Week 2 Flashcards
What is a reference genome
Digital DNA sequence data based as representative of species genome
Not one individual
Often various versions
What does HGVS stand for
Human genome varation society
what does g stand for in HGVS
genomic
what does c stand for in HGVS
coding
what does n stand for in HGVS
non coding
what does r stand for in HGVS
RNA
what does p stand for in HGVS
protein
what does NC stand for in HGVS
complete genomic sequence
what does NG stand for in HGVS
incomplete genomic sequence
what does NM stand for in HGVS
mRNA
what does NP stand for in HGVS
protein
explain each part of:
F5NM_000130.3:c1601G>A(p.Arg534Gin)
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
What does number 1 mean in genomic numbering?
first nucleotide
what does number 1 mean in coding DNA
ATG- start codon of translation
how denotes non coding sequence
first half of intron is + then after – from next
deletion annotation
c.123delA
_ gives range and write full bases (TATCC)
duplication annotation
c.123dupA
_ gives range and write full bases (TATCC)
Insertion annotation
Insertion c.123_124insC
indel annotation
c.123delinsGTAT
Nonsense annotation
- or Ter
What does star allele nomeclature identify
CYP3A5*2 identifies genetic variant need to go onto database to look at
Rule 1 of star allele
if letter after number then gives other variants that don’t have an effect
Rule 2 of star allele
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
problems with star allele
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
What is an rs number
Reference SNP cluster ID specific number for SNPS
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
UCSC annotation
hg
genome reference consortium annotation
CRCh
What is a trasncript
Single gene can be transcribed to multiple RNA single gDNA cahnge can result in different cDNAs
What enzyme metabolises codeine and where does this occur
CYP2D6 in the liver this is highly polymorphic with over 100*
ultra rapid codeine metabolisers, activity score frequency and guidelines
> 2- more than 2 copies of functional- avoid- 1-2%
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)
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%
codeine metabolisers, activity score frequency and guidelines
0- no functional alleles avoid (5-10%)
Phase 1 reactions and product
oxidation reduction and hydrolysis
Phase 1 effect on active drug
Either inactivate active drug- metabolites inactive or metabolites less active than original drug
Phase 1 effect on pharmacologically inactive drug
one of metabolites is active - prodrug
Cytochrome P450
monooxygenases- use heam to oxidise molecules often making more water soluble for clearance by adding or unmasking polar group
Hydroxylation mechanism
hydrogen on drug hydroxylated to Ok group
What does hydroxylation do
small increase in hydrophilicity exposing functional group
Phase II effect
changes Phase I metabolite into compound soluble enough for excretion
conjugation
large increase in hydrophilicity, polar compound added to functional group, facilitates excretion
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
action of Tramadol
Some activity at Mu-opiod receptor and inhibits synaptic reuptake of serotonin and norepinephrine inhibit pain transmission at spinal cord
activity of tramadol pre and post metabolism
Active drug but Metabolism- one main metabolite M1 tramadol contributes significantly higher than tramadol
enzymes invovled in tramadol metabolism
CYP2D6 catalyzes production of M1
CYP2B6 and CYP3A4 catalyse M2 which is inactive
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
Thiopurine use
Used for treatment of inflame, autoimmune, leukaemia and to prevent rejection
TPMTs
Thiopurine methyl transferases (TPMT methylate’s thipures to inactive non-toxic form in phase II metabolism
side effects of thipurines
neutropenia- bone marrow suppression, hepatotoxicity, nausea and comiting and pancreatities
frequency fo variation for thiopurines
89% have normal TPMT enzyme actvicty
11% low TPMT
0.3% have undetectable levels
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
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
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
when is genotyping done for thiopurines in UK
deficient TPMT or previous sever reaction or blood transfusion
issue with testing enzyme activity
can miss if blood transfusion
