High-performance xenograft read-sorting for DNA methylation analysis

Altendorfer, S.; Zentgraf, J.; Schmitz, J. E.; Plass, C.; Gerhauser, C.; Rahmann, S.

doi:10.64898/2026.10.06.756952

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bioRxiv · 10.64898/2026.10.06.756952

High-performance xenograft read-sorting for DNA methylation analysis

Altendorfer, S.·Zentgraf, J.·Schmitz, J. E.·Plass, C.·Gerhauser, C.·Rahmann, S.

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Abstract

Xenograft sorting tools separate sequenced DNA reads by species. We have enhanced the computational method and tool Xengsort to enable efficient epigenetic profiling of patient-derived xenograft models; it now supports cytosine-converted whole genome or reduced-representation data. Benchmarking Xengsort against several established methods (ICRG, bamcmp, XenofilteR) revealed consistently high accuracy across tools, but Xengsort outperformed the other tools in computational efficiency due to its alignment-free design.

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Altendorfer, S., Zentgraf, J., Schmitz, J. E., Plass, C., Gerhauser, C., Rahmann, S.. 2026-10-12. High-performance xenograft read-sorting for DNA methylation analysis. https://doi.org/10.64898/2026.10.06.756952

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