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Medical Genomics > Module > Flashcards

Module Flashcards

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USMLE® Step 1 flashcards
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
Q

How do enhancers increase gene expression?

A

promoter-enhancer loops

allow transfer of regulatory elements (TF’s) over a long distance

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26
Q

Give 4 reasons why it is hard to identify enhancers:

A
  • found at various distances from target promoter
  • found/regulate upstream and downstream genes
  • scattered across 98% of the genome
  • many enhancers not evolutionarily conserved
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27
Q

What is gene panel sequencing?

A

targeted sequencing to detect changes in a selected panel of genes known to cause the phenotype

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28
Q

What is Clinical Exome Sequencing?

A

targeted sequencing of exons of known disease genes

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29
Q

What is Whole Exome Sequencing?

A

sequencing of all exons of all genes

30
Q

How many disease causing variants are found within Exons?

A

> 85%

31
Q

What are the 2 Purine bases?

A

A

G

32
Q

What are the 2 Pyramidine bases?

A

T

C

33
Q

What type of mutation are ‘point mutations’?

A

Base Substitution

34
Q

What are Transition point mutations?

A

purine substituted for another purine

pyramidine substituted for another pyramidine

35
Q

What are Transversion point mutations?

A

purine substituted to pyramidine (vice versa)

36
Q

What is a silent mutation?

A

mutation that results in a synonymous codon

amino acid sequence stays the same

37
Q

What is a missense mutation?

A

base substitution resulting in a different codon

38
Q

What are the 2 types of missense mutations?

A

conservative (similar structure+function)

non-conservative (different structure+properties)

39
Q

What is a nonsense mutation?

A

base substitution resulting in a stop codon

40
Q

What are deletions?

A

deletion of one or more base pairs deleted from DNA sequence

causes altered translational frame

41
Q

What are insertions?

A

insertions of additional base pairs, if it’s not a multiple of 3 then causes frameshift

42
Q

What are INDEL mutations?

A

length difference between 2 alleles and can’t be known if it’s due to an Insertion or Deletion

43
Q

How long is the mitochondrial genome?

A

16,569 bp’s

44
Q

List 3 features of mtDNA?

A
  • double stranded
  • circular
  • encodes 37 genes
45
Q

what is the mutation rate in mtDNA?

A

1/33 generations

46
Q

What is Heteroplasmy?

A

The presence of more than one organellar genome within a cell/individual

47
Q

What are the risks of mitochondrial transfer procedures?

A
  • mtDNA carryover
  • technicality of procedure
  • operator dependent
  • virsuses used (karyoplast removal)
48
Q

What are the + and - of Polar body mitochondrial transfers?

A

+ easier to obtain polar bodies
+ simple procedure-> micropipette
+ lower mtDNA carryover

  • more invasive
49
Q

What ae the relative risks of mTDNA carryover in mitochondrial transfer procedures?

A

PB1T

50
Q

What is linkage disequilibrium?

A

The non-random association of alleles at different lociu

51
Q

How can you tell when linkage disequilibrium has occurred?

A

When 2 alleles are inherited together more often than you’d expect by chance

52
Q

What are 3 characteristics of mendelian disorders?

A
  • Rare
  • Specific pattern of inheritance
  • Caused by pathogenic variant
53
Q

List 6 limitations of GWAS studies?

A
  • 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
Q

What is Y chromosomal testing useful for?

A

for ancestry DNA testing in men

55
Q

What is mitochondrial DNA testing useful for?

A

determining maternal lineage

56
Q

What are Short Tandem Repeats?

A

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
Q

what characteristic of mtDNA makes it ideal for studying relationships between individuals?

A

Hypervariable region
DNA lasts longer - double membrane
Constant mutation rate

58
Q

List 4 uses of autosomal testing:

A
  • paternity
  • Relationship e.g. siblings
  • DNA fingerprint test
  • Inherited Disease
59
Q

In genetic testing, what do 12-18 markers show?

A

proves non-relationship

60
Q

In genetic testing, what do 23-26 markers show?

A

non-relationship

61
Q

In genetic testing, what do 37-43 markers show?

A

family markers become clean (e.g. cousins, 2nd cousins)

62
Q

In genetic testing, what do 67 markers show?

A

perfect matches-> related

63
Q

List 4 disadvantages of DTC Genetic Testing?

A
  • false positives are common
  • upsetting results
  • little oversight/regulation of companies (privacy)
  • Cause decisions based on incorrect info
64
Q

List 4 advantages of DTC Genetic Testing?

A

+ promotes awareness of disease (better choices)
+ personalised health info
+ cheap
+ further medical genomics research

65
Q

What percentage of cancer is sporadic?

A

80-90% (somatic mutations)

66
Q

What percentage of cancer is hereditary?

A

5-10% (germline mutations)

67
Q

What are driver mutations in cancer?

A

changes to a gene that drive cancer mutation

68
Q

What are passenger mutations in cancer?

A

Mutations that don’t do anything to affect the cancer phenotype

69
Q

In cancer, what can RT-qPCR be used for?

A
  • Diagnosis + monitoring response to treatment of CML

- Recurrence risk in breast cancer

70
Q

What is OncotypeDX?

A

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 (2 decks)

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