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Identity by descent genome segmentation based on single nucleotide polymorphism distributions.

T W Blackwell1, E Rouchka, D J States

  • 1Institute for Biomedical Computing, Washington University, St. Louis, MO 63110, USA. blackwel@ibc.wustl.edu

Proceedings. International Conference on Intelligent Systems for Molecular Biology
|April 29, 2000
PubMed
Summary

Researchers analyzed human genome sequences from two individuals to study single nucleotide polymorphisms (SNPs). They found non-uniform SNP distribution and a recent large duplication, providing insights into human genome evolution and mutation rates.

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Area of Science:

  • Human Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Comparing independently sequenced human genomic regions from different individuals reveals sequence discrepancies.
  • These discrepancies, primarily single nucleotide polymorphisms (SNPs), offer insights into genome variation and accuracy of large-scale sequencing data.

Purpose of the Study:

  • To analyze the frequency and distribution of SNPs in the human genome.
  • To identify large-scale genomic structures like duplications.
  • To develop a population genetic model for SNP distribution and estimate the human mutation rate.

Main Methods:

  • Comparative analysis of independently sequenced human genomic regions (BAC sequences).
  • Statistical analysis of single nucleotide polymorphism (SNP) frequencies and distribution.

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  • Development of a probabilistic algorithm for segmenting genomic sequence into regions of identity by descent (IBD).
  • Fluorescence in situ hybridization (FISH) mapping to analyze population polymorphism.

    • Main Results:

    • Observed transition/transversion frequencies support biological origins for sequence differences, validating large-scale sequencing data for SNP analysis.
    • Single nucleotide polymorphism distribution is non-uniform across the human genome.
    • A large duplication (>130 kb) between chromosomes 1p34 and 16p13 was identified, with highly identical sequences suggesting a recent event.
    • Human populations may be polymorphic for this duplication, as indicated by FISH mapping.
    • A population genetic theory and algorithm for IBD segmentation were developed.

    Conclusions:

    • The human genome exhibits non-uniform SNP distribution and recent large-scale duplications.
    • The developed methods allow for accurate SNP analysis and estimation of the human mutation rate.
    • Findings contribute to understanding human genome evolution and variation.