Single Nucleotide Polymorphisms and Pharmacogenomics

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Single Nucleotide Polymorphisms and
Pharmacogenomics MEHMET GÜNDÜZ, MD,
PhD Department of Oral Pathology and Medicine,
Okayama University Graduate School of Medicine,
Dentistry and Pharmaceutical Sciences,
Okayamashi, Japan Department of Otolaryngology,
Head and Neck Surgery, Wakayama Medical
University, Japan
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The Human Genome

• 30,000 Genes
• ?? 200,000 Proteins
• alternative mRNA splicing
• post-translational modifications (2-7 millions?
  )
• -Phosphorylation
• -Acetylation
• -Sumolation
• -Ubiquitination

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Some facts about human genome

• Less than 2 of the genome codes for proteins.
• Repeated sequences that do not code for proteins
  ("junk DNA") make up at least 50 of the human
  genome.
• Repetitive sequences are thought to have no
  direct functions, but they shed light on
  chromosome structure and dynamics.
• The human genome has a much greater portion
  (50) of repeat sequences than the mustard the
  worm (7), and the fly (3).

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Some facts about human genome

• The human genome contains 3 billion chemical
  nucleotide bases (A, C, T, and G). 
• The average gene consists of 3000 bases, but
  sizes vary greatly, with the largest known human
  gene being dystrophin at 2.4 million bases.
• The total number of genes is estimated at around
  30,000--much lower than previous estimates of
  80,000 to 140,000.
• Almost all (99.9) nucleotide bases are exactly
  the same in all people.
• The functions are unknown for over 50 of
  discovered genes.

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Some facts about human genome

• The human genome's gene-dense "urban centers"
  are predominantly composed of the DNA building
  blocks G and C.
• In contrast, the gene-poor "deserts" are rich in
  the DNA building blocks A and T. GC- and AT-rich
  regions usually can be seen through a microscope
  as light and dark bands on chromosomes.
• Genes appear to be concentrated in random areas
  along the genome, with vast expanses of noncoding
  DNA between.
• Stretches of up to 30,000 C and G bases
  repeating over and over often occur adjacent to
  gene-rich areas, forming a barrier between the
  genes and the "junk DNA." These CpG islands are
  believed to help regulate gene activity.
• Chromosome 1 has the most genes (2968), and the
  Y chromosome has the fewest (231).

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Basic Gene Structure
Promoter
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Genetic Terminologies
Allele Alternative form of a genetic locus a
single allele for each locus is inherited
separately from each parent. Genotype Each
person has two copies of all chromosomes except
the sex chromosomes. The set of alleles that a
person has is called a genotype.
The term genotype can refer to the SNP alleles
that a person has at a particular SNP, or for
many SNPs across the genome. Genotyping A
method that discovers what genotype a person has
is called genotyping.
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Variations in Genome
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What is SNP ?

• A SNP is defined as a single base change in a DNA
  sequence that occurs in a significant proportion
  (more than 1 percent) of a large population.
• A SNP is a single nucleotide site where exactly
  two (of four) different nucleotides occur in a
  large percentage of the population
• For example, 30 of the chromosomes may have an
  A, and 70 may have a G (on a specific site)
• These two forms, A and G, are called variants or
  alleles of that SNP
• An individual may have a genotype for that SNP
  that is AA, AG, or GG.

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SNP facts

• SNPs are found in coding and (mostly) noncoding
  regions.
• There are probably between 10 and 30 million
  SNPs in humans, about one every 100 to 300 bases
• The abundance of SNPs and the ease with which
  they can be measured make these genetic
  variations significant.
• SNPs close to particular gene acts as a marker
  for that gene.
• SNPs in coding regions may alter the protein
  structure made by that coding region.
• Of these SNPs, perhaps 4 million are common
  SNPs, with both alleles of each SNP having a
  frequency above 20 percent

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SNP Profiles

• Genome of each individual contains distinct SNP
  pattern.
• People can be grouped based on the SNP profile.
• SNPs Profiles important for identifying response
  to Drug Therapy.
• Correlations might emerge between certain SNP
  profiles and specific responses to treatment.

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Classification of SNPs

• SNPs may occur at any position in the above gene
  structure and
• based on its location it can be classified as
  intronic, exonic or promoter region etc.
• Coding SNPs can be further subdivided into two
  groups
• Synonymous when single base substitutions do not
  cause a change
• in the resultant amino acid
• Non-synonymous when single base substitutions
  cause a change
• in the resultant amino acid.

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SNPs may / may not alter protein structure
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SNPs act as gene markers
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SNP Profiles
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Techniques to detect polymorphisms

• Direct Sequencing
• Microarray
• Restriction Length Fragment Polymorphism (RLFP)

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Sequence-based SNP Identification
Amplify DNA (PCR)
Sequence
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Sequence each end of the fragment.
ATAGACG ATACACG ATAGACG ATACACG
ATAGACG ATACACG
Homozygotes
Heterozygote
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Polymorphic Sites Revealed in Sequencing
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SNPGenotyping
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TSC and HGP High Resolution SNP Map
Feb. 2001 - Human Genome Project and TSC
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• 1.58 millions SNPs genotyped
• 71 individuals from 3 American populations
  European, African and Asian ancestry

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What is Pharmacogenomics?
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Pharmacogenomics-personalized medicine
Selection of patients
Drug-response related genes

Rationalized dosage regimen
Pharmacokinetics related genes
Drug metabolizing enzymes, transporters, etc.
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Evans, W. E. et. al. N Engl J Med 2003348538-549
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Evans, W. E. et. al. N Engl J Med 2003348538-549
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Watters, JW et. al. BBA 2003160399-11
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Watters, JW et. al. BBA 2003160399-11
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PharmGKB
The Pharmacogenetics and Pharmacogenomics
Knowledge Base URL http//www.pharmgkb.org/index
.jsp
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There is no gene for the human spirit