Sub-discapline of pharmacogenetics that surverys the entire genome to assess genetic determinants of drug response

Variation in DNA sequence present in at least 1% of a population

1.  Better screening of potential drug candidates for efficacy, toxicity, and side effects in clinical trials

2.  Better ID of therapeutic dose

3.  Improved ability to select potential protein targets for drug development

4.  Better ability to ID patients hwo might be at higher risk for therapeutic failure or development of an adverse drug reaction

Before = "Phenotype to Genotype approach" compare drug response outliers to normal population

Now = "reverse genetic, genotype-to-phenotype approach"

-GWAS (genome wide association studies) use genomic approach to ID genetic polymorphisms, then determine if these polymorphisms translate into phenotypic variability

Monogenic traits determiend by alleles that encode proteins with different activities, the different genotypes may result in distinct phenotypes

Multigenic traits are determiend by multiple genes and alleles, the large # of genotypes will prodcue a broad range of phenotypes that do not reveal a any distinct groups (cant say are dominant, codominant, or recessive)

1.  Single Nucleotide Polymorphisms (SNPs)

  -Present in the human genome at ~1 SNP every few hundred to 1000 bp

2.  Indels (Insertions/Deletions)

3.  Copy Number Variations

-caused by genomic rearrangements including duplications, deletions, and inversions

-10% of genome

SNPs in coding region of genome

1.  Non-synonymous (missense) - base pair change results in amino acid change

2.  Synonymous (sense) - base pair change does not result in amino acid change

  -Can still have direct affect on phenotypic trait (change to less preferred codon for same AA)

3.  Nonsense - bp change introduces a stop codon

1.  5' and 3' untranslated regions of mRNA

  -may alter cis-elements that determine mRNA translatability or stability (altering protein levels)

2.  Promoter and Enhancer regions of genes

  -may alter cis-elements that regulate gene transcription

3.  Introns

  -If by exon-intron border may affect transcript splicing, often leading to frame shift and early stop codon

4.  Intergenic regions

May affect:

a.  DNA tertiary structure

b.  Interaction with chromatin

c.  Interaction with topoisomerases

d.  DNA replication

The impact of a non-synonymouse SNP on protein function can be tested experimentally

-Express various SNPs and test their efficacy of function by comparing it to a normal phenotype.  Ex: transport activity

1.  Frequency of a variant allele

2.  Penetrance of a variant allele

3.  Narrowness of therapeutic index or sharpness of dose-response curve of drug

4.  Limited availability of alternate clearance pathways

5.  Absense of alternative drugs

1.  Intronic

2.  Intergenic Regions

Proportion of individuals carrying a variant allele that express an associated phenotype

A set of SNPs on a single chromosome that is stastically associated

A gene is likely to have more than one SNP, the haplotype is the particular combination of all SNPs that occur together for a gene

Linkage is the extent to which the genotypes at two genetic loci are independent of one another

Linkage equilibrium - the genotype present at one locus is independent of the genotype at a second locus

Linkage disequilibrium - the genotypes at two loci are not independent of one another

  -Complete linkage disequilibrium = genotypes at two loci always occur together

1.  Genes that encode determinants of a drug's pharmacokinetics

  -ex: drug metabolizing enzymes, transporters

2.  Genes that encode drug receptors and targets

  -variants that alter function greatly may cause disease and face negative selective pressure to be passed on

  -variats with subtle changes can be maintained in population without causing disease but may cause variation in drug response

3.  Genes involved in the disease being treated but do not direclty interact with a drug (modifiers)

Debrisoquine is an anti-hypertensive drug that is metabolized by CYP2D6

CYP2D6 polymorphisms can result in:

1.  Poor metabolizers which contain mutant CYP2D6 alleles that reduce or abolish enzyme activity

2.  Ultra rapid metabolizers via copy number variant polymorphism inducing gene duplications of CYP2D6

If pt is a poor metabolizer and takes debrisoquine, may result in dizziness and orthostatic hypotension

NAT2 (N-acetyletransferase-2) catalyzes the N acetylation of many drugs and chemicals (procainamide, caffeine, 4aminobiphenyl)

Genetis:

-Human actylation polymorphism is controlled by 4 major allels at a single locus on chromosome 8

-3 alleles encode for slow activity; 1 allele encodes for fast activity

-Fast activity is dominant, Slow activity is recessive

NAT shows considerable ethnic variation: Slow acetylators account for <10% in some groups and >90% in others

Consequences of Slow Acetylation:

1.  More prone to polyneuropathy during isoniazid treatment

2.  More likely to develop hemolytic anemia during treamtent with sulfa drugs

3.  Greater incidence of bladder cancer when exposed to arylamine carcingoens

Fast acetylators require larger doses to get desired effect

ADH2 (Alcohol dehydrogenase 2) encodes B polypeptide

Individuals with ADH2*2 genotype metabolize ethanol more rapidly than do those with the ADH2*1. 

  -Faster ethanol metabolism results in increased acetaladehyle production, which is the toxic metabilite that causes alcohol-induced flushing (asian glow)

  -Flushing also occurs with polymorphism to aldehyde dehydrogenase enzyme ALDH2*2 that decreases its ability to convert acetaldehyde into acetic acid