{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T03:39:34Z","timestamp":1792640374690,"version":"4.5.0"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T00:00:00Z","timestamp":1770336000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T00:00:00Z","timestamp":1773100800000},"content-version":"vor","delay-in-days":32,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Hum Genomics"],"DOI":"10.1186\/s40246-026-00921-2","type":"journal-article","created":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T22:34:46Z","timestamp":1770417286000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["DUCKS4: a comprehensive workflow for Nanopore sequencing analysis of facioscapulohumeral muscular dystrophy (FSHD)"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-9196-2097","authenticated-orcid":false,"given":"Tamara","family":"L\u00f6wenstern","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4995-7351","authenticated-orcid":false,"given":"Silvia","family":"Madritsch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3561-653X","authenticated-orcid":false,"given":"David","family":"Horner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9289-3453","authenticated-orcid":false,"given":"Nadja","family":"Brait","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naz","family":"G\u00fcleray Lafci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Schachner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6840-1802","authenticated-orcid":false,"given":"Maria","family":"Gerykova Bujalkova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tadeusz","family":"Ka\u0142u\u017cewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pawel","family":"Szyld","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Hengstschl\u00e4ger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Dremsek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franco","family":"Laccone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,2,6]]},"reference":[{"issue":"12","key":"921_CR1","doi-asserted-by":"publisher","first-page":"1056","DOI":"10.1212\/WNL.0000000000000797","volume":"83","author":"JC Deenen","year":"2014","unstructured":"Deenen JC, Arnts H, van der Maarel SM, et al. Population-based incidence and prevalence of facioscapulohumeral dystrophy. Neurology. 2014;83(12):1056\u20139. https:\/\/doi.org\/10.1212\/WNL.0000000000000797. (PMID: 25122204; PMCID: PMC4166358).","journal-title":"Neurology"},{"issue":"1","key":"921_CR2","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1007\/s00415-020-10144-7","volume":"268","author":"L Vercelli","year":"2021","unstructured":"Vercelli L, Mele F, Ruggiero L, et al. A 5-year clinical follow-up study from the Italian National Registry for FSHD. J Neurol. 2021;268(1):356\u201366. https:\/\/doi.org\/10.1007\/s00415-020-10144-7.","journal-title":"J Neurol"},{"issue":"4","key":"921_CR3","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1016\/j.nmd.2013.01.008","volume":"23","author":"JM Statland","year":"2013","unstructured":"Statland JM, McDermott MP, Heatwole C, et al. Reevaluating measures of disease progression in facioscapulohumeral muscular dystrophy. Neuromuscul Disord. 2013;23(4):306\u201312. https:\/\/doi.org\/10.1016\/j.nmd.2013.01.008.","journal-title":"Neuromuscul Disord"},{"key":"921_CR4","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1002\/ana.410430303","volume":"43","author":"R Tawil","year":"1998","unstructured":"Tawil R, Figlewicz DA, Griggs RC, et al. Facioscapulohumeral dystrophy: a distinct regional myopathy with a novel molecular pathogenesis. Ann Neurol. 1998;43:279\u201382. https:\/\/doi.org\/10.1002\/ana.410430303.","journal-title":"Ann Neurol"},{"key":"921_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/mus.20522","volume":"34","author":"R Tawil","year":"2006","unstructured":"Tawil R, Van Der Maarel SM. Facioscapulohumeral muscular dystrophy. Muscle Nerve. 2006;34:1\u201315. https:\/\/doi.org\/10.1002\/mus.20522.","journal-title":"Muscle Nerve"},{"key":"921_CR6","doi-asserted-by":"publisher","DOI":"10.1186\/2044-5040-4-12","volume":"4","author":"R Tawil","year":"2014","unstructured":"Tawil R, van der Maarel SM, Tapscott SJ. Facioscapulohumeral dystrophy: the path to consensus on pathophysiology. Skelet Muscle. 2014;4:12. https:\/\/doi.org\/10.1186\/2044-5040-4-12.","journal-title":"Skelet Muscle"},{"issue":"5999","key":"921_CR7","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1126\/science.1189044","volume":"329","author":"RJ Lemmers","year":"2010","unstructured":"Lemmers RJ, van der Vliet P, Klooster R, et al. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science. 2010;329(5999):1650\u20133. https:\/\/doi.org\/10.1126\/science.1189044. (PMID:20724583;PMCID:PMC4677822).","journal-title":"Science"},{"issue":"12","key":"921_CR8","doi-asserted-by":"publisher","first-page":"1370","DOI":"10.1038\/ng.2454","volume":"44","author":"RJ Lemmers","year":"2012","unstructured":"Lemmers RJ, Tawil R, Petek L, et al. Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2. Nat Genet. 2012;44(12):1370\u20134. https:\/\/doi.org\/10.1038\/ng.2454.","journal-title":"Nat Genet"},{"key":"921_CR9","doi-asserted-by":"publisher","first-page":"729","DOI":"10.3390\/ijms21030729","volume":"21","author":"KRQ Lim","year":"2020","unstructured":"Lim KRQ, Nguyen Q, Yokota T. DUX4 signalling in the pathogenesis of Facioscapulohumeral muscular dystrophy. Int J Mol Sci. 2020;21:729. https:\/\/doi.org\/10.3390\/ijms21030729.","journal-title":"Int J Mol Sci"},{"issue":"23","key":"921_CR10","doi-asserted-by":"publisher","first-page":"e2441","DOI":"10.1212\/WNL.0000000000009617","volume":"94","author":"K Hamanaka","year":"2020","unstructured":"Hamanaka K, \u0160ikrov\u00e1 D, Mitsuhashi S, et al. Homozygous nonsense variant in LRIF1 associated with facioscapulohumeral muscular dystrophy. Neurology. 2020;94(23):e2441\u20137. https:\/\/doi.org\/10.1212\/WNL.0000000000009617.","journal-title":"Neurology"},{"key":"921_CR11","doi-asserted-by":"publisher","unstructured":"Lemmers RJ, van der Vliet P, van der Gaag K, et al. Worldwide Population Analysis of the 4q and 10q Subtelomeres Identifies Only Four Discrete Interchromosomal Sequence Transfers in Human Evolution. Am J Human Genet. 2010;86(3):364\u2013377. ISSN 0002\u20139297. https:\/\/doi.org\/10.1016\/j.ajhg.2010.01.035.","DOI":"10.1016\/j.ajhg.2010.01.035"},{"issue":"5","key":"921_CR12","doi-asserted-by":"publisher","first-page":"1020","DOI":"10.1016\/j.ajhg.2016.03.013","volume":"98","author":"ML van den Boogaard","year":"2016","unstructured":"van den Boogaard ML, Lemmers RJ, Balog J, et al. Mutations in DNMT3B Modify Epigenetic Repression of the D4Z4 Repeat and the Penetrance of Facioscapulohumeral Dystrophy. Am J Hum Genet. 2016;98(5):1020\u20139. https:\/\/doi.org\/10.1016\/j.ajhg.2016.03.013. (PMID:27153398;PMCID:PMC4863565).","journal-title":"Am J Hum Genet"},{"key":"921_CR13","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/ng999","volume":"32","author":"RJ Lemmers","year":"2002","unstructured":"Lemmers RJ, de Kievit P, Sandkuijl L, et al. Facioscapulohumeral muscular dystrophy is uniquely associated with one of the two variants of the 4q subtelomere. Nat Genet. 2002;32:235\u20136. https:\/\/doi.org\/10.1038\/ng999.","journal-title":"Nat Genet"},{"issue":"2","key":"921_CR14","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1006\/geno.2002.6690","volume":"79","author":"M Van Geel","year":"2002","unstructured":"Van Geel M, Dickson MC, Beck AF, et al. Genomic analysis of human chromosome 10q and 4q telomeres suggests a common origin. Genomics. 2002;79(2):210\u20137. https:\/\/doi.org\/10.1006\/geno.2002.6690.","journal-title":"Genomics"},{"issue":"3","key":"921_CR15","doi-asserted-by":"publisher","DOI":"10.1212\/NXG.0000000000200076","volume":"9","author":"M Delourme","year":"2023","unstructured":"Delourme M, Charlene C, Gerard L, et al. Complex 4q35 and 10q26 rearrangements: a challenge for molecular diagnosis of patients with facioscapulohumeral dystrophy. Neurol Genet. 2023;9(3):e200076.","journal-title":"Neurol Genet"},{"issue":"1","key":"921_CR16","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1111\/cge.14533","volume":"106","author":"E Giardina","year":"2024","unstructured":"Giardina E, Cama\u00f1o P, Burton-Jones S, et al. Best practice guidelines on genetic diagnostics of facioscapulohumeral muscular dystrophy: update of the 2012 guidelines. Clin Genet. 2024;106(1):13\u201326. https:\/\/doi.org\/10.1111\/cge.14533.","journal-title":"Clin Genet"},{"key":"921_CR17","doi-asserted-by":"publisher","unstructured":"Lemmers, RJ, van der Vliet; P, Blatnik; A, et al. Chromosome 10q-linked FSHD identifies DUX4 as principal disease gene. J Med Genet. 2022;59(2):180\u2013188. https:\/\/doi.org\/10.1136\/jmedgenet-2020-107041. PMID: 33436523; PMCID: PMC8273184.","DOI":"10.1136\/jmedgenet-2020-107041"},{"issue":"2","key":"921_CR18","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1093\/brain\/awad312","volume":"147","author":"RJLF Lemmers","year":"2024","unstructured":"Lemmers RJLF, Butterfield RJ, van der Vliet PJ, de Bleecker JL, van der Pol L, Dunn DM, et al. Autosomal dominant in cis D4Z4 repeat array duplication alleles in facioscapulohumeral dystrophy. Brain. 2024;147(2):414\u201326. https:\/\/doi.org\/10.1093\/brain\/awad312. (PMID:37703328).","journal-title":"Brain"},{"issue":"10","key":"921_CR19","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1002\/humu.23304","volume":"38","author":"K Nguyen","year":"2017","unstructured":"Nguyen K, Puppo F, Roche S, et al. Molecular combing reveals complex 4q35 rearrangements in Facioscapulohumeral dystrophy. Hum Mutat. 2017;38(10):1432\u201341.","journal-title":"Hum Mutat"},{"key":"921_CR20","unstructured":"Preston, MK, Wang, L. Facioscapulohumeral muscular dystrophy. In: Adam MP, Feldman J, Mirzaa GM, et al., eds. GeneReviews\u00ae [Internet]. Seattle (WA): University of Washington, Seattle; 1993\u20132025. Updated 2025 Jul 10. Available from: https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK1443\/."},{"key":"921_CR21","doi-asserted-by":"publisher","DOI":"10.1136\/jmedgenet-2019-106638","author":"L Qiu","year":"2020","unstructured":"Qiu L, Ye Z, Lin L, et al. Clinical and genetic features of somatic mosaicism in facioscapulohumeral dystrophy. J Med Genet. 2020. https:\/\/doi.org\/10.1136\/jmedgenet-2019-106638.","journal-title":"J Med Genet"},{"issue":"6","key":"921_CR22","doi-asserted-by":"publisher","DOI":"10.1212\/NXG.0000000000200107","volume":"9","author":"NM Guruju","year":"2023","unstructured":"Guruju NM, Jump V, Lemmers R, et al. Molecular diagnosis of facioscapulohumeral muscular dystrophy in patients clinically suspected of FSHD using optical genome mapping. Neurol Genet. 2023;9(6):e200107. https:\/\/doi.org\/10.1212\/NXG.0000000000200107.","journal-title":"Neurol Genet"},{"key":"921_CR23","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2021.07.021","author":"AA Stence","year":"2021","unstructured":"Stence AA, Thomason JG, Pruessner JA, et al. Validation of optical genome mapping for the molecular diagnosis of facioscapulohumeral muscular dystrophy. J Mol Diagn. 2021. https:\/\/doi.org\/10.1016\/j.jmoldx.2021.07.021.","journal-title":"J Mol Diagn"},{"issue":"4","key":"921_CR24","doi-asserted-by":"publisher","DOI":"10.1212\/NXG.0000000000000039","volume":"1","author":"C Angelini","year":"2015","unstructured":"Angelini C. LGMD phenotype due to a new gene and dysferlinopathy investigated by next-generation sequencing. Neurol Genet. 2015;1(4):e39. https:\/\/doi.org\/10.1212\/NXG.0000000000000039.","journal-title":"Neurol Genet"},{"key":"921_CR25","doi-asserted-by":"publisher","DOI":"10.3390\/genes15111409","volume":"15","author":"A Luglio","year":"2024","unstructured":"Luglio A, Maggi E, Riviello F, et al. Hereditary neuromuscular disorders in reproductive medicine. Genes. 2024;15:1409. https:\/\/doi.org\/10.3390\/genes15111409.","journal-title":"Genes"},{"key":"921_CR26","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2024.1522203","volume":"15","author":"M Tan","year":"2025","unstructured":"Tan M, Huo H, Feng J, et al. Facioscapulohumeral muscular dystrophy type 1 combined with becker muscular dystrophy: a family case report. Front Genet. 2025;15:1522203. https:\/\/doi.org\/10.3389\/fgene.2024.1522203.","journal-title":"Front Genet"},{"issue":"9","key":"921_CR27","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1101\/gr.277871.123","volume":"33","author":"RJ Butterfield","year":"2023","unstructured":"Butterfield RJ, Dunn DM, Duval B, Moldt S, Weiss RB. Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing. Genome Res. 2023;33(9):1439\u201354. https:\/\/doi.org\/10.1101\/gr.277871.123.","journal-title":"Genome Res"},{"issue":"1","key":"921_CR28","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-022-03743-7","volume":"20","author":"Y Hiramuki","year":"2022","unstructured":"Hiramuki Y, Kure Y, Saito Y, Ogawa M, Ishikawa K, Mori-Yoshimura M, et al. Simultaneous measurement of the size and methylation of chromosome 4qA-D4Z4 repeats in facioscapulohumeral muscular dystrophy by long-read sequencing. J Transl Med. 2022;20(1):517. https:\/\/doi.org\/10.1186\/s12967-022-03743-7.","journal-title":"J Transl Med"},{"key":"921_CR29","doi-asserted-by":"publisher","DOI":"10.1016\/j.gimo.2024.101817","volume":"2","author":"K Li","year":"2024","unstructured":"Li K, Quiat D, She F, Liu Y, He R, Haghighi A, et al. Genetic diagnosis of facioscapulohumeral muscular dystrophy type 1 using rare-variant linkage analysis and long-read genome sequencing. Genet Med Open. 2024;2:101817. https:\/\/doi.org\/10.1016\/j.gimo.2024.101817.","journal-title":"Genet Med Open"},{"issue":"12","key":"921_CR30","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1136\/jmg-2023-109832","volume":"61","author":"Y Wang","year":"2024","unstructured":"Wang Y, Zhao Z, Meng F, Kong X. Accurate prenatal diagnosis of facioscapulohumeral muscular dystrophy 1 using nanopore sequencing. J Med Genet. 2024;61(12):1096\u2013102. https:\/\/doi.org\/10.1136\/jmg-2023-109832.","journal-title":"J Med Genet"},{"key":"921_CR31","doi-asserted-by":"publisher","unstructured":"Xiao LC, Semwal A, St John B, Zeglinski K, Su S, Lancaster J, et al. D4Z4End2End: complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS and reference cohorts. medRxiv. 2025. 2025.04.24.25326320. https:\/\/doi.org\/10.1101\/2025.04.24.25326320. PMID: not available (preprint).","DOI":"10.1101\/2025.04.24.25326320"},{"key":"921_CR32","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-024-05259-8","volume":"22","author":"M Huang","year":"2024","unstructured":"Huang M, Zhang Q, Jiao J, et al. Comprehensive genetic analysis of facioscapulohumeral muscular dystrophy by Nanopore long-read whole-genome sequencing. J Transl Med. 2024;22:451. https:\/\/doi.org\/10.1186\/s12967-024-05259-8.","journal-title":"J Transl Med"},{"issue":"7","key":"921_CR33","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1016\/j.nmd.2023.05.004","volume":"7","author":"P Yeetong","year":"2023","unstructured":"Yeetong P, Kulsirichawaroj P, Kumutpongpanich T, et al. Long-read Nanopore sequencing identified D4Z4 contractions in patients with facioscapulohumeral muscular dystrophy. Neuromuscul Disord. 2023;7(7):551\u20136. https:\/\/doi.org\/10.1016\/j.nmd.2023.05.004.","journal-title":"Neuromuscul Disord"},{"issue":"10","key":"921_CR34","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.1038\/s41587-023-01662-6","volume":"10","author":"M Rautiainen","year":"2023","unstructured":"Rautiainen M, Nurk S, Walenz BP, et al. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotechnol. 2023;10(10):1474\u201382. https:\/\/doi.org\/10.1038\/s41587-023-01662-6.","journal-title":"Nat Biotechnol"},{"key":"921_CR35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0253830","volume":"16","author":"A Jones","year":"2021","unstructured":"Jones A, Torkel C, Stanley D, et al. High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing. PLoS ONE. 2021;16:e0253830. https:\/\/doi.org\/10.1371\/journal.pone.0253830.","journal-title":"PLoS ONE"},{"key":"921_CR36","unstructured":"R Core Team. R: A language and environment for statistical ## computing. R Foundation for Statistical Computing, Vienna, Austria; 2021. https:\/\/www.R-project.org\/"},{"key":"921_CR37","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. https:\/\/doi.org\/10.1186\/1471-2105-10-421.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"921_CR38","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1086\/521986","volume":"81","author":"RJ Lemmers","year":"2007","unstructured":"Lemmers RJ, Wohlgemuth M, van der Gaag K, et al. Specific sequence variations within the 4q35 region are associated with facioscapulohumeral muscular dystrophy. Am J Hum Genet. 2007;81(5):884\u201394. https:\/\/doi.org\/10.1086\/521986.","journal-title":"Am J Hum Genet"},{"key":"921_CR39","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","volume":"37","author":"H Li","year":"2021","unstructured":"Li H. New strategies to improve minimap2 alignment accuracy. Bioinformatics. 2021;37:4572\u20134. https:\/\/doi.org\/10.1093\/bioinformatics\/btab705.","journal-title":"Bioinformatics"},{"issue":"2","key":"921_CR40","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. https:\/\/doi.org\/10.1093\/gigascience\/giab008.","journal-title":"GigaScience"},{"key":"921_CR41","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1038\/s43588-022-00387-x","volume":"2","author":"Z Zheng","year":"2022","unstructured":"Zheng Z, Li S, Su J, et al. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nat Comput Sci. 2022;2:797\u2013803. https:\/\/doi.org\/10.1038\/s43588-022-00387-x.","journal-title":"Nat Comput Sci"},{"key":"921_CR42","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1007\/978-1-0716-2819-5_8","volume":"2590","author":"M Martin","year":"2023","unstructured":"Martin M, Ebert P, Marschall T. Read-Based Phasing and Analysis of Phased Variants with WhatsHap. Methods Mol Biol. 2023;2590:127\u201338. https:\/\/doi.org\/10.1007\/978-1-0716-2819-5_8. (PMID: 36335496).","journal-title":"Methods Mol Biol"},{"key":"921_CR43","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1038\/s41587-023-02024-y","volume":"42","author":"M Smolka","year":"2024","unstructured":"Smolka M, Paulin LF, Grochowski CM, et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol. 2024;42:1571\u201380. https:\/\/doi.org\/10.1038\/s41587-023-02024-y.","journal-title":"Nat Biotechnol"},{"key":"921_CR44","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"2","author":"P Cingolani","year":"2012","unstructured":"Cingolani P, Platts A, le Wang, L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;2:80\u201392 (PMID: 22728672).","journal-title":"Fly"},{"key":"921_CR45","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2012.00035","volume":"3","author":"P Cingolani","year":"2012","unstructured":"Cingolani P, Patel VM, Coon M, et al. Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift. Front Genet. 2012;3:35.","journal-title":"Front Genet"},{"issue":"1","key":"921_CR46","doi-asserted-by":"publisher","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","volume":"42","author":"M Landrum","year":"2014","unstructured":"Landrum M, Lee J, Riley G, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42(1):D980\u20135. https:\/\/doi.org\/10.1093\/nar\/gkt1113. (PMID: 24234437).","journal-title":"Nucleic Acids Res"},{"key":"921_CR47","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.191","author":"W Shen","year":"2024","unstructured":"Shen W, Sipos B, Zhao L. Seqkit2: a swiss army knife for sequence and alignment processing. iMeta. 2024. https:\/\/doi.org\/10.1002\/imt2.191.","journal-title":"iMeta"},{"issue":"15","key":"921_CR48","doi-asserted-by":"publisher","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","volume":"34","author":"W De Coster","year":"2018","unstructured":"De Coster W, D\u2019Hert S, Schultz D, et al. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34(15):2666\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/bty149.","journal-title":"Bioinformatics"},{"key":"921_CR49","unstructured":"Posit team. RStudio: integrated Development Environment for R. Boston MA: Posit Software, PBC; 2025. Available from http:\/\/www.posit.co\/."},{"key":"921_CR50","unstructured":"Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. 2016. ISBN 978-3-319-24277-4. https:\/\/ggplot2.tidyverse.org."},{"issue":"2","key":"921_CR51","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1212\/01.WNL.0000078889.51444.81","volume":"61","author":"RJ Lemmers","year":"2003","unstructured":"Lemmers RJ, Osborn M, Haaf T, et al. D4F104S1 deletion in facioscapulohumeral muscular dystrophy: phenotype, size, and detection. Neurology. 2003;61(2):178\u201383.","journal-title":"Neurology"},{"issue":"5","key":"921_CR52","doi-asserted-by":"publisher","first-page":"748","DOI":"10.1093\/hmg\/ddab250","volume":"31","author":"RJ Lemmers","year":"2022","unstructured":"Lemmers RJ, van der Vliet P, Granado D, et al. High-resolution breakpoint junction mapping of proximally extended D4Z4 deletions in FSHD1 reveals evidence for a founder effect. Hum Mol Genet. 2022;31(5):748\u201360.","journal-title":"Hum Mol Genet"},{"issue":"9","key":"921_CR53","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1136\/jmedgenet-2018-105949","volume":"56","author":"K Nguyen","year":"2019","unstructured":"Nguyen K, Broucqsault N, Chaix C, et al. Deciphering the complexity of the 4q and 10q subtelomeres by molecular combing in healthy individuals and patients with facioscapulohumeral dystrophy. J Med Genet. 2019;56(9):590\u2013601.","journal-title":"J Med Genet"},{"key":"921_CR54","doi-asserted-by":"publisher","unstructured":"Lemmers RJ, O\u2019Shea S, Padberg G, et al. Best practice guidelines on genetic diagnostics of Facioscapulohumeral muscular dystrophy: Workshop 9th June 2010, LUMC, Leiden, The Netherlands. Neuromusc Disord. 2012;22(5):463\u2013470, ISSN 0960\u20138966: https:\/\/doi.org\/10.1016\/j.nmd.2011.09.004.","DOI":"10.1016\/j.nmd.2011.09.004"},{"issue":"6","key":"921_CR55","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics11060982","volume":"11","author":"NV Zernov","year":"2021","unstructured":"Zernov NV, Guskova AA, Skoblov MY. FSHD1 diagnosis in a Russian population using a qpcr-based approach. Diagnostics. 2021;11(6):982. https:\/\/doi.org\/10.3390\/diagnostics11060982.","journal-title":"Diagnostics"},{"key":"921_CR56","doi-asserted-by":"publisher","DOI":"10.1136\/jmg-2025-110827","author":"M Huang","year":"2025","unstructured":"Huang M, Zhang Q, Wu S, et al. Accurate detection of D4Z4 repeats, methylation and allele haplotype in facioscapulohumeral muscular dystrophy 1 using nanopore long-read adaptive sampling sequencing: a pilot study. J Med Genet. 2025. https:\/\/doi.org\/10.1136\/jmg-2025-110827.","journal-title":"J Med Genet"}],"container-title":["Human Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40246-026-00921-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40246-026-00921-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40246-026-00921-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T12:48:59Z","timestamp":1773146939000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s40246-026-00921-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,6]]},"references-count":56,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["921"],"URL":"https:\/\/doi.org\/10.1186\/s40246-026-00921-2","relation":{},"ISSN":["1479-7364"],"issn-type":[{"value":"1479-7364","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,6]]},"assertion":[{"value":"17 November 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 January 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 February 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This study was approved by the ethics committee of the Medical University of Vienna under EK Nr. 1078\/2024. Informed consent was obtained from all the patients included in this study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"48"}}