Medical Genomics > Module > Flashcards

Module Flashcards

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1
Q

What is a nucleosome?

A

Unit of chromatin- DNA wound around 8 histone

proteins 1.65 times

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2
Q

What charge are histones?

A

positive

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3
Q

What charge is DNA and why?

A

negative, due to the phosphate groups

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4
Q

What is the function of H1?

A

stabilising chromatin in higher order chromosomal structures e.g. 30 nm fibres of chromatin

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5
Q

Name 2 mechanisms to make chromatin more accessible:

A
  • Histone modifications e.g. HATs

- chromatin remodelling complexes

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6
Q

What are HATs and HDACs?

A
  • Histone Acetyl Transferases

- Histone Deacetylases

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7
Q

What do HATs do?

A

transfer acetyl groups to histones,associated with euchromatin, linked to increased gene expression

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8
Q

What do HDACs do?

A

remove acetyl groups from histones, allow histones to wrap more tightly, less accessible

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9
Q

What are the 3 stages of Transcription?

A

Initiation
Elongation
Termination

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10
Q

What does RNA Pol I transcribe?

A

rRNA

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11
Q

What does RNA Pol II transcribe?

A

mRNA

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12
Q

What does RNA Pol III transcribe?

A

tRNA

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13
Q

What happens in transcription initiation?

A
  • RNA pol and transcription factors bind to promoter
  • form a closed pre-initiation complex
  • complex opening separates 2 DNA strands and moves template strand to active site of RNA Pol
  • Abortive synthesis
  • Promoter escape
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14
Q

What happens in transcription elongation?

A
  • RNA pol travels along template DNA strand in 5’ to 3”
  • Synthesises RNA strand 5’ to 3’
  • Transcription bubble
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15
Q

In Transcription, what 2 sequences is the cleavage site found between?

A

AAUAAA - upstream

GU- rich - Downstream

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16
Q

How is transcription terminated when the cleavage sequences have been transcribed?

A
  • CPSF binds to AAUAAA
  • CstF binds to GU-rich
  • Forms protein complex
  • CPSF cleaves downstream of AAUAAA site
  • Poly(A) polymerase adds a 3’ polyA tail
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17
Q

List 3 aims of the 100,000 genomes project:

A
  • Increase understanding of genetic variants -> new treatments
  • Bring about personalised medicine
  • Greater understanding of genomic medicine benefits
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18
Q

What are the aims of the gnoMAD project?

A
  • Bring together exome and genome sequencing data from large scale sequencing projects
  • Summarise data for wider scientific community
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19
Q

What are the aims of the EXAC project?

A

To create a browser to display large population datasets of genetic variation and display gene variation

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20
Q

What Biochemical evidence shows that the non-coding

genome is important?

A
  • Pervasive Transcription

- Functional genomic elements

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21
Q

What Genetic Evidence shows that the non-coding genome is important?

A
  • GWAS
  • Non-coding mutations -> mendelian disease
  • higher non-coding conservation across mammalian evolution
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22
Q

What is a silencer?

A

combination of short DNA sequence elements that suppress transcription of a gene

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23
Q

What is an insulator?

A

DNA element that acts as a barrier or a blocker of enhancers

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24
Q

What is an enhancer?

A

short region of DNA that can be bound by activators to increase the likelihood of a gene being transcribed

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25
How do enhancers increase gene expression?
promoter-enhancer loops | allow transfer of regulatory elements (TF's) over a long distance
26
Give 4 reasons why it is hard to identify enhancers:
- found at various distances from target promoter - found/regulate upstream and downstream genes - scattered across 98% of the genome - many enhancers not evolutionarily conserved
27
What is gene panel sequencing?
targeted sequencing to detect changes in a selected panel of genes known to cause the phenotype
28
What is Clinical Exome Sequencing?
targeted sequencing of exons of known disease genes
29
What is Whole Exome Sequencing?
sequencing of all exons of all genes
30
How many disease causing variants are found within Exons?
>85%
31
What are the 2 Purine bases?
A | G
32
What are the 2 Pyramidine bases?
T | C
33
What type of mutation are 'point mutations'?
Base Substitution
34
What are Transition point mutations?
purine substituted for another purine | pyramidine substituted for another pyramidine
35
What are Transversion point mutations?
purine substituted to pyramidine (vice versa)
36
What is a silent mutation?
mutation that results in a synonymous codon | amino acid sequence stays the same
37
What is a missense mutation?
base substitution resulting in a different codon
38
What are the 2 types of missense mutations?
conservative (similar structure+function) | non-conservative (different structure+properties)
39
What is a nonsense mutation?
base substitution resulting in a stop codon
40
What are deletions?
deletion of one or more base pairs deleted from DNA sequence | causes altered translational frame
41
What are insertions?
insertions of additional base pairs, if it's not a multiple of 3 then causes frameshift
42
What are INDEL mutations?
length difference between 2 alleles and can't be known if it's due to an Insertion or Deletion
43
How long is the mitochondrial genome?
16,569 bp's
44
List 3 features of mtDNA?
- double stranded - circular - encodes 37 genes
45
what is the mutation rate in mtDNA?
1/33 generations
46
What is Heteroplasmy?
The presence of more than one organellar genome within a cell/individual
47
What are the risks of mitochondrial transfer procedures?
- mtDNA carryover - technicality of procedure - operator dependent - virsuses used (karyoplast removal)
48
What are the + and - of Polar body mitochondrial transfers?
+ easier to obtain polar bodies + simple procedure-> micropipette + lower mtDNA carryover - more invasive
49
What ae the relative risks of mTDNA carryover in mitochondrial transfer procedures?
PB1T
50
What is linkage disequilibrium?
The non-random association of alleles at different lociu
51
How can you tell when linkage disequilibrium has occurred?
When 2 alleles are inherited together more often than you'd expect by chance
52
What are 3 characteristics of mendelian disorders?
- Rare - Specific pattern of inheritance - Caused by pathogenic variant
53
List 6 limitations of GWAS studies?
- Large sample size needed - Effect sizes are small - Causal pathway not always determined - SNPs aren't responsible for all variation e.g. CNVs - Limited ethnic studies - Pleiotropy common (variants associated with multiple traits)
54
What is Y chromosomal testing useful for?
for ancestry DNA testing in men
55
What is mitochondrial DNA testing useful for?
determining maternal lineage
56
What are Short Tandem Repeats?
small sequences of the genome that are repetitive and relatively spaced out. Primer site son wither side are the same but no. of repeats between them varies
57
what characteristic of mtDNA makes it ideal for studying relationships between individuals?
Hypervariable region DNA lasts longer - double membrane Constant mutation rate
58
List 4 uses of autosomal testing:
- paternity - Relationship e.g. siblings - DNA fingerprint test - Inherited Disease
59
In genetic testing, what do 12-18 markers show?
proves non-relationship
60
In genetic testing, what do 23-26 markers show?
non-relationship
61
In genetic testing, what do 37-43 markers show?
family markers become clean (e.g. cousins, 2nd cousins)
62
In genetic testing, what do 67 markers show?
perfect matches-> related
63
List 4 disadvantages of DTC Genetic Testing?
- false positives are common - upsetting results - little oversight/regulation of companies (privacy) - Cause decisions based on incorrect info
64
List 4 advantages of DTC Genetic Testing?
+ promotes awareness of disease (better choices) + personalised health info + cheap + further medical genomics research
65
What percentage of cancer is sporadic?
80-90% (somatic mutations)
66
What percentage of cancer is hereditary?
5-10% (germline mutations)
67
What are driver mutations in cancer?
changes to a gene that drive cancer mutation
68
What are passenger mutations in cancer?
Mutations that don't do anything to affect the cancer phenotype
69
In cancer, what can RT-qPCR be used for?
- Diagnosis + monitoring response to treatment of CML | - Recurrence risk in breast cancer
70
What is OncotypeDX?
Genomic test that analyzes the activity of a group of genes that can affect how a cancer is likely to behave and respond to treatment
Medical Genomics
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