• nucleotide sequence between any two indivuals (not counting identical twins) is nearly identical at 99.5-99.9%

functional consequences of different types of

polymorphism

• SNP in protein coding region of genes can alter AA sequence
  • effect drug metabolizing enzymes (CYP2D6) and protein stability (TPMT)
• SNP near the exon-intron boundaries of genes (they don't alter AA sequence)
  • may affect mRNA splicing (ex: DPD)
• SNP or insertion polymorphisms in promotor or regulatory regions of genes (ex: TS)
• SNP in other regions (ex: intergenic region)

• loss of exons
• inclusion of introns
• loss of exon or inclusion of intron can result in change in reading frame and/or premature termination of mature mRNA

• synonymous (sense) mutation- change in codon does not lead to change in AA
• missense (conservative) mutation- change in codon leads to change in AA with similar chemistry
• missense (nonconservative) mutation- change in codon leads to change in AA with a different chemistry (can lead to inactive enzyme)
• nonsense mutation- change in codon will cause premature termination of polypeptide sequence

• bimodal/trimodal distribution
• patterns of inheritance
  • autosomal dominant (ex: Hunington's)
  • autosomal recessive (ex: CF)
  • X linked recessive (ex: Duchenne muscular dystrophy)

• affecting pharmacokinetics
  • drug metabolizing enzymes- metabolized drugs into active and inactive forms
  • drug transporters- drug mov't btw or out of body compartments; move drugs into or out of cells (ex: MDR1)
• affecting pharmacodynamics
  • target proteins- bind drugs to modulate cell physiology (ex: beta and alpha adrenergic R's)

study of SNP's and their role in determing an individuals pharmacokinetic (metabolism) and pharmacodynamic response to drugs

1. give drug
2. observe ADR
3. conduct family studies to elucidate drug patterns
4. clone involved gene sequences (SNP's) that conferred inheritance in phenotypes

• Phenotype driven (forward genetics)
• advantage- mongenic traits for ADR's are in many instances metabolism related, and hence readily phenotyped (ex: measure drug metabolites in urine to determine phenotype)

• N-acetylation by NAT2
• metabolism by P450 CYP2D6
• TPMT activity

• limited number of drug responses that behave as simple monogenic trait
  • most responses to drugs, and certainly most diseases, are polygenic
• many studies have not examined a sufficient number of pts of different racial backgrounds and/or have not been reproduced in a second study

• fast acetylators have a faster rate of  metabolism and a positive therapeutic response
• slow acetylators are subject to neurotoxicity by INH

• aliphatic oxication
• aromatic hydroxylation
• deamination
• N-/S-oxidation and N-hydroxylation
• N-/S-/O-dealkylation
• oxidative dehalogenation

• ultra-rapid metabolizers (due to gene duplication) have a suprafunctional enzyme, so we need to increase their dose
• extensive metabolizers have a normal enzyme and a good therapeutic response
• poor metabolizers (no functional enzyme)- subject to exaggerated hypotensive response due to high plasma levels of drug, so we decrease the dose

• CYP2D6
• CYP2C9
• other CYP2 enzymes
• CYP3A4

• remember a particular polymorphism does not treat all drugs equally
  • ex: you could have a poor metabolizer or ultra metabolizer of imipramine and need to dosage adjust, but that polymorphism has no effect on sertraline dosage

• poor metabolizer- poor efficacy and accumulation of prodrug
• extensive metabolizer- good efficacy and rapid therapeutic onset

ex: codeine is metabolized to morphine

• poor metabolizer phenotype: patients with homozygous variants have been associated with susceptibility to tardive dyskinesis in response to antipsychotics
• extensive metabolizer phenotype: less likely to suffer from extrapyramidal symptoms like tardive dyskinesia

ex: antipsychotics (ex: haloperidol, risperidone) are metabolized to inactive form

• poor metabolizer phenotype- accumulation causing drowsiness, orthostatic hypotension, urinary retention, constipation, rapid or irregular heartbeat and seizure
• extensive metabolizer phenotype- good efficacy (ultra metabolizer- may need to increase dose)

1. azothioprine (prodrug) metabolized to 6 mercaptopurine
2. 6 mercaptopurine metabolized to inactive form via TPMT methylation(phase 2 metabolism)

TPMT phenotype is very important to potential toxicity, because azothioprine has a very low TI

1. forms an unstable protein that is ubiquinated and degraded, so it has no activity
2. poor metabolizers lead to increase level of drugs
3. increased toxicity
4. death to myeloid lineage
5. lead to life threatening myelosuppression

recommend genotype testing before dosing so that dosage can be adjusted for potential toxicity if you are homozygous for the variant allele

1. warfarin decreases CF's that are vitamin K dependent
2. metabolized to inactive form via CYP2C9
3. in various polymorphisms, increase bleeding propensity
4. this leads to a need to decrease the dosage
   • other factors include protein C levels and age

1. flurouracil inhibits TS and decreases replication (useful in breast and colon cancer)
2. dihydropyrimidine DH is needed for 5-FU metabolism
3. if it has a polymorphism that loses an exon, it leeds to synthesis of a nonfunctional protein
4. no 5-FU metabolism
5. leads to toxicity and death

• alpha 1 polymorphism leading to a decrease in negative feedback cause increase NE release
• beta1 polymorphism causing hyperfunctional receptor leads to further increase in HR and contractility

• CYP2D6 and CYP2C19
• warfarin metabolism by CYP2C9
• NAT2
• TPMT
• required for CCR5 (HIV receptor)

• study of all gene variants/polymorphisms that influence a patient's response to a given drug

• process (reverse genetics)
  1. genotype first and look at all polymorphisms
  2. give a drug
  3. finally, phenotype persons associated with different response
• advantage
  • genome wide SNP data availabe
  • whever a patient is prescribed a drug, his/her SNP profile is minded for known associations between specific gene alleles and drug response
• disadvantages
  • need a very large database
  • for polygenic traits, genotyping does not always predict phenotype due to imperfect knowledge of gene-gene and gene-environment interactions

• during a clinical trial, genetic samples are collected from all patients and SNP's are read from gene chips
• when drug has responders and nonresponders (or individuals with ADR), SNP's are identified that are common to all responders while other SNP's are IDed that are common for all nonresponders or to all ADR individuals
• this information is archived in database and becomes apart of FDA approval for drug
• physician determines genotype of patine (orders SNP analysis) prior to prescribing a drug
• physician selects a drug appropriate for genotype
• determine functional consequences of SNP for future drug development

• life insurance
• disability
• long term care insurance market