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Flashcards in Sudbery - Human Genetics Deck (81)
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1
Q

describe the differences in genetic diseases in foetuses, babies and children, and adults and the elderly

A

Foetuses: Up to 50% of all conceptions result in miscarriage
- Chromosomal defects not compatible with life
New-born babies and children: 0.1% chromosomal eg Downs Syndrome
~5-6% single gene rare diseases
Mitochondrial
Adults and the elderly: Common diseases
Genetic and environmental
Many alleles
Complex

2
Q

explain the phrase ‘genetic disorders are individually rare but collectively common’

A

each individual genetic disorder is by itself rare, however collectively, genetic diseases are common.

3
Q

what pattern of inheritance do single gene disorders follow?

A

mendelian inheritance

4
Q

state the differences in single gene disorders and complex disorders

A
Single gene disorders:
Simple ‘Mendelian’ Inheritance
Individually rare but collectively common
High penetrance 
Tests are predictive
Alleles at single genes
Complex diseases and phenotypic traits:
Runs in families, no simple inheritance pattern
Common
Influenced by environment 
No reliable tests yet
Susceptibility not deterministic
Risk alleles at many polygenes
5
Q

how many kb long is mitochondrial DNA?

A

16

6
Q

what are the problems associated with mitochondrial disorders?

A
Multi system failures:
Basal ganglia of brain
Heart
Endocrine system, especially pancreas
Sight and hearing
Skeletal muscles
7
Q

define heteroplasmy

A

A mixture of wild-type and mutant mitochondrial DNA within the cell.

8
Q

what is the effect of heteroplasmy in a mother’s children?

A

as mtDNA is maternally inherited when a mother has heteroplasmy it can result in variable phenotypes (severity) within offspring or within one organism.

9
Q

what is the significance between the disease phenotypes of damaged mtDNA and aging?

A

mtDNA damage results in multisystem failures eg sight/hearing loss. This is similar to the effects of aging, this suggests that the accumulation of mtDNA damage may be involved in aging.

10
Q

how many base pairs are there in the human genome? what % of the genome is protein encoding sequence? how many protein encoding genes are there?

A

3.2gb (3.2x10^9) bp
protein encoding sequence: ~1.1% genome
~20,500 protein encoding genes

11
Q

at what point in protein synthesis are genes spliced?

A

genes transcribed into primary mRNA. this undergoes splicing to form mature mRNA which is then translated (mostly)

12
Q

describe the significance of NGS in genome sequencing

A

NGS takes a few hours and is less than $1000
100,000s genomes now being sequenced
Whole genome sequencing massive amount of info
Whole exome sequencing just the protein encoding sequences (1% of the whole genome)

13
Q

describe the different types of single gene disorders (ie sex-linked/autosomal etc)

A
1) autosomal recessive 
(both copies are defective and the parents are unaffected heterozygotes
2) autosomal dominant
One copy of the gene mutant
Gain of function or haploinsufficient 
50% transmission from affected parent
But often occur de novo
3) Sex-linked
Generally only affects boys passed on through the female line (X-linked)
14
Q

what is a de novo mutation?

A

A genetic alteration that is present for the first time in one family member as a result of a mutation in a germ cell of one of the parents, or a mutation that arises in the fertilized egg itself during early embryogenesis.

15
Q

describe the class III, IV and VI cystic fibrosis mutations and the medication that treats them

A

Class III: reduced gating - the CFTR gate is closed (Gly551Asp; Phe508del)
Class IV: reduced conductance (restriction of movement of Cl- through channel)
Class VI: high surface turnover (Phe508del) (CFTR internalised and degraded too rapidly)
Medication:
Potentiators - Ivacaftor (forces the gate to be open)

16
Q

describe the class II cystic fibrosis mutations and the medication that treats them

A

Class II: Misfolded and degraded (Phe508del) Correctors - Lumacaftor (correct folding)

17
Q

describe the class I and V cystic fibrosis mutations and the medication that treats them

A

Class I: no CFTR (Gly542X)
Could get ribosome to not read STOP - would result in protein that works slightly
Class V: v low CFTR levels (3849 + 10kb C→T mutation 10kb into intron affects splicing)
Medication:
Production correctors - Ataluren

18
Q

what is Orkambi?

A

a combined drug therapy of lumacaftor and ivacaftor

which may be a more effective treatment for CF

19
Q

what is NICE and what do they do?

A

The National Institute for Health and Care Excellence

they weigh benefit of cost and effectiveness with drugs

20
Q

what is ‘standard of care’ and how is it used in drug trials?

A

SOC (standard of care): the treatments already available - what you compare new treatment to

21
Q

what is ppFEV?

A

predicted forced expiratory volume

22
Q

define: annual rate of exacerbations

A

how often patients have to go into hospital due their condition and its related conditions

23
Q

define quality-adjusted life years and explain how its used in drug trials

A

how many (good quality) years the patient survives for (has to be economically viable, eg incremental cost-effectiveness ratio (ICER) (£/QALY) has to be

24
Q

describe the results of trials with ivacaftor and CF, how much it costs and who the treatment is approved for

A

~5% of CF patients have the mutation(s) that can be treated by Ivacaftor
Trials show 10% increase in ppFEV and a reduction to half in the rate of exacerbations, reduced sweat salt concs, reduced Pseudomonas infections and improved QoL
Costs:
- $30,000
- ICER £335-1,274,000
- Treatment approved in 2016 for children 2-5

25
Q

what are the symptoms and associated problems with CF?

A

Symptoms:
thick, dehydrated mucous
chronic inflammation, overproduction of elastase and irreversible lung damage
Associated problems:
repeated bacterial infections by Staphylococcusaureus, Pseudomonasauruginosa
Pancreatic exocrine deficiency, diabetes, Congenital Bilateral absence of the vas deferens, congenital bowel obstruction, salty sweat (this can be used in diagnostics)

26
Q

what are the majority of CF mutations

A

Phe508del

~15 mutations responsible for 1/2 remaining cases among Europeans

27
Q

what does the CFTR do?

A

pumps Cl- ions across the plasmamembrane

28
Q

what is the effect of the CFTR not pumping out Cl- ions?

A

Cl- stays in the cell, H2O enters the cells for osmoregulation. this means the pericillary layer isnt as large and the mucus on top of this cannot move

29
Q

name 5 methods of treating the symptoms of CF

A
physio
DNAse to reduce mucus viscosity
antbiotics
anti-inflammatories (eg steroid)
mannitol spray to increase osmolarity of mucus
30
Q

name 2 gene therapies for treating CF and the problems with each

A
viral vectors (uses virus to insert WT allele) - immune response prevents repeated therapy
Liposomes - innate response to CpG (modified nucleotide) in vector
31
Q

describe the trait pattern of Huntington’s disease, its incidence and its effects

A
late onset autosomal dominant
incidence 1;6700
movement disorder - chorea
personality changes
cognitive decline
weight loss
32
Q

describe the neuropathology of Huntington’s disease

A

in the corpus striatum:

  • neuronal death
  • generalised atrophy
  • general brain shrinkage
  • multisystem CNS disorder
33
Q

when was the Huntington’s gene mapped and cloned?

A

mapped: ‘84
cloned: ‘94

34
Q

what is the mutation that causes Huntington’s disease?

A

trinucleotide repeat expansion in ORF
CAG repeated 6-35: normal
CAG repeated 40 times: adult onset
CAG repeated 70 times: juvenile onset

35
Q

what does CAG encode? what is the effect of the expansion of this trinucleotide

A

glutamine - expanded forms insoluble protein inclusion body

36
Q

what is the most abundant body tissue?

A

muscle

23%♀, 40%♂

37
Q

what is the age of onset for Duchenne Muscular Dystrophy (DMD)

A

3-5yrs
wheelchair bound by 12
<30yrs die of respiratory failure

38
Q

describe the morphology of skeletal muscle

A
cells called fibres run length of muscle
striated appearance (orderly arrangement of actin and myosin)
39
Q

how big is the DMD gene? which protein does it encode? what does this protein do? is it sexlinked or autosomal? what are most mutations? what is BMD and name its mutation

A

V large (2.4Mb) - 79 exons
Encoded protein called dystrophin
Dystrophin links F-actin to sarcolemma which is attached to basal lamina
Sarcolemma can’t repair damage => muscle degradation
sex-linked (on X-chromosome)
Most mutations are newly arisen deletions (exon deletions => frameshift => nonsense)
Exon 45 or 47 missing (PCR test shows this)
Becker Muscular Dystrophy: no frameshift ∴ no nonsense

40
Q

describe antisense oligonucleotide treatment for DMD

A

Morpholino - chemically modified AON that base-pairs with mRNA so it can’t be translated
In DMD pre-mRNA the exons 49-50 can be removed which leads to a premature STOP codon (in exon 51), producing a frameshift mutation and therefore no dystrophin
If exon 51 is also removed then a shortened but functional dystrophin protein is produced

41
Q

are there many or a few undocumented single gene disorders?

A

OMIM catalogues 8575 suspected Mendelian phenotypes of which 5225 are known at a molecular level. There may be many more that aren’t documented.

42
Q

why identify variants (mutations) responsible for a single gene disorder?

A

Stopping repeated, invasive, distressing medical tests
Introducing appropriate treatment and stopping inappropriate treatment
Psychological benefits to affected and family
Scientific knowledge

43
Q

describe the issues with allelic heterogeneity in diagnosing a disorder

A

Allelic heterogeneity: a similar phenotype is produced by different alleles within the same gene
therefore we don’t know the exact mutation that has caused the disease - this can be problematic in working out whether parents will pass on a disease to their children (2 diff mutations = no disease)

44
Q

what is atypical disease presentation and how is it problematic in diagnosis?

A

phenotype is different to normal disease phenotype - the common symptoms/signs lead you to believe its another disease = incorrect tests therefore no evidence of disorder

45
Q

explain why novel variants in a known gene are problematic in diagnosis

A

patient presenting with a disease may have a new/unknown mutation therefore the tests will no give proof of disorder

46
Q

why choose whole exome sequencing and not whole genome sequencing when diagnosing diseases? name a disadvantage of this

A

Mendelian disorders so far are all in coding sequence
CF complex disease variants nearly all outside coding sequence
Mutation in exon disrupts splicing downstream
Cheaper
Fewer variants to analyse
WES will miss some causative alleles and WGS is becoming increasingly feasible

47
Q

how can a causative variant of a SGD be identified after whole exome sequencing?

A

each individual will show ~20,000 variants after WES so:
Predicted effect on protein function
Disease allele will be rare – use population databases to see if this is the case
Pedigree information
Same allele in unrelated individuals with same disorder
Expert appraisal of biological relevance to disorder phenotype - (Recapitulation (the repetition of an evolutionary or other process) in model system/organism)

48
Q

how can predicting the deleterious effect on protein function help in identifying the causative variant of a SGD?

A

Likely to lead to LoF: frameshift (FS), protein terminating variant (PTV), splice sites, exon deletion (how will that change the function eg polar substitution in transmembrane domain)
Sequence conservation across organisms
Assessed by computer programs - computer can list variants that may cause disease

49
Q

how can the exome aggregation consortium help in identifying the causative variant of a SGD?

A

60,000 exomes and is used to identify v rare alleles
We all carry 100s of potentially harmful mutations
Population frequency – identify which alleles are very rare and which potentially harmful alleles occur frequently in apparently healthy individuals.
- Size of database is key in determining this

50
Q

how can pedigree information help in identifying the causative variant of a SGD?

A

Allows a comparison in known genetic trait patterns
Recessive
- May be compound heterozygote (2 different mutant alleles at a particular gene locus 1 on each chromosome)
- Heterozygous parents
- Heterozygous siblings not affected
Consanguineous
- Same allele in each gene
- Only affected members of pedigree are homozygous
De novo dominant
- New allele mutation in gamete
- Not present in either parent

51
Q

briefly describe the case study of the consanguineous autosomal recessive disease (include: her symptoms/her treatment/whether it was successful/the mutation she carried)

A

16yr old Saudi Arabian girl with complex symptoms shared with a total of 8 consanguineous relatives
Suggestive of complex neurotransmitter disorders:
- Dopamine: Parkinson’s symptoms, couldn’t walk, global development delay, decreased muscle tone
- Serotonin: sleep and mood disturbance
- Epinephrine – diaphoresis, temperature instability
Neurotransmitter levels normal, but dopamine breakdown products elevated in urine
Was treated by increasing dopamine levels – immediate worsening of condition
A 3.2Mb region of homozygosity was found:
- 8 genes in homozygous region, 1 gene associated with neurotransmitter function (transmembrane protein)
- Identified p.pro387leu (p. = protein location, 387th protein has been substituted) mutation in SLC18A2 encoding the VMAT2 dopamine transporter
- Highly conserved residue
- Homozygous in all affected but not in unaffected
- Not in >1000 patients with Parkinson’s

52
Q

what does VMAT2 do? in the consanguineous relationship case study how was the patient treated?

A

VMAT2 transports serotonin and dopamine into presynaptic vesicles
Expressed WT and mutant VMAT2 in tissue culture – reduction in activity in mutant VMAT2
Treatment with dopamine receptor agonist (chemical that binds to a receptor and activates it):
- Resulted in dramatic improvement in the patient within 7 days and maintained for 32 months

53
Q

describe the characteristics of a complex disease. give 2 other names for a complex disease

A

Relatives of affected have higher than population risk but no Mendelian inheritance
- Familial
Common major diseases
Complex genetic and environmental factors and complex interactions between and within each
2 other names:
- Multifactorial
- Polygenic

54
Q

state the evidence for and against psychiatric disorders being genetic

A

44 risk variants for major depression
But only explains 1.9% of the population variation in liability
Top decile of risk variant profile 2.4x more likely to suffer depression than the bottom decile
Genes identified enriched in brain function and overlap with genes associated with other psychiatric disorders
Families share same genes but also the same environment, need to distinguish between these

55
Q

define heritability

A

The amount of the observed variance in a population that can be attributes to genetic variance

56
Q

how can phenotypic variance be calculated?

A

phenotypic variance = genetic variance + environmental variance

57
Q

give the equation to work out total genetic variance/broad sense heritability (H2)

A

genetic variance / (genetic variance + environmental variance)

58
Q

name the 3 components that make up genotypic variance

A

G = A + D + I
additive (A): the mean of 2 expressed alleles (eg tall allele + short allele = medium)
dominance (D): interaction between alleles that results in phenotypic expression that is not purely additive
interaction/epistasis (I): interactions between genes at different loci that act on the same characteristic

59
Q

give the equation to work out narrow sense heritability/additive genetic variance (h2)

A
h2 = A/P
h2 = A/(A+D+E)
60
Q

how can we estimate heritability in a human context?

A

use of identical and non-identical twin studies

61
Q

define monozygotic and dizygotic twins

A

MZTs – monozygotic twins – identical

DZTs – dizygotic twins – non-identical

62
Q

describe the ACE model in studying twins

A

ACE model:

  • Additive variance A
  • Common environment C
  • Non-shared environment E
63
Q

give the correlation due to genetics; due to common environment and due to non-shared environment for MZTs

A

Correlation due to their genetics = 1 (same genetics)
Correlation due to their common environment = 1 (same environment)
Correlation due to their non-shared environment

Phenotype of MZTs (rMZ) = A+C

64
Q

give the correlation due to genetics; due to common environment and due to non-shared environment for DZTs

A

Correlation due to their genetics = 0.5 (50% same genes)
Correlation due to their common environment = 1 (same environment)
Correlation due to their non-shared environment

Phenotype of DZTs (rDZ) = 0.5(A+C)

65
Q

what is the equation that gives A (additive variance) using the phenotype values of MZTs and DZTs

A

Additive variance = 2(rMZ - rDZ)

66
Q

give the equation to work out E (non-shared env)

A

E = 1-rMZ

67
Q

what are association studies?

A

population studies
answers the question: Is there a particular allele that is more frequent in a population of cases (of disease) compared to a population of controls (not affected)?
not looking for an exact correlation, looking for small numbers

68
Q

what are SNPs?

A

single nucleotide polymorphisms - single base changes in individuals

69
Q

what is the minor allele frequency? what value does the MAF have to be to be considered a common allele?

A

The frequency of the SNP’s less frequent allele in a given population.
common = MAF >5%
MAFs used in HapMap project

70
Q

name the 2 major alleles for complex disease

A

apolipoprotein E ε4

HLA locus DQβ1 self/non‐self

71
Q

describe the effect of the presence of the ε4 allele

A

allele increases risk of Alzheimer’s disease

  • Transports lipids round the bloodstream
  • 16% gene pool have the ε4 allele that codes for apolipoprotein E
  • 1 copy = 3x risk of general population
  • 2 copies 8x population risk
72
Q

describe the effect of the presence of the HLA locus DQβ1 allele

A

Allows immune system to differentiate between self and non-self – protein presented on cell surfaces

  • Reside 57 Asp–>any other a/a = greatly increases risk of Type I diabetes
  • 1 copy 6x population risk
  • 2 copies 18x population risk
73
Q

describe Genome Wide Association Studies

A

Identify panel of SNPs that span the genome ~1 million
Assemble a set of cases and unaffected controls
- Each subject examined for 1 million SNPs
- Microarrays or DNA chips (not genome sequencing) – specifically examine 1 million different positions in genome
Identify SNPs that have a higher frequency in the cases compared to controls.
- The SNP is associated with the disease
- The SNP is unlikely to be the causative allele – it marks the region of the genome where the real risk allele is located

74
Q

what is the value for genome-wide significance? how was this value reached?

A

genome-wide significance p value = <10^-8
Nominal significance: result less than 1 time in 20 by chance (p=<0.05)
Each SNP = independent test
So million SNPs expect 10^6/20 = 50,000 false positive

75
Q

what is the problem with using the genome-wide significance value? how can this be partially overcome?

A

false negatives

use a massive sample size - the smaller the risk allele contributes the more subjects needed (meta-analysis used)

76
Q

how is the risk of an allele measured in GWAS?

A

using the odd ration (OR)
Most risk alleles OR<1.2
OR=1.2, 12 people with risk allele result in 10 people with disease

77
Q

name the 2 genes and 1 gene family that when mutated increases the risks of breast cancer. how much does each mutation increase risk?

A

5% cases due to BRCA1/2 autosomal dominant alleles
- 60-85% risk (10-50x pop risk)
- High risk ovarian cancer
Other rare alleles with high risk (10x pop risk)
- Eg Li Fraumeni syndrome (TP53)
Genes in DNA repair pathway
- Moderate effect 2-4x pop risk

78
Q

describe a Manhattan plot

A

Chromosome number along the bottom (autosome)
Each dot on the graph represents a SNP
The y-axis is the probability that the SNP is more common in cases compared to controls (-log of P value)
p=0.05 (nominal significance) covers a large number of SNPs
p=10^-8 (genome-wide) covers a small number of SNPs

79
Q

what is genetic ‘dark matter’? how does it relate to GWAS?

A

the genetic material that is unknown or poorly understood. GWAS only explains a maximum of 20% of genetic variance

80
Q

describe the law of diminishing returns in relation to the GWAS

A

as you have more subjects you have more power to detect those contributing SNPs, but there is a point at which number of subjects won’t influence the number of SNPs detected

81
Q

what is a possible cause for the lack of genetic variance shown by GWAS?

A

V large number of risk alleles each with a v small effect
Can show the existence of more risk alleles in the grey area (between genome-wide threshold and nominal significance) of the probability spectrum, but can’t distinguish genuine alleles from false positives