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Related Experiment Videos

Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map.

Circe Tsui1, Laura E Coleman, Jacqulyn L Griffith

  • 1Department of Biochemistry, Center for Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA.

Nucleic Acids Research
|August 9, 2003
PubMed
Summary

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The current human genome map lacks sufficient single nucleotide polymorphisms (SNPs) for the HapMap project. Researchers discovered over 140,000 new SNPs, significantly improving genomic coverage for future genetic studies.

Area of Science:

  • Human Genomics
  • Bioinformatics
  • Genetic Variation

Background:

  • The Human Genome Project aims to create a comprehensive haplotype map (HapMap) using 300,000 to 1 million tag single nucleotide polymorphisms (SNPs).
  • Current SNP density is insufficient for the HapMap project, with significant genomic regions lacking adequate SNP coverage.

Purpose of the Study:

  • To assess the current density of the human SNP map in relation to HapMap project requirements.
  • To identify and characterize new SNPs to improve genome coverage and support the HapMap initiative.
  • To enhance the utility of the human SNP map for genetic linkage studies.

Main Methods:

  • Analysis of existing human SNP map density and coverage.
  • Development and application of a novel bioinformatics pipeline for SNP discovery.

Related Experiment Videos

  • Mapping of newly identified SNPs to existing genomic gaps.

    • Main Results:

    • 24.6% of the genome lacks sufficient SNPs for a conservative tag SNP map.
    • 140,696 additional SNP candidates were identified.
    • Over 51,000 new SNPs were mapped to large gaps, significantly improving coverage in these regions.

    Conclusions:

    • The newly discovered SNPs are crucial for the HapMap project, enabling the inclusion of more genomic intervals.
    • Additional SNP discovery efforts are necessary to fully define human genome haplotype architecture.
    • Enhanced SNP maps are vital for comprehensive human genetic linkage studies.