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

• Published in: BMC bioinformatics Vol. 25; no. 1; pp. 299 - 5
• Main Authors: Radtke, Maximilian, Moch, Johanna, Hentschel, Julia, Schumann, Isabell
• Format: Journal Article
• Language: English
• Published: London BioMed Central 12.09.2024; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; AltAFplotter; Applications programs; Bioinformatics; Biological effects; Biomedical and Life Sciences; Chromosome abnormalities; Chromosomes; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Data science; Diagnosis; DNA sequencing; Genetics; Genomes; Heterodisomy; High-Throughput Nucleotide Sequencing - methods; Humans; Internet; Isodisomy; Life Sciences; Methods; Microarrays; Molecular diagnostic techniques; NGS-diagnostics; Nucleotide sequencing; Python; Software; Source code; Underpotential deposition; UPD; UPD-detection; Web applications; Germany; UPD; NGS-diagnostics; Isodisomy; AltAFplotter; Heterodisomy; UPD-detection
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05922-3

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.