CnQuant: high-resolution chromosomal copy number profiling for precision oncology in the clinics

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CnQuant is an interactive Python suite designed for chromosomal copy number variation (CNV) analysis from DNA methylation array files.
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The tool enhances clinical diagnostics by providing detailed CNV annotations and cohort-level frequency analyses.
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CnQuant features a user-friendly interface, low computational requirements, and is scalable for broad clinical implementation.
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An internal validation study showed 98.71% concordance with routine diagnostic data in analyzing brain tumors.
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CnQuant is the first open-source software offering high-resolution CNV exploration with interactive features for methylation arrays.

Acta Neuropathologica

by Benjamin Maciej Freyter, Claus Hultschig, Jon Brugger, Ivana Bratic Hench, Stephan Frank, Juergen Hench
May 8, 2026

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