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popSTR2 enables clinical and population-scale genotyping of microsatellites

Snædis Kristmundsdottir1,2, Hannes P Eggertsson1, Gudny A Arnadottir2

  • 1deCODE genetics/Amgen, Reykjavík 102, Iceland.

Bioinformatics (Oxford, England)
|December 6, 2019
PubMed
Abstract

Insights

popSTR2 enhances population-scale microsatellite genotyping by improving sensitivity to sample differences and enabling clinical detection of pathogenic repeat expansions. This updated tool facilitates analysis in association studies and clinical sequencing.

Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Microsatellites are repetitive DNA sequences crucial for genetic variation and disease association studies.
  • Accurate and scalable genotyping of microsatellites is essential for population genetics and clinical diagnostics.
  • Previous tools like popSTR provided foundational capabilities for microsatellite genotyping.

Purpose of the Study:

  • To introduce popSTR2, an advanced tool for population-scale microsatellite genotyping.
  • To enhance genotyping accuracy by incorporating sample-specific slippage rate estimation.
  • To facilitate clinical applications by identifying pathogenic repeat expansions.

Main Methods:

  • Development of a kernel for estimating sample-specific microsatellite slippage rates.
  • Inclusion of a pathogenic repeat expansion panel and scanning script for clinical utility.
  • Implementation of a binning method for integrating genotypes into standard association pipelines.

Main Results:

  • popSTR2 offers increased sensitivity to inter-sample variations in microsatellite genotyping.
  • The tool enables the detection and flagging of potential pathogenic repeat expansions.
  • A novel binning method improves the amenability of microsatellite genotypes for association analyses.

Conclusions:

  • popSTR2 represents a significant advancement in population-based microsatellite genotyping.
  • The tool enhances both research capabilities in population genetics and clinical diagnostic potential.
  • popSTR2 is available for download, promoting wider adoption and further research.

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