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Blair Genetic disease Flashcards

1
Q

How big is the human genome?

A

3300mb/ 21,000 nuclear genes

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2
Q

How many mitochondrial genes?

A

37 genes, 16.6kb

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3
Q

What proportion of the genome is exonic?

A

2.5%

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4
Q

What does extragenic DNA consist of?

A

mostly repetitive sequences

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5
Q

What length of extragenic repeat is significant to implicate disease?

A

1x10^5

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6
Q

What are the 2 types of DNA repeat?

A

tandem and interspersed

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7
Q

What is polymorphic DNA?

A

DNA that varies between individuals

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8
Q

What are the classes of tandem DNA repeat?

A

satellite repeats, microsatellites, minisatellites

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9
Q

Where do minisatellites exist?

A

telomeres

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10
Q

Where do satellites exist?

A

heterochromatin

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11
Q

What size are microsatellites?

A

mostly dinucleotides (STRs)

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12
Q

Where are microsatellites found?

A

All chromosomes

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13
Q

What are VNTRs?

A

Variable number tandem repeats- minisatellites

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14
Q

What are microsatellites also known as?

A

STRs

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15
Q

Which type of tandem repeat has most repeats?

A

STR

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16
Q

What can polymorphisms be used to detect?

A

Paternity, forensics, inheritable disease

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17
Q

How are VNTRs detected?

A

restriction fragment polymorphisms change length in electrophoresis and southern blotting. Multi-locus probes detects many related sequences of different lengths. Single Locus Probes detect adjacent sequences for high specificity- sequencing for copy number

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18
Q

What are the failures of SLP probing?

A

Allele drop out caused by PCR of low copy numbers, easily contaminated

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19
Q

What are SNPs?

A

Single nucelotide polymorphisms.

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20
Q

Mismatch probes will not anneal in high stringency conditions…

A

T close to Tm, low salt

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21
Q

How are SNPs directly detected?

A

Oligonucleotide Ligation Assay, Amplification Refractory Mutation System, Single Stranded Chain Polymorphism.

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22
Q

How does OLA work?

A

2 probes, common probe fluoresces to detect with capillary electrophoresis. Ligates if mutant probe has 3’ complementary base. Varying length Polyethoxy tail for normal and mutant

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23
Q

Which detection of SNPs requires a known mutation?

A

OLA ARMS

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24
Q

How does ARMS work?

A

Primer has 3’ mutant and extension only if mutant present due to altered Tm

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25
Does SSCP require a known SNP?
No
26
How does SSCP work?
PCR amplification. Secondary structure lost after heating and cooling to increase PAGE migration
27
What techniques are used in clinical diagnostics?
high throughput: capillary electrophoresis, fluorescence/chemiluminescence, solid phase capture
28
What are the high throughput methods used to detect sequences?
Taqman, SybrGreen, Lux, qPCR, molecular beacons, scorpion probes, sp FRET, DGGE, gene chips
29
How does Taqman probes work?
Fluoresce when displaced by Pol 2
30
How does qPCR work?
fluorescent nucleotides extend proportional to starting DNA concentration
31
How do Lux probes work?
Fluoresce when extended
32
What does SybrGreen bind?
non specific for dsDNA
33
How do molecular beacons work?
annealing releases quencher for fluorescence
34
How do scorpion probes work?
Molecular beacon attached to PCR primer. amplification causes self annealing and releases quencher
35
How does spFRET work?
OLA with 2 fluorophores, ligation, denaturation, produces secondary structure for FRET
36
How does DGGE work?
Progressive denaturation of discrete domains produces single strand which anneals to gel. separates oligonucleotides, small DNA fragments, PCR products
37
How are gene chips synthesised?
3'-5' on using light to block addition of nucleotides. Can be made to any sequence.
38
What do microarrays do?
different regions for each mutant, fragment annealing can be detected for complementary sequence
39
Why is sequencing not used?
expensive to sequence whole genome
40
When is sequencing used?
for small fragments, detected by RNA bait on strepatividin beads
41
What is first generation sequencing?
Sanger/dieoxy NTP sequencing uses termination, electrophoresis then colour reading
42
What are the types of second generation sequencing?
Illumina, Roche, ABI
43
How does Illumina sequencing work?
fluorescent reversible terminators
44
How does Roche sequencing work?
PCR amplification releases PPi for ATP for luciferase. one base at a time.
45
How does ABI sequencing work?
Fragment bound to bead with P1 primer tag. Mutating primer gives sequence by moving along fragment
46
What is gene therapy?
Deliberate introduction of nucleic acids into human somatic cells for therapeutic, prophalatic or diagnostic purposes
47
What does gene therapy treat?
Single locus gene defects, eradicate tumour growth, stimulate immune response or control autoimmune disease
48
Why are vectors needed for gene therapy?
Cells are resistant to free nucleic acids. Targetting of specific cell types.
49
What are the 2 main types of Gene therapy vectors?
liposomes and viruses
50
How do liposomes bind DNA?
Phosphates bind on outside of weakly cationic phospholipids.
51
What are the advantages of liposomes?
No immunological response allows multiple treatments. Can administer large genes.
52
What are the disadvantages of liposomes?
Poor targetting, poor uptake and poor delivery into the nucleus. Epichromosome is less stable.
53
What are the advantages of viral vectors?
Efficient targetting and entry
54
What are the 3 modes of viral DNA containing?
Sustained integrated; Non-integrating transient; non-integrating sustained
55
Which type of DNA incorporation in viral vectors is most common?
integrating
56
What are the disadvantages of viral vectors?
Produce inflammation. Transient requires multiple administrations but immune response. Integrating can disrupt host genes. Expensive to produce replication deficient species.
57
What are the integrating viral vectors?
reteroviruses and adeno-associated viruses
58
How do reteroviruses carry genes for therapy?
RNA for reverse transcriptase inserted into dividing cells
59
Why are reteroviruses replication deficient?
No PS1 coat protein. (produced in packaging cells)
60
When do adeno-associated viruses become active?
Insert ssDNA into Chromosome 19 in presence of adenovirus.
61
What type of viral vector is Herpes?
A sustained, non-integrating
62
Why is herpes virus used?
Many non-essential genes, latent infection established in non dividing cells evades immune response
63
What do adeno-associated viruses treat?
occular disease
64
What do herpes virus treat?
Neurological disease
65
What type of vector is Adenovirus?
An integrating viral vector
66
What cells does adenovirus target?
non-dividing epithelial cells (51 total targets)
67
Which genes of adenovirus are used as vector?
E1A/B for growth and activation of packaging late genes, E3. Replacement with insert up to 10kb.
68
How is adenovirus produced?
E1A constitutively expressed in 293 packaging cells
69
How does adenovirus target cells?
fibre structure within capsid: CAR receptor D1 domain bound by knob, penton RGD motif binds integrins.
70
How has adenovirus been modified for second generation therapies?
ONYX-015 targets p53 deficient cells, E2 DNA binding protein replacement is replication defiecient, "gut" viruses have only terminal repeats requiring cotransfection modification of fibre for novel receptors
71
How is gene therapy administered in vivo?
intravenous, topical, direct, nebulisation
72
Which disorder has been treated by ex vivo gene therapy?
SCID treated with reterovirus using cytokine receptor subunit, but random integration upregulated transcription factors causing leukaemia.
73
What barriers are there for adenovirus?
CAR in tight junctions (growth inhibitor), loss of CAR (tumour supressor) in cancer, immune response
74
Why is lentivirus a better viral vector?
Reterovirus can target non dividing cells, 3 genes for simple modification

Health and Disease: Genes (6 decks)

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