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

Maximilian Radtke; Johanna Moch; Julia Hentschel; Isabell Schumann

doi:10.1186/s12859-024-05922-3

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

BMC Bioinformatics. 2024 Sep 12;25(1):299. doi: 10.1186/s12859-024-05922-3.

Authors

Maximilian Radtke¹, Johanna Moch², Julia Hentschel², Isabell Schumann^{2

3}

Affiliations

¹ Institute of Human Genetics, Medical Facility, Leipzig University, Leipzig, Germany. maximilian.radtke@medizin.uni-leipzig.de.
² Institute of Human Genetics, Medical Facility, Leipzig University, Leipzig, Germany.
³ Centre of Medical Genetics, Department of Medical Genetics, University of Münster, Münster, Germany.

Abstract

Background: The detection of uniparental disomies (the inheritance of both chromosome homologues from a single parent, UPDs) is not part of most standard or commercial NGS-pipelines in human genetics and thus a common gap in NGS diagnostics. To address this we developed a tool for UPD-detection based on panel or exome data which is easy to use and publicly available.

Results: The app is freely available at https://altafplotter.uni-leipzig.de/ and implemented in Python, using the Streamlit framework for data science web apps. It utilizes bcftools and tabix for processing vcf files. The source code is available at https://github.com/HUGLeipzig/altafplotter and can be used to host your own instance of the tool.

Conclusion: We believe the app to be a great benefit for research and diagnostic labs, which struggle identifying and interpreting UPDs in their NGS diagnostic setup. The information provided allows a quick interpretation of the results and thus is suitable for usage in a high throughput manner by clinicians and biologists.

Keywords: AltAFplotter; Heterodisomy; Isodisomy; NGS-diagnostics; UPD; UPD-detection.

MeSH terms

High-Throughput Nucleotide Sequencing* / methods
Humans
Internet
Software*