{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:42:48Z","timestamp":1785426168524,"version":"3.56.0"},"posted":{"date-parts":[[2025,9,15]]},"group-title":"Genetics","reference-count":40,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T00:00:00Z","timestamp":1757894400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["LUAUS24087"],"award-info":[{"award-number":["LUAUS24087"]}],"id":[{"id":"https:\/\/ror.org\/037n8p820","id-type":"ROR","asserted-by":"publisher"}]},{"name":"the MULTIOMICS_CZ (Programme Johannes Amos Comenius, Ministry of Education, Youth and Sports of the Czech Republic","award":["Project CZ.02.01.01\/00\/23_020\/0008540"],"award-info":[{"award-number":["Project CZ.02.01.01\/00\/23_020\/0008540"]}]},{"name":"the European Union; and the National Center for Medical Genomics","award":["LM2023067"],"award-info":[{"award-number":["LM2023067"]}]},{"award":["UNCE\/24\/MED\/022"],"award-info":[{"award-number":["UNCE\/24\/MED\/022"]}],"id":[{"id":"https:\/\/ror.org\/024d6js02","id-type":"ROR","asserted-by":"publisher"}]},{"award":["Cooperation"],"award-info":[{"award-number":["Cooperation"]}],"id":[{"id":"https:\/\/ror.org\/024d6js02","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Start MD RCSI 2025"},{"name":"ADTKD Net A European registry based clinical research platform HRB"},{"name":"EU joint funding"},{"name":"HRB RD-CAt research award 2024"},{"name":"The Carlos Slim Health Foundation"},{"name":"The Black Brogan Foundation"},{"name":"The Rassmuss Foundation"},{"name":"Critical Path Institute US Food and Drug Administration Contract","award":["75F40124C00106"],"award-info":[{"award-number":["75F40124C00106"]}]},{"name":"CKD Biomarkers Consortium Pilot and Feasibility Studies Program funded by NIH-NIDDK","award":["U01 DK103225"],"award-info":[{"award-number":["U01 DK103225"]}]},{"name":"Soli Deo Gloria"},{"name":"National Center for Advancing Translational Sciences Wake Forest Clinical and Translational Science Award","award":["UL1TR001420"],"award-info":[{"award-number":["UL1TR001420"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>\n                    ADTKD-\n                    <jats:italic>MUC1<\/jats:italic>\n                    is caused by frameshift mutations in\n                    <jats:italic>MUC1<\/jats:italic>\n                    gene that produce a frameshifted protein (MUC1fs) toxic to kidney cells. The gene\u2019s variable number of tandem repeats (VNTR), with high GC content, makes it largely inaccessible to standard sequencing. As a result, both the reference sequence and natural variation in this region remain poorly defined, complicating mutation detection and data interpretation. Standard methods also fail to pinpoint the exact VNTR unit affected, limiting insight into mutation mechanisms and genotype\u2013phenotype correlations.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>\n                    We employed Single Molecule, Real-Time (SMRT) sequencing and characterized the genomic sequence of\n                    <jats:italic>MUC1<\/jats:italic>\n                    in 300 individuals including 279 individuals from 143 families suspected of having ADTKD-\n                    <jats:italic>MUC1<\/jats:italic>\n                    . We compared these results to those obtained using the CLIA-approved mass spectrometry-based probe extension (PE) assay, which specifically detect the most prevalent 59dupC mutation. We correlated the structural features of the\n                    <jats:italic>MUC1<\/jats:italic>\n                    VNTR with the rate of kidney function decline in affected individuals.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    We identified\n                    <jats:italic>MUC1<\/jats:italic>\n                    consensus sequences for 205 unique VNTR alleles, with 9 distinct types of frameshift mutations present on 52 distinct mutated VNTR alleles.\n                    <jats:italic>MUC1<\/jats:italic>\n                    frameshift mutations were identified in 71 of 143 families (50%) with suspected ADTKD, comprising 135 genetically affected individuals (48%). The SMRT assay exhibited complete concordance and revealed that the PE assay is capable of detecting frameshift mutations in approximately 85% of affected families. The constellation of VNTR structures supports a genotype\u2013progression model, in which fast progressors exhibit a significantly lower number of repeat units on the wild-type allele and a higher number of repeats on the mutation-bearing allele, including an increased number of frameshifted repeat units.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>\n                    SMRT sequencing outperforms current diagnostic methods for ADTKD-\n                    <jats:italic>MUC1<\/jats:italic>\n                    and reveals the prognostic value of VNTR structures. Although their contribution to disease progression is modest (\u223c6% variance explained), it remains biologically and clinically meaningful.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Key Points 3<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>\n                        Single Molecule, Real-Time (SMRT) sequencing of\n                        <jats:italic>MUC1<\/jats:italic>\n                        outperforms existing genetic and immunohistochemical methods for ADTKD-\n                        <jats:italic>MUC1<\/jats:italic>\n                        diagnosis.\n                      <\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>\n                        CLIA-approved mass spectrometry-based genotyping assay, complemented by SMRT sequencing, can detect nearly all ADTKD-\n                        <jats:italic>MUC1<\/jats:italic>\n                        patients.\n                      <\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Disease progression correlates with VNTR pattern: fast progressors have fewer WT repeats and more mutant\/frameshifted repeats<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>","DOI":"10.1101\/2025.09.06.673538","type":"posted-content","created":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T15:15:13Z","timestamp":1757949313000},"source":"Crossref","is-referenced-by-count":4,"title":["Long-Read Sequencing of the\n                  <i>MUC1<\/i>\n                  VNTR: Genomic Variation, Mutational Landscape, and Its Impact on ADTKD Diagnosis and 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