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Week 2 Flashcards

1
Q

What is a reference genome

A

Digital DNA sequence data based as representative of species genome
Not one individual
Often various versions

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2
Q

What does HGVS stand for

A

Human genome varation society

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3
Q

what does g stand for in HGVS

A

genomic

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4
Q

what does c stand for in HGVS

A

coding

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5
Q

what does n stand for in HGVS

A

non coding

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6
Q

what does r stand for in HGVS

A

RNA

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7
Q

what does p stand for in HGVS

A

protein

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8
Q

what does NC stand for in HGVS

A

complete genomic sequence

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9
Q

what does NG stand for in HGVS

A

incomplete genomic sequence

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10
Q

what does NM stand for in HGVS

A

mRNA

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11
Q

what does NP stand for in HGVS

A

protein

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12
Q

explain each part of:

F5NM_000130.3:c1601G>A(p.Arg534Gin)

A 
F5 official gene symbol
 NM is reference sequence
c means coding DNA
 G>A sub at position 1601
 p. means protein Arg to Gln at codon 534
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13
Q

What does number 1 mean in genomic numbering?

A

first nucleotide

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14
Q

what does number 1 mean in coding DNA

A

ATG- start codon of translation

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15
Q

how denotes non coding sequence

A

first half of intron is + then after – from next

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16
Q

deletion annotation

A

c.123delA

_ gives range and write full bases (TATCC)

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17
Q

duplication annotation

A

c.123dupA

_ gives range and write full bases (TATCC)

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18
Q

Insertion annotation

A

Insertion c.123_124insC

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19
Q

indel annotation

A

c.123delinsGTAT

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20
Q

Nonsense annotation

A
  • or Ter
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21
Q

What does star allele nomeclature identify

A

CYP3A5*2 identifies genetic variant need to go onto database to look at

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22
Q

Rule 1 of star allele

A

if letter after number then gives other variants that don’t have an effect

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23
Q

Rule 2 of star allele

A

if variant identifies splice variant ad others travel other variants travel with that may have an effect but not as strong an effect- less relevant

24
Q

problems with star allele

A

Interpretations should be consistent- not all genes have committees
Need to be maintained on ref tables
Some Pgx genes use more than 1 nomenclature systems
variation

25
What is an rs number
Reference SNP cluster ID specific number for SNPS
26
international workgroup reccomendations (see if this is actually improtant)
Use HGNC to specify Report using HGVS Report rs IDs Use haplotype translation tables to convert * alleles Indicate each variant observed List of variations can be detected with a test Describe test including limitations Test description should be publicly available
27
UCSC annotation
hg
28
genome reference consortium annotation
CRCh
29
What is a trasncript
Single gene can be transcribed to multiple RNA single gDNA cahnge can result in different cDNAs
30
What enzyme metabolises codeine and where does this occur
CYP2D6 in the liver this is highly polymorphic with over 100*
31
ultra rapid codeine metabolisers, activity score frequency and guidelines
>2- more than 2 copies of functional- avoid- 1-2%
32
Normal codeine metabolisers, activity score, frequency and guidelines
1-2-two alleles for full or reduced function – use label recommended age or weight on label (77%-92% of individuals)
33
Intermediate codeine metabolisers, activity score, frequency and guidelines
0.5 one reduced function and one non functional - use label recommended age or weight on label if don’t react then possibly change 2-11%
34
codeine metabolisers, activity score frequency and guidelines
0- no functional alleles avoid (5-10%)
35
Phase 1 reactions and product
oxidation reduction and hydrolysis
36
Phase 1 effect on active drug
Either inactivate active drug- metabolites inactive or metabolites less active than original drug
37
Phase 1 effect on pharmacologically inactive drug
one of metabolites is active - prodrug
38
Cytochrome P450
monooxygenases- use heam to oxidise molecules often making more water soluble for clearance by adding or unmasking polar group
39
Hydroxylation mechanism
hydrogen on drug hydroxylated to Ok group
40
What does hydroxylation do
small increase in hydrophilicity exposing functional group
41
Phase II effect
changes Phase I metabolite into compound soluble enough for excretion
42
conjugation
large increase in hydrophilicity, polar compound added to functional group, facilitates excretion
43
action of opiods
Decreased AC activity so decreased cAMP Binding to opioid receptor block CA channels in presynaptic so ca doesn’t enter so less synaptic vesicles released Binding of opioid to post synaptic causes more K to be released so more inhibition of synaptic vesicles from presynaptic side Overall reduced neuronal release
44
action of Tramadol
Some activity at Mu-opiod receptor and inhibits synaptic reuptake of serotonin and norepinephrine inhibit pain transmission at spinal cord
45
activity of tramadol pre and post metabolism
Active drug but Metabolism- one main metabolite M1 tramadol contributes significantly higher than tramadol
46
enzymes invovled in tramadol metabolism
CYP2D6 catalyzes production of M1 | CYP2B6 and CYP3A4 catalyse M2 which is inactive
47
Tramadol guidelines
CYP2D6 poor metabolizers often don’t have as much analgesia and ultra rapid could have a lot more but no individual CPIC guidelines
48
Thiopurine use
Used for treatment of inflame, autoimmune, leukaemia and to prevent rejection
49
TPMTs
Thiopurine methyl transferases (TPMT methylate's thipures to inactive non-toxic form in phase II metabolism
50
side effects of thipurines
neutropenia- bone marrow suppression, hepatotoxicity, nausea and comiting and pancreatities
51
frequency fo variation for thiopurines
89% have normal TPMT enzyme actvicty 11% low TPMT 0.3% have undetectable levels
52
testing different levels of TPMT activity
1- conventional dosagesgiven to all apteitns Higher cellulr contc of active thioguanine nucleotides in TPMY deficient- more toxicity 2- genotype specific dosing Similar thiopurines levels achieve, less toxicity Show by indivdiaulising dose can get therapeutic effect
53
Thiopurine FDA guidelines
genotyping *1/*1 standard Heterozygous for low 30-70% standard Homozygous for low activity- consider alternative medication or 10% of standard dose
54
UK guidelines for thiopurines
10% of pop have low- measure TPMT activity prior to start and if undetectable generally not treated an with low then receive reduced dose
55
when is genotyping done for thiopurines in UK
deficient TPMT or previous sever reaction or blood transfusion
56
issue with testing enzyme activity
can miss if blood transfusion

Pharmacogenomics (11 decks)

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