The International HapMap Project

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The International HapMap Project

• Ryan Tarpine

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What is it?

• The International HapMap Project is a
  multi-country effort to identify and catalog
  genetic similarities and differences in human
  beings.

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Why?

• Using the information in the HapMap,
  researchers will be able to find genes that
  affect health, disease, and individual responses
  to medications and environmental factors.

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The Hypothesis

• According to an idea known as the common
  disease-common variant hypothesis, the risk of
  contracting common diseases is influenced by
  genetic variants that are relatively common in
  populations.

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http//www.hapmap.org
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Finding SNPs
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Enter the gene name
Or choose an example
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Results
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Default Plots
Click to jump
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Available Plots
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LD Plot
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Haplotype Display
Click anywhere to see data
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Phased Haplotypes
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Turning it off
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Available Data
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SNP Genotype Frequency Data

• rs11620542 Chr13 59952072 ncbi_b35 perlegen
  urnlsidperlegen.hapmap.orgProtocolGenotyping_1
  .0.02 urnlsidperlegen.hapmap.orgAssay25768.61
  508381 urnlsiddcc.hapmap.orgPanelCEPH-30-trio
  s1 QC T/T 0.533 32 C/T 0.45 27 C/C 0.017 1 60
• rs11841623 Chr13 59941224 ncbi_b35 sanger
  urnLSIDillumina.hapmap.orgProtocolGolden_Gate_
  1.0.01 urnLSIDsanger.hapmap.orgAssay41908051
  urnlsiddcc.hapmap.orgPanelCEPH-30-trios1
  QC T/T 1 60 G/T 0 0 G/G 0 0 60
• ...

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SNP Genotype Data

• rs1341840 A/G Chr13 59883193 ncbi_B35 sanger
  urnlsidillumina.hapmap.orgProtocolGolden_Gate_
  1.0.01 urnlsidsanger.hapmap.orgAssay4935111
  urnlsiddcc.hapmap.orgPanelCEPH-30-trios1 QC
  AA AA AA AA AA AA AA AA AA AA AA AA AG AG AA AG
  AG AA AA AA AA AA AA AG AG AA AA AA AA AA AG AA
  AA AG AA AA GG AG AA AA AG AA AA AA AA AA AA AA
  AA AA AA AA AG AA GG AG AA AA AA AA AA AA AG AG
  AG AA AA AA AA AG AG AA AG AG AA AA AA AG AA AA
  AA AA AG AA AA AG AG AG AG AA
• rs1341841 A/G Chr13 59883309 ncbi_B35 perlegen
  urnlsidperlegen.hapmap.orgProtocolGenotyping_1
  .0.02 urnlsidperlegen.hapmap.orgAssay25771.21
  294471 urnlsiddcc.hapmap.orgPanelCEPH-30-trio
  s1 QC AG AA AG AG AG AG AG AG AA AG GG AG AA AA
  AA AA AA AA AG AG AG AG AG AG AA AG AA AA AA AA
  AG AA NN AA AA GG AA AA AG AG AA AA AG AG AG AG
  AG AA AA AG AA AA AG AA AA AA AA AG AA AG NN AG
  AA AG AA AG AA AA AA AG AG AG AA AA AG AA AG AA
  AA AG AA AA AG AA AA AA AG AA AG AG
• ...

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Other Resources

• dbSNP http//www.ncbi.nlm.nih.gov/SNP/
• To integrate with GenBank
• Perlegen http//genome.perlegen.com