Treatment of Parasitic Diseases

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HIV Genomics How do we get there from here?
David W. Haas, M.D. Vanderbilt AIDS Clinical
Trials Center
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Objectives

• To provide an overview of the history and current
  status of pharmacogenomics.
• To briefly discuss selected laboratory approaches
  to pharmacogenomic analysis.
• To discuss strategies for pharmacogenomic studies
  design.
• To suggest attractive areas for future
  pharmacogenomic study.

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The Origins of Pharmacogenomics

• 1950s inherited difference in drug effect
  reported...
• Primaquine hemolysis G6PD deficiency
• Science 124484,1956
• Isoniazid neuropathy slow acetylators
• Am Rev Tuberc 70266,1954
• Suxamethonium apnea plasma cholinesterase
• Lancet 211576,1956
• Early pharmacogenetic studies required no
  knowledge of gene structure or sequence.

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Origins of Molecular Genetic Basis of Effect
Debrisoquine 4-hydroxylase

• 4-OH debrisoquine is inactive.
• No major alternate routes of metabolism.
• In 7 of British subjects (poor metabolizers),
  with 4-hydroxylation deficiency caused high
  systemic concentrations cause severe postural
  hypotension
• Debrisoquine 4-hydroxylase CYP2D6

Mahgoub Lancet 1584, 1977
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Genetic Variants

• Mutation a rare DNA variant (ltlt1 of population)
• Polymorphism a common DNA variant (gt1 of
  population)
• Base substitution, deletion, or insertion.
• Most common are Single Nucleotide Polymorphisms
  (SNP).
• May be in coding or non-coding region.
• Alter amino acid (non-synonymous) or not
  (synonymous).
• May alter function or expression level of protein.

C/A
C/C
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Haplotypes and Linkage Disequilibrium
NNNNNNNNN
NNNNNNNNN
NNNNNNNNN
NNNN
A B
P Q
X Y

• Recombination between nearby polymorphisms should
  be unlikely LINKAGE DISEQUILIBRIUM

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Evans et al. Ann Rev Gen Hum Genet 29, 2001.
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The Future???A Patient-Specific Leukemia
Microarray
Wilson et al. Nature Genetics 29265, 2001.
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The Challenge of Genome SNP Scanning

• The human genome 3 billion base pairs.
• About 1 SNP per 1,000 base pairs.
• about 3 million SNPs per person.
• Cost for genome scan 10 cents per SNP.
• Cost for total genome SNP scan 300,000 per
  person.
• Can reduce cost by
• Scanning only non-synonymous SNPs.
• Scanning only coding regions.
• Only scan occasional SNPs (linkage
  disequilibrium).

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Complex Environment of Drug Effect
Roden et al. Nature Reviews Drug Discovery
137,2002.
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Interindividual Variability in Drug Effect
Roden et al. Nature Reviews Drug Discovery
137,2002.
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Interindividual Variability in Drug Effect
Roden et al. Nature Reviews Drug Discovery
137,2002.
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Strategies to identify genetic predictors of
variable drug response

• Candidate gene approach
• Genome-wide screening approach
• Not mutually exclusive

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Lab Methods to Identify Polymorphisms
Hybridization with specific probes
Allele-specific primer extension
Minisequencing single nucleotide primer extension
Oligonucleotide ligation
Invasive cleavage
Restriction site cleavage
Syvanen Nature Reviews Genetics 2930, 2001.
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Single stranded conformational polymorphism
analysis
YI G FLGFI
YI D FLGFI
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(No Transcript)
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Candidate Gene Approach Success
Mallal et al. Lancet 359727, 2002
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HLA Haplotype Predicts Abacavir Hypersensitivity
Reaction
Mallal et al. Lancet 359727, 2002
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Genome Scanning for Alzheimers Disease Proof of
Principle

• Compares cases-to-control allelic frequency.
• Chromosome 19.

Roses. Human Molec Genetics 112261,2001.
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Microarray For SNP Analysis