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Population genetic implications from DNA polymorphism in random human genomic sequences.

Peidong Shen1, Molly Buchholz, Raphael Sung

  • 1Stanford Genome Technology Center, Palo Alto, California, USA.

Human Mutation
|August 31, 2002
PubMed
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This study surveyed genomic sequence tagged sites (STSs) for genetic variations across diverse ethnic groups. Random genomic sequences exhibit higher nucleotide diversity than intragenic regions, suggesting selection pressures on genes.

Area of Science:

  • Human genetics
  • Population genetics
  • Genomics

Background:

  • Understanding human genetic variation is crucial for population genetics and disease research.
  • Previous studies have focused on specific genes, but a broader survey of random genomic regions is needed.

Purpose of the Study:

  • To survey a large number of random genomic sequence tagged sites (STSs) for genetic polymorphisms in a diverse US population.
  • To compare nucleotide diversity and evolutionary pressures between random genomic regions and intragenic non-coding regions.

Main Methods:

  • Denaturing high performance liquid chromatography (DHPLC) and dye-terminator sequencing were employed.
  • 516 random genomic STSs were analyzed in 24 individuals from major US ethnic groups.
  • Polymorphisms, including simple sequence polymorphisms (SSPs), were identified and characterized.

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Main Results:

  • 58.3% of surveyed STSs were polymorphic, with varying numbers of SSPs per locus.
  • Transitions were the most common type of SSP (63%), followed by transversions (28%) and indels (9%).
  • Nucleotide diversity was 50% higher in random genomic sequences (theta = 8.23 x 10(-4)) compared to intragenic non-coding regions (theta = 5.52 x 10(-4)).

Conclusions:

  • Random genomic regions harbor substantial genetic variation, with higher nucleotide diversity than non-coding intragenic regions.
  • The observed differences in Tajima's D statistic suggest directional selection acting on genes, rather than population growth, as a primary driver of genetic patterns.