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Collapsed haplotype pattern method for linkage analysis of next-generation sequence data.

Gao T Wang1, Di Zhang1, Biao Li1

  • 1Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

European Journal of Human Genetics : EJHG
|April 16, 2015
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Summary
This summary is machine-generated.

Next-generation sequencing (NGS) enables direct genome analysis for Mendelian diseases. A new collapsed haplotype pattern (CHP) method enhances linkage analysis using NGS data, proving more powerful than individual variant analysis.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Genomic analysis

Background:

  • Next-generation sequencing (NGS) advances allow direct sequencing of genomes and exomes for Mendelian diseases.
  • Decreasing NGS costs facilitate family-wide DNA sequencing and direct linkage analysis.

Purpose of the Study:

  • To develop a novel method for linkage analysis using NGS data.
  • To improve the power and accuracy of identifying causal variants in Mendelian diseases.

Main Methods:

  • Developed the collapsed haplotype pattern (CHP) method for linkage analysis, inspired by 'burden' tests.
  • Applied the CHP method to NGS data from families with deafness genes.
  • Implemented the CHP method in the SEQLinkage software package.

Main Results:

  • The CHP method demonstrated substantially greater power compared to analyzing individual variants in linkage analysis.
  • CHP provides statistical evidence for gene involvement in disease etiology.
  • The method is robust against phenocopies and reduced penetrance, reducing the exclusion of causal variants.

Conclusions:

  • The collapsed haplotype pattern (CHP) method is a powerful tool for linkage analysis with NGS data.
  • SEQLinkage software facilitates linkage analysis on NGS data and compatibility with existing programs.
  • This approach enhances the identification of genes underlying Mendelian diseases.