What is a SNP

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What is a SNP?
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Lecture topics

• What is a SNP?
• What use are they?
• SNP discovery
• SNP genotyping
• Introduction to Linkage Disequilibrium

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Readings in the text

• Pp 241-251, 271-291

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Recognizing Heterozygotes for a SNP
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SNPs

• Non-Coding (5 or 3 UTR, regulatory regions or
  inter-genic)
• Coding
• Synonymous
• Non-Synonymous (Replacement)
• Non-coding, and synonymous SNPs may be functional

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Haplotypes An Introduction

• A distinct collection of a number of (usually
  bi-allelic) SNPs along a gene (or chromosome
  region)
• Certain alleles may segregate together
• Much more on this next lecture

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Why are we interested in SNPs?

• Population genetics (population demography and
  evolution
• Quantitative Genetics (mapping allelic variants
  causing diseases)
• We often only use the SNPs as markers, and we
  are not interested in them in particular

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A little Population Genetics

• What causes SNPs to be maintained in a
  population? Why do they vary?
• Mutation vs. Drift (Neutral)
• Positive or purifying selection (fixation)
• Balancing Selection
• Ps and qs
• Hardy Weinberg Equilibrium

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SNP discovery

• Currently re-sequencing is the major method for
  SNP discovery
• This can be coupled with database searches for
  putative SNPs that need to be verified
• One major challenge is the frequency of the rare
  alleles
• P 1 (1-p)2N

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Genotyping methods

• New methods are developing at an extremely rapid
  pace
• Cost, efficiency and error rate must all be
  considered carefully
• Depending upon the question, and organism being
  utilized, different approaches may be useful
  (Drosphila vs. humans)

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Recognizing Heterozygotes for a SNP
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PCR-Restriction Fragment Length polymorphism
(RFLP)
Also known as Cleaved Amplified Polymorphic
Sequence (CAPS)
Wild Type CTCACTCTCACGCGCATACACAGTGAAATGTAAACACC
Mutant CTCACTCTCACGCGCACACACAGTGAAATGTAAACA
CC
DraIII Recognition site CACNNNGTG
Wild Type CTCACTCTCACGCGCATACACAGTGAAATGTAAACACC
Mutant CTCACTCTCACGCGCACACACAGTGAAATGTAAACA
CC
Mutant cuts, wild type does not
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But, what if there is no restriction site???

• You make one of course!!!
• Derived CAPS (dCAPS)
• Using Primer mismatch, you engineer a restriction
  site
• Depending upon the length of your primer, the
  difference
• in size between the two fragments is
  usually 20 bp.

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ASO (Figure 5.20)
Allele Specific oligo-hybridization
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Single Base Extension (SBE)
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Pyro-sequencing (5.23)