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Related Experiment Videos

Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data.

Igor Leykin1, Ke Hao, Junsheng Cheng

  • 1Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA. ileykin@hsph.harvard.edu

BMC Genetics
|February 17, 2005
PubMed
Summary
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New software, CompareLinkage and dChipLinkage, automates SNP array data formatting and analysis for disease gene identification. These tools enable visualization of linkage results alongside genome data, improving genetic studies.

Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Single nucleotide polymorphisms (SNPs) are increasingly used to identify disease-associated genes.
  • High-density SNP microarray platforms offer large-scale, cost-effective genotyping for linkage analysis.
  • Analyzing large SNP datasets and visualizing linkage scores on genome maps is challenging with current software.

Purpose of the Study:

  • To develop novel software for automated formatting and analysis of SNP array data.
  • To integrate visualization of linkage analysis results with genome annotations.
  • To implement parametric linkage analysis and haplotyping for SNP array data.

Main Methods:

  • Developed CompareLinkage software for automated data formatting into "Linkage" format.

Related Experiment Videos

  • Integrated CompareLinkage with multi-point linkage software (Merlin, Allegro).
  • Implemented a variant of the Lander-Green algorithm in dChipLinkage for parametric analysis and haplotyping.
  • Utilized dChip software for visualization of results alongside genome annotations and cytoband information.

    • Main Results:

    • CompareLinkage successfully formats Affymetrix Mapping 10 K genotype data.
    • The software enables visualization of linkage analysis results from Merlin and Allegro within dChip.
    • Parametric linkage analysis and haplotyping were performed using the dChipLinkage module.
    • Analysis of three families with different disease types demonstrated the software's utility.

    Conclusions:

    • CompareLinkage and dChipLinkage are freely available software tools.
    • These packages automate SNP array data processing for linkage analysis programs.
    • Results are visualized in dChip, contextualized with gene and cytoband information.
    • The integrated Lander-Green algorithm variant supports parametric linkage analysis and haplotyping.