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Related Experiment Videos

How well do HapMap SNPs capture the untyped SNPs?

Erwin Tantoso1, Yuchen Yang, Kuo-Bin Li

  • 1Bioinformatics Institute, 30 Biopolis Street, 07-01 Matrix, 138671, Singapore. erwint@bii.a-star.edu.sg

BMC Genomics
|September 20, 2006
PubMed
Summary
This summary is machine-generated.

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HapMap single nucleotide polymorphisms (SNPs) show limited ability to capture untyped variants across most human genes. While some genes show good coverage, resequencing may be necessary for comprehensive SNP discovery.

Area of Science:

  • Genomics
  • Human Genetics
  • Bioinformatics

Background:

  • Human genome sequencing reveals millions of single nucleotide polymorphisms (SNPs) crucial for understanding human variation.
  • The International HapMap Project provides a catalog of human genetic variation for disease association studies.
  • National Institute of Environmental Health Sciences Environmental Genome Project (NIEHS EGP) offers valuable SNP data for analysis.

Purpose of the Study:

  • To assess the transferability of HapMap genotype data to NIEHS EGP SNPs.
  • To evaluate the capacity of HapMap SNPs in capturing untyped SNPs within genomic regions.
  • To establish guidelines for selecting robust HapMap SNPs for comprehensive SNP coverage.

Main Methods:

  • Analysis of HapMap genotype data against NIEHS EGP SNPs.

Related Experiment Videos

  • Assessment of HapMap SNP performance in capturing untyped variants across different ethnic panels.
  • Identification of factors influencing SNP coverage, such as SNP density and linkage disequilibrium.

    • Main Results:

    • HapMap data demonstrated insufficient robustness for capturing untyped variants in most human genes.
    • European and Asian panels showed marginal performance (approx. 55%) in capturing untyped variants.
    • The HapMap YRI panel captured only about 30% of variants, with some genes exhibiting excellent coverage in European/Asian panels but not African.

    Conclusions:

    • HapMap SNPs are transferable to NIEHS SNPs, but do not capture all untyped SNPs.
    • SNP density and inter-SNP association are critical for robust SNP reference panels.
    • Resequencing may be required to identify SNPs in regions with inadequate HapMap coverage.