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altAFplotter: a web app for reliable UPD detection in NGS diagnostics.

Maximilian Radtke1, Johanna Moch2, Julia Hentschel2

  • 1Institute of Human Genetics, Medical Facility, Leipzig University, Leipzig, Germany. maximilian.radtke@medizin.uni-leipzig.de.

BMC Bioinformatics
|September 12, 2024
PubMed
Summary
This summary is machine-generated.

A new tool detects uniparental disomies (UPD), a gap in genetic diagnostics. This user-friendly app analyzes next-generation sequencing (NGS) data, aiding researchers and clinicians in identifying UPDs.

Keywords:
AltAFplotterHeterodisomyIsodisomyNGS-diagnosticsUPDUPD-detection

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Area of Science:

  • Genetics
  • Bioinformatics
  • Molecular Biology

Background:

  • Uniparental disomies (UPD) detection is often missing in standard next-generation sequencing (NGS) pipelines.
  • This gap limits comprehensive genetic diagnostics.
  • A need exists for accessible tools to identify UPDs.

Purpose of the Study:

  • To develop an easy-to-use tool for UPD detection.
  • To enable UPD analysis from panel or exome sequencing data.
  • To address the diagnostic gap in human genetics.

Main Methods:

  • Developed a Python-based application utilizing the Streamlit framework.
  • Employed bcftools and tabix for efficient processing of VCF files.
  • Ensured public availability of the tool and its source code.

Main Results:

  • The tool, Altafplotter, is publicly accessible online.
  • It provides a streamlined process for UPD detection.
  • Source code is available for custom hosting and further development.

Conclusions:

  • The app benefits research and diagnostic laboratories facing UPD identification challenges.
  • Facilitates rapid interpretation of UPD results for clinicians and biologists.
  • Supports high-throughput analysis in clinical and research settings.