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Epidemiology > Genetic Epidemiology > Flashcards

Genetic Epidemiology Flashcards

1
Q

what does genetic epidemiology study

A

influence of genes and environment on measures of health and disease susceptibility in populations
uncover the role of genetic factors in determining health and disease

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2
Q

outline basic genetics DNA

A

DNA is series of nucleotides - adenine, guanine, cytosine, thymine
genome = 23 pairs of chromosomes - 1 pair sex chromosome

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3
Q

what is an allele

A

alternative form of genetic material at a locus

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4
Q

what is a genotype

A

combination of alleles at a locus (different chromosomes)

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5
Q

what is a haplotype

A

combination of alleles at different loci (same chromosome)

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6
Q

how identical are genetic sequences of unrelated humans

A

99.9% identical
the differences are mostly single nucleotide polymorphisms

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7
Q

what are single nucleotide polymorphisms

A

deletions
inversions (opposite sequence)
copy number variants or short tandem repeats

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8
Q

what is a polymorphism

A

a DNA variation that is relatively common in the population

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9
Q

what is a mutation

A

DNA variation that is relatively rare in the population

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10
Q

what is the mechanism of inheritance

A

each organism carries two factors that determine together the organisms phenotype
an adult organism can only transmit one of the two factors to each of its offspring

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11
Q

what is Mendels law of segregation

A

when a parent passes one of their two inherited alleles to offspring, these are transmitted with probability 0.5

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12
Q

what is Mendels law of independant assortment

A

alleles located sufficiently far apart (or on different chromosomes) will be inherited independantly of eachother
in families though this depends on physical proximity of loci on the DNA strands

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13
Q

what is Mendels law of dominance

A

interaction between the two alleles of a gene in a given individual such that the dominant allele masks the influence of the recessive allele on the individuals phenotype

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14
Q

outline dominant and recessive disorders

A

dominant - one disease allele required for an individual to get the disease
recessive - two disease alleles are required for an individual to get the disease

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15
Q

what is the first step to identifying disease in genetics

A

family aggregation studies
clustering of disease within families
family history
measured by relative recurrence risk (RRR) or familial risk ratios (FRR)

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16
Q

are family aggregation studies sufficient to infer the importance of genetic susceptibility?

A

no
environmental and cultural influences can aggregate in families and increase risk

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17
Q

what is monogenic

A

one gene with a large effect

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18
Q

what is oligogenic

A

few genes each with a moderate effect

19
Q

what is polygenic

A

many genes each with small effect

20
Q

what is non-classical inheritance?

A

mitochondrial diseases, genomic imprinting

21
Q

what is the purpose of genetic linkage studies

A

associate functionality of genes to their location on chromosomes - find the location of disease genes

22
Q

what is the purpose of genetic association studies

A

find candidate genes or genome regions that contribute to specific disease by testing for correlation between disease status and genetic variation

23
Q

outline linkage analysis

A

large pedigrees each containing affected individuals
tests the hypothesis that a particular locus is linked to a locus that causes disease

24
Q

outline co-segregation of linkage studies

A

co-transmission
of alleles at 2 or more genetic marker loci
alleles at markers close together tend to be transmitted together
there will be correlation between disease alelles and phenotype resulting in co-segregation of alleles at other locus

25
Q

outline genome association analysis

A

determine whether particular genetic variant influences risk of developing disease
is association is present allele will be seen more often than expected
indicates direct or indirect causal relationship. and is a statistical finding

26
Q

what are the main types of genetic association study

A

family based
case/control
total association

27
Q

outline family based genetic association analysis

A

investigate transmission of particular high risk alleles through a number of pedigrees
avoids problem of population heterogeneity

28
Q

outline case/control studies as genetic association analysis

A

compare distribution of alleles or genotype at locus in affected and unaffected people or population-based control sample
easy to collect

29
Q

outline total association studies as genetic association analysis

A

e.g all individuals with quantitative trait
need to account for correlations in genotype and phenotype due to relatedness

30
Q

what does the word linkage refer to

A

the relationship of loci

31
Q

what are genome wide association studies

A

examination of many common genetic variants in a group of individuals to see if any variant is associated with a trait

32
Q

what is linkage disequilibrium

A

correlation between alleles at 2 or more loci that lie close together at population level
occurs due to consideration of population history as in the past everyone had identical haplotypes at any given stretch of DNA
new alleles arise due to rare mutations
over generations LD decays as recombination breaks up haplotype as new mutations occur

33
Q

how do we visualise linkage disequilibrium

A

haplotype blocks
haplotype = set of SNP on single chromatid of chromosome pair which are statistically associated
haplotype blocks = regions over which there is little evidence for historical recombination only few common haplotypes observed

34
Q

outline tagging SNPs

A

if 2 SNP are in strong LD then genotype at SNP2 will be predicted by genotype at SNP1
they can be correlated with disease phenotype
can pick a reduced set of SNPs to genotype that provide us with as much info as the full set

35
Q

what statistic does GWAS provide

A

p value
GWAS requires stringent significance levels to overcome the multiple testing problem when we test too many SNPs

36
Q

what is needed for GWAS to be valid

A

large sample size (1000s of individuals) to have sufficient power and detect a true association

37
Q

what do we expect to see in GWAS at any location showing significant association

A

several SNPs in same region showing association with phenotype due to correlation (LD) between neighbouring SNPs

38
Q

what is used in GWAS to visualise the strength of association

A

Manhattan plots

39
Q

why should we identify environmentally modifiable factors that influence disease risk (mendelian randomisation)

A

it is fundamental to public health improvement strategies

40
Q

outline models of gene environment interaction

A
  1. genotype exacerbates effect of risk factor e.h UV radiation, genetic mutation, skin cancer
  2. risk factor exacerbates effect of genotype mutation, baribiturates, skin irritation
  3. both genotype and risk factor are required
  4. genotype and risk factor influence independantly e.g mutation of clotting factor V Leiden, oral contraceptive pill -> thrombosis
41
Q

what is the gold standard for mendelian randomisation

A

randomised controlled trials
but its expensive and could require very long follow up
not every intervention is ethical

42
Q

outline mendelian randomisation

A

its a method of assessing the causal nature of some environmental exposures in observational studies
based on Mendel’s law of segregation, instead of randomising, populations are separated according to their genetic profile
genetic variation is NOT influenced by life style, geographical or other confounding factors

43
Q

what statistical method is mendelian randomisation

A

it is an instrumental variable (IV) analysis
instrument is a variable that is only related to the outcome through its association with exposure
MR uses genetic variants as IVs

44
Q

what is the future of genetic epidemiology

A

identification of genetic factors affecting disease prognosis
understanding the contribution of different aspects of genetics - copy number variation, epigenetics, rare variants
refine risk estimates
use genes as tools to better understand the environmental processes

Epidemiology (23 decks)

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