MucOneUp: A Simulation Framework for MUC1 -VNTR Variant Benchmarking

Abstract Summary Variable number tandem repeats (VNTRs) in the MUC1 gene cause autosomal dominant tubulointerstitial kidney disease when disrupted by frameshift variants, but the GC-rich 60-bp repeat structure (20-125 copies) challenges variant detection. While tools like VNtyper enable MUC1 variant calling, no gold-standard benchmarking datasets exist for systematic performance evaluation. We present MucOneUp, a specialized simulation framework for generating MUC1-VNTR reference sequences with targeted variants and platform-specific sequencing reads (Illumina, Oxford Nanopore, PacBio). MucOneUp employs Markov chain-based repeat generation, supports diploid simulation with customizable variant placement, and includes additional analysis modules for SNaPshot assay simulation and exploratory frameshift analysis. We validate MucOneUp through a multi-variant, cross-platform benchmark of six tool-platform combinations using 13 distinct frameshift variants and investigate VNTR length effects on detection. Availability and implementation MucOneUp is accessible at no cost under the MIT License at https://github.com/berntpopp/MucOneUp and archived on Zenodo (DOI: 10.5281/zenodo.19740406). Contact bernt.popp{at}charite.de Supplementary information Supplementary data are provided with this manuscript. Competing Interest Statement B.P. is employed by Labor Berlin - Charite Vivantes GmbH, a diagnostic laboratory offering genetic testing services. H.S. developed the original VNtyper implementation; B.P. and H.S. developed VNtyper 2, which is benchmarked in this study. No other conflicts are declared by any author.