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Related Experiment Videos

A 4-Mb high-density single nucleotide polymorphism-based map around human APOE

E Lai1, J Riley, I Purvis

  • 1US Discovery Genetics, GlaxoWellcome, Inc., 5 Moore Drive, Research Triangle Park, North Carolina, 27709, USA.

Genomics
|November 10, 1998
PubMed
Summary
This summary is machine-generated.

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High-density single-nucleotide polymorphism (SNP) maps are feasible for complex disease research. This pilot study efficiently generated SNP maps with <100-kb spacing, paving the way for genome-wide association studies.

Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Whole-genome association studies (WGS) are crucial for identifying complex disease loci.
  • High-density single-nucleotide polymorphism (SNP) maps are needed for effective WGS.
  • Generating dense SNP maps has been a technical challenge.

Purpose of the Study:

  • To assess the feasibility of generating high-density SNP maps (<100-kb spacing).
  • To compare SNP detection efficiencies using different mapping and sequencing strategies.
  • To evaluate SNP detection software.

Main Methods:

  • Pilot study focused on a 4-Mb region of human chromosome 19 around the APOE locus.
  • Compared YAC-based vs. BAC/PAC-based maps.
  • Sequenced individual DNA vs. pooled DNA samples.

Related Experiment Videos

  • Evaluated three polymorphism detection software applications.

    • Main Results:

    • Identified 121 SNPs, with 25 in coding regions, at a frequency of 1 SNP/1.1 kb.
    • Achieved average marker spacing of ~30 kb across a 2-Mb region.
    • Observed allele frequency differentials in 10 out of 51 genotyped SNPs across five populations.

    Conclusions:

    • High-density SNP maps can be efficiently generated using current technologies.
    • A genome-wide map with 60,000-100,000 SNPs is achievable within a practical timeframe.
    • This facilitates advancements in complex disease genetics research.