F' Single Nucleotide Polymorphisms SNPs

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F. Single Nucleotide Polymorphisms (SNPs)

• F. Single Nucleotide Polymorphisms
• F.1. Variation and inheritance
• F.2. Lets watch a movie!
• F.3. Why do we care? Mostly pharmacogenomics
  designer drugs!
• F.4. The HapMap project
• Read 3.2 of DGPB (including Math. Minute 3.3)
• Read HapMap project page http//www.hapmap.org/wha
  tishapmap.html.en
• You are responsible for the material covered in
  the video

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F.1 Variation and Inheritance Genes and Alleles

• A human egg cell and a human sperm cell both
  contain 23 single chromosomes. Fertilization
  brings these two sets of single chromosomes
  together to make 23 pairs of chromosomes in the
  embryo.

Life is more complicated recombination
Brown eye
Brown eye
Blue eye
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F.1 Variation and Inheritance From Genotype to
Phenotype
Some human characteristics are controlled by just
one pair of genes Shape of the upper eyelid,
earlobe, color of iris and ability to taste.
Others are controlled by more than one pair of
genes (allele). A set of alleles inherited by an
individual is called a genotype. The way the
genes express themselves in the individual's
appearance is their phenotype.
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F.1 Variation and Inheritance SNP Distribution
Low kb per SNP
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F.1 Variation and Inheritance Genome Variations

• Microsatellite A region where multiple mutations
  occurred.
• Single Nucleotide Polymorphisms (SNPs) A single
  base mutation. Occurred in roughly 1 out of 1200
  bases.
• Questions
• If a SNP happens in the CDS of a gene does it
  always result in a different protein encoding?
  Explain your answer.
• If a SNP appears outside the CDS, does it matter?

AAGGTaCCAACAAAC AAGGTcCCAACAAAC AAGGTcCCAACAAAC AA
GGTaCCAACAAAC
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F.2 Lets watch movie
http//www.hhmi.org/biointeractive/genomics/lectur
es.html
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F.3. Why are SNPs Interesting?

• Study of evolution
• DNA Fingerprinting
• Markers for disease or propensity for disease
• Pharmacogenomics DESIGNER DRUGs

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F.3 Why SNPs? Some definitions
Locus alleles (genes) Linkage How close two
loci are to each other on a chromosome. Linkage
Disequilibrium If two alleles (or two SNPs) tend
to be inherited than by chance then we say it is
in linkage disequilibrium. Haplotype The set
of alleles on a particular chromosome.
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F.3 Why SNPs? Simple Comparison of SNPs
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F.3 Why SNPs? Polygenic Analysis