Pharmacogenetics

Question 1

What is pharmacogenetics?

Answer 1

• genetically controlled variations in drug response
• genetic factors that alter an individual’s drug response to a drug
  
  • genetic polymorphisms
  • less common genetic variants

Question 2

State the importance in recognizing genetic differences in individuals:

Answer 2

1. Genetic differences can cause significant differences in the dose of a drug required to achieve the desired effect.
2. Genetic differences in drug metabolism can significantly alter drug clearance and pharmacokinetics.
3. Genetic differences can alter susceptibility to toxic effects of drugs and other chemicals.
4. Genetic differences can cause or exacerbate adverse drug reactions, some of which used to be called “idiosyncratic”.
5. These patients do not become apparent until they are exposed to a particular chemicalor drug.

Question 3

Genetic locus:

Answer 3

chromosomal location at which two alleles are possible

Question 4

Genotype:

Answer 4

• an individual’s **composition at the gene level **
• i.e. the specific genes they have

Question 5

Phenotype:

Answer 5

an individual’s expression of their genotype

Question 6

Genetic polymorphism:

Answer 6

• Mendelian trait that exists in the population in at least two phenotypes neither of which is rare
• i.e. at least one variant that represents greater than 1% of total pool

Question 7

Allele:

Answer 7

• an alternative form of a gene
• one of the different forms of a gene that can exist at a single locus

Question 8

Single nucleotide polymorphism (SNP):

Answer 8

• a change in one single base pair in the DNA sequence that differs from the “wild type” or predominant sequence
• may or may not result in an altered phenotype
  
  • 99% do not change the phenotype
• most common polymorphism

Question 9

How do we categorize individuals based off of SNPs?

Answer 9

• Haplotypes
• Halotypes

Question 10

Haplotype:

Answer 10

• refers to closely linked genetic markers on a chromosome that tend to be inherited together
• • often within a gene or closely linked genes

Question 11

Halotypes:

Answer 11

• refers to a cluster of SNPs that occur together in an individual (andare of interest to a phenotype)

1. useful for categorizing individuals to understand how clusters of SNPs can contribute to phenotype
2. multiple SNPs may be:
   
   • in a single gene (similar to a haplotype)
   • multifactorial, multiple genes not necessarily inherited as a unit

Question 12

Types of inheritance:

Answer 12

• Autosomal co-dominance: each allele contributes to phenotype
• Autosomal recessive: wild-type allele has predominant effect; it takes two recessive alleles to see the effect
• Autosomal dominant: a single allele predominates over the presence of other possible alleles
• X-linked inheritance: genes inherited on X chromosome; all males will express these traits (males are hemizygous)

Question 13

Hardy Weinberg equilibrium:

Answer 13

• In populations with random mating and no selection pressure, the incidence of the various genotypes can be determined mathematically
• This description is the Hardy Weinberg formula:

1 = (p+q)²=p² +2pq +q²

where:

• p = proportion of wild type alleles
• 2pq = frequency of heterozygote
• q = proportion of variant alleles
• p² = frequency of homozygous WT
• q² = frequency of homozygous variant
• If frequencies of observed phenotypes fit the equation, a variant is said to be
  consistent with Mendelian inheritance

Question 14

homozygous:

Answer 14

have 2 identical alleles

• e.g. AA or aa

Question 15

Pharmacogenetics versus pharmacogenomics:

Answer 15

1. Pharmacogenetics: variation at selected loci
2. Pharmacogenomics: whole genome variation

Question 16

What are some potential genetic polymorphic impacts on drug efficacy & toxicity:

Answer 16

• Polymorphisms which could impact pharmacokinetics:
  
  1. Transporters (uptake, distribution)
  2. Plasma protein binding
  3. Metabolism
  4. Excretion
• Polymorphisms which could impact pharmacodynamics:
  
  1. Receptors
  2. Ion channels
  3. Enzymes
  4. Signaling events

Question 17

NAT-2 polymorphism:

Answer 17

Initial observations

1. Increased neurologic side effects in some patients were correlated with increased plasma concentrations of isoniazid
2. Plasma half-life phenotype in population identified two groups, and implicated a difference in elimination/metabolism
3. Subsequently established that genetic differences in NAT-2 explain “fast” versus “slow” acetylators
   
   • autosomal recessive trait

Question 18

____________ responsible for metabolism of the anti-tuberculosis drug isoniazid

Answer 18

• N-acetyltransferase-2 (NAT-2)

Question 19

Other drugs influenced by N-acetylation phenotype:

Answer 19

• hydralazine
• nitrazepam
• procainamide
• phenelzine
• dapsone
• clonazepam
• sulfonamides
• others

Question 20

Slow acetylator phenotype has been associated with:

Answer 20

• increased incidence of neuropathy due to isoniazid
• arylamine-associated bladder cancer
• hypersensitivity to sulfonamides
• higher incidence of lupus erythematosus with long-term hydralazine therapy

Question 21

CYP2D6 Polymorphism:

Answer 21

• First identified from those that suffered severe hypotension following administration of the anti-hypertensive debrisoquine
• Severe hypotension associated with increased debrisoquine concentrations, and decreased metabolism of debrisoquine
• Subsequently linked to “poor metabolizer” variants of CYP2D6

Question 22

Poor metabolizer variants of CYP2D6:

Answer 22

1. CYP2D6 variant alleles
   
   • Autosomal gene
   • >75 variants identified
2. Frequency of poor metabolizer allele and phenotype:
   
   • Mutant allele frequency about 30%
   • Poor metabolizer phenotype frequency:
     
     • 2–10% of population
     • (ethnic variation)

Question 23

Ultrafast CYP2D6 metabolizers

Answer 23

• CYP2D6 gene duplication (up to 13 copies) of the normal allele

1. Incidence among different ethnic groups (varies from 1–30%)
2. Clinical trials of nortriptyline clearance in patients show much more rapid drug clearance in those with multiple copies of functional CYP2D6

Question 24

Why are CYP2D6 polymorphisms important?

Answer 24

• CYP2D6 metabolizes about 25% of metabolized prescription drugs, including:
  
  • β-blockers
  • antiarrhythmics
  • antidepressants
  • neuroleptics
  • some opiates
  • others

Question 25

CYP2C19 polymorphism:

Poor metabolizer phenotype

Answer 25

• Population incidence: 3–20%
  
  • homozygous poor
• primarily 2 variant alleles

Question 26

What classes of drugs do CYP2C19 affect?

Answer 26

• anti-convulsants (e.g. mephenytoin, phenytoin):
  
  • Increased drug levels and side effects
• proton pump inhibitors (e.g. omeprazole, lansoprazole)
  
  • higher drug levels, higher gastric pH, and better control of GERD
• anti-platelet drugs (e.g. clopidogrel)
  
  • clopidogrel is activated by CYP2C19
  • those with even one slow allele have less active drug and >50% increase in M.I. and stroke
• omeprazole decreases the activation of clopidogrel and increases the risk for:
  
  • serious cardiovascular events, even in those with a normal genotype
• anti-depressants (e.g. amitriptyline)
• anti-cancer (e.g. cyclophosphamide)
• hormones (e.g. progesterone)

Question 27

CYP2C9 polymorphism:
Poor metabolizer phenotype

Answer 27

• 2 predominant variants (CYP2C9*2 and CYP2C9*3)
  
  • alleles in up to 31% of patients
• Several substrates including some drugs with a narrow therapeutic window, e.g.
  
  • phenytoin (anticonvulsant)
  • tolbutamide (type 2 diabetes)

Question 28

CYP2C9 polymorphism:

Warfarin

Answer 28

• S-warfarin cleared almost entirely by CYP2C9
• *3 allele has a much larger impact on warfarin clearance and dosing than *2
• *2 and *3 alleles:
  
  • decrease warfarin clearance
  • increase warfarin half-life
  • increased risk of serious bleeding
  • need lower maintenance doses

Question 29

Vitamin K Receptor (VKORC1) Polymorphism:

Answer 29

VKORC1:

• Subunit of the vitamin K epoxide reductase complex
• Warfarin, a vitamin K antagonist, inhibits the activity of this complex
• Haplotypes and clades predict successful warfarin dose

Question 30

Vitamin K Receptor (VKORC1) Polymorphism:

Haplotypes & Clades

Answer 30

10 common SNPs:

• A clade:
  
  • haplotypes H1 and H2 require lower warfarin doses
  • associated with lower expression of VKORC1
• B clade:
  
  • haplotypes H7, H8, H9 require higher warfarin doses
  • associated with higher expression of VKORC1

Question 31

How does VKORC1 gene expression correlate to dose?

Answer 31

• gene expression: B/B > B/A > A/A
• warfarin dose: B/B > B/A > A/A

Question 32

Pseudocholinesterase Polymorphism:

Answer 32

• Variant response to succinylcholine
  
  • depolarizing muscle relaxant
• Due to reduced activity variants of pseudocholinesterase
  
  • butyrylcholinesterase in
    plasma and liver
• 30–90% decrease in cholinesterase activity
• 1–6% of population (ethnic variation)
• Rare silent variants

Question 33

How does TPMT Polymorphism present?

Answer 33

• Presents as increased risk for life-threatening bone marrow suppression in cancer patients treated with thiopurine drugs
  
  • 6-mercaptopurine, 6-MP

Question 34

Describe the variants in TPMT polymorphism?

Answer 34

• Due to variants with decreased activity of thiopurine methyltransferase (TPMT)
• Low activity allele has 2 SNPs in the TPMT gene
• TPMT allele frequency:
  
  • 0.3% are homozygous for low activity allele
  • 11% heterozygous
• DNA testing recommended by FDA

Question 35

TPMT genotype (alleles):

1. normal/normal
2. normal/slow
3. slow/slow

Answer 35

Resulting phenotype:

1. Normal risk of marrow suppression from 6-MP
2. Elevated risk of marrow suppression from 6-MP
3. High risk of marrow suppression from 6-MP

Question 36

P-glycoprotein (Pgp or MDR-1):

Answer 36

ATP-binding protein that effluxes drugs from the gastrointestinal mucosa

Question 37

What happens with a P-glycoprotein (Pgp) polymorphism?

Answer 37

• result in increased net uptake of the cardiac glycoside digoxin
  
  • decreased levels of Pgp protein
  • low expression alleles found in 16–57% of patients
• Pgp polymorphisms affect other drugs also

Question 38

Parameters that increase the clinical significance of genetic polymorphisms:

Answer 38

1. When the drugs are used relatively frequently (on a population basis)
2. The pathway affected by the polymorphism must be the predominant one
3. If the parent drug and the metabolite are equally active, metabolic genetic polymorphisms will NOT likely alter efficacy/toxicity.
4. Polymorphisms are more important for drugs with a **relatively narrow therapeutic **window
5. Polymorphisms are more important when the drug’s side effects are potentially serious

Question 39

Describe’s codeine’s narrow therapeutic window:

Answer 39

• CYP2D6 activates a portion of codeine to morphine
  
  • Poor metabolizers will not get expected therapeutic benefit from codeine
• Tylenol #3 with codeine:
  
  • codeine → morphine

1. CYP2D6 Poor metabolizer:
   
   • CODEINE → morphine
   • no benefit
2. CYP2D6 Ultrafast metabolizer:
   
   • codeine → MORPHINE
   • morphine side effects