is genotyped to identify which are most common in a group of interest (putative associations)

41
Q

phase 2/3 of GWAS

A

SNPs identified from phase 1 are retested in populations that are larger or of a similar size. can distinguish the few true-positive associations from phase 1 from the false-positives that occur by chance

42
Q

difficulties with statistical methods: general

A

claims often refuted bc of lack of consistency in results

43
Q

difficulties with statistical methods: segregation analysis

A
  • choice of families affects results (change population lose genetic correlation)
  • multiple genes analyzed together
44
Q

difficulties with statistical methods: association analysis

A
  • small areas of genome examined

- larger areas = false positives

45
Q

environmental influences on well known medically important chronic conditions: diet, obesity, lifestyle

A
  • type 2 diabetes

- hypertension

46
Q

environmental influences on well known medically important chronic conditions: diet and lifestyle

A
  • obesity

- cancer

47
Q

environmental influences on well known medically important chronic conditions: developmental issues?

A

schizophrenia

48
Q

environmental influences on well known medically important chronic conditions: head trauma, aluminum exposure, vascular disease

A

alzheimer’s

49
Q

allele identification/mapping with SNPs: current trend for mapping/GWAS is to use SNPs

A
  • most frequently seen type of polymorphisms
  • 3 million pairs of SNPs present in human genome
  • technically easier and less expensive to genotype (only 2 alleles; require less DNA)
50
Q

t/f: whole population are being mapped to identify traits

A

true; an ex is entire population of Iceland is being sequenced

51
Q

IDDM and HLA Super-Locus

A

region that encodes 6 classical transplantation HLA genes and at least 132 protein coding genes which has important roles in regulating immune sys. also, this region is associated with more than 100 different diseases ie autoimmune disorders; (particular variants in those genes contribute to a type of disorder)

52
Q

IDDM and HLA Super-Locus: candidate loci sequenced

A
  • higher frequency of DQB1 allele in IDDM
  • the protein encoded by this gene is one of two proteins that are required to form the DQ heterodimer, a cell surface receptor essential to the fcn of the immune sys
53
Q

IDDM proposed cause:

A

oligogenic (small # of genes may interact genetically to manifest a phenotype) + environment
60 genes were linked to diabetes

54
Q

Alzheimer’s disease characteristics:

A
  • most common form of senile dementia
  • neurons lost in cerebral cortex and hippocampus
  • two formations in brain are characteristic: neurofibrillary tangles (tau proteins) and amyloid plaques
55
Q

genetics of Alzheimer disease (2)

A

autosomal dominant form:

  1. mutations in APP (AB peptide precursor): greater aggregation and production of plaques
  2. mutations in presinilin I (part of y-secretase): enzyme that cleaves APP fragments
56
Q

most cases of familial AD are attributable to completely

A

penetrant missense mutations in this subunit (presinilin I)

57
Q

concordance of 80% MZ and 35% DZ in Alzheimer

A
  • suggests that disease is familial or that there is a genetic influence
  • conduct heritability studies, but it is difficult to separate genetic from shared environmental influences
58
Q

APOEe4 allele in 25-35%; what is the function of APOE

A 
function of APOE is cholesterol transport and found in plaques and tangles 
*certain alleles of certain genes make you more susceptible, in this case, Alzheimers*
59
Q

why does loss of function variants in ABCA7 confer greater risk to Alzheimer disease?

A

protein encoded by this gene is a member of transporters; transport various molecules across extra- and intracellular membranes. this changes the biochemical properties of a cell and could favor plaque/tangle formation

60
Q

GWAS and SPON1 gene variant

A

to identify the heritability of various brain connections, used MRIs; discovered genetic variants that affect the human brain’s wiring with specific SPON1 variant. SPON1 variant was significantly associated with bilateral differences in regional brain volumes;

61
Q

GWAS found what in influencing dementia severity

A

a significant genome-wide association for dementia severity was found btwn a common genetic variant on chromosome 11 and anatomical fiber connectivity regional brain volumes

62
Q

GWAS and autism

A

GWAS study of common risk alleles for autism revealed their involvement neuronal development and increased cognitive ability (contribution of many genes in numerous molecular mechanisms of the human brain)

63
Q

polygenic background and monogenic risk variant

A

depending on your genetic background, the combination of genes that you have, risk for disease can go up with or without a defect/mutation; genetic background can modify penetrance of disease in tier 1 genomic conditions ex hereditary breast cancer

Genetics (37 decks)

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