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The International HapMap Project

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Title: The International HapMap Project


1
The International HapMap Project
  • Ryan Tarpine

2
What is it?
  • The International HapMap Project is a
    multi-country effort to identify and catalog
    genetic similarities and differences in human
    beings.

3
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.

4
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.

5
http//www.hapmap.org
6
Finding SNPs
7
Enter the gene name
Or choose an example
8
Results
9
Default Plots
Click to jump
10
Available Plots
11
LD Plot
12
Haplotype Display
Click anywhere to see data
13
Phased Haplotypes
14
Turning it off
15
Available Data
16
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
  • ...

17
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
  • ...

18
Other Resources
  • dbSNP http//www.ncbi.nlm.nih.gov/SNP/
  • To integrate with GenBank
  • Perlegen http//genome.perlegen.com
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