{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T17:38:29Z","timestamp":1787506709494,"version":"build-2736575974"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T00:00:00Z","timestamp":1770249600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100004923","name":"AFM Telethon","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004923","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Agence Nationale pour la recherche","award":["ANR-24-CE17-0115-01"],"award-info":[{"award-number":["ANR-24-CE17-0115-01"]}]},{"DOI":"10.13039\/100007586","name":"Aix-Marseille University-A*Midex","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100007586","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Marseille Maladies Rares"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Facioscapulohumeral dystrophy (FSHD) is primarily associated with contraction of the D4Z4 macrosatellite array at the 4q35 locus. Unaffected individuals carry 11\u2013150 D4Z4 repeats, whereas \u223c95% of FSHD patients (FSHD1) exhibit a contraction to 1\u201310 units, along with reduced DNA methylation. In another \u223c3% of patients (FSHD2), the disease results from a digenic mechanism associated with the presence of a pathogenic variant in the SMCHD1 gene, leading to the epigenetic deregulation of the 4q35 locus. However, 1%\u20132% of clinically diagnosed patients lack a defined genetic cause, highlighting diagnostic gaps. In prior work, we identified &amp;gt;70 patients, clinically diagnosed with FSHD and carrying a complex structural variant of the 4q35 or 10q26 loci. A potential pathogenicity of these structural variants was evoked in some cases, in the absence of other FSHD-associated genetic features.<\/jats:p>\n                  <jats:p>Given their diagnostic relevance, here we performed detailed structural analyses of these rearrangements in seven representative cases carrying different structural variants of the 4q35 or 10q26 loci using high-resolution long-read sequencing technologies (Oxford Nanopore and PacBio) and suspected of FSHD. By comparing the advantages and limitations of several methodological long-read sequencing strategies, we resolved the architecture and methylation patterns across the 4q35 and 10q26 loci at the nucleotide level. We show that duplicated alleles arise from intrachromosomal recombination between LSau elements contained within D4Z4 and distal subtelomeric \u03b2-satellite elements, producing variable deletions within the proximal D4Z4 region, with breakpoints differing among patients. These complex structural variants are not detectable using standard technologies, such as Bionano Optical Genome Mapping, and require manual curation for identification during routine molecular diagnosis procedures. Importantly, determining the pathogenic relevance of these rearrangements necessitates integration of structural and epigenetic features typically associated with FSHD.<\/jats:p>\n                  <jats:p>Our results underscore the importance of in-depth molecular characterization for patients with clinical FSHD who test negative for FSHD1\/FSHD2 by conventional diagnostic methods. We also show that structural variants might be considered as likely to be pathogenic, in the absence of an SMCHD1 variant. Overall, as structural variants at 4q35 are increasingly identified in patients clinically diagnosed with FSHD, their comprehensive analysis is crucial to refine diagnosis, guide genetic counselling and, ultimately, improve clinical care for individuals clinically suspected of FSHD but presenting with an atypical molecular profile.<\/jats:p>","DOI":"10.1093\/brain\/awag029","type":"journal-article","created":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T12:41:50Z","timestamp":1769172110000},"page":"1750-1767","source":"Crossref","is-referenced-by-count":2,"title":["Benchmarking long-read sequencing approaches to resolve facioscapulohumeral dystrophy locus complexity"],"prefix":"10.1093","volume":"149","author":[{"given":"Charlotte","family":"Tardy","sequence":"first","affiliation":[{"name":"Aix-Marseille Univ-INSERM, Marseille Medical Genetics , Marseille 13005 ,","place":["France"]},{"name":"Service de G\u00e9n\u00e9tique M\u00e9dicale, H\u00f4pitaux Universitaires de Marseille, H\u00f4pital Timone Adulte, Biog\u00e9nop\u00f4le , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean Philippe","family":"Trani","sequence":"additional","affiliation":[{"name":"Aix-Marseille Univ-INSERM, Marseille Medical Genetics , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6286-5526","authenticated-orcid":false,"given":"Victor","family":"Murcia Pienkowski","sequence":"additional","affiliation":[{"name":"Aix-Marseille Univ-INSERM, Marseille Medical Genetics , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Loeva","family":"Morin","sequence":"additional","affiliation":[{"name":"Aix-Marseille Univ-INSERM, Marseille Medical Genetics , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christel","family":"Castro","sequence":"additional","affiliation":[{"name":"Aix-Marseille Univ-INSERM, Marseille Medical Genetics , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louis","family":"Souville","sequence":"additional","affiliation":[{"name":"Aix-Marseille Univ-INSERM, Marseille Medical Genetics , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"Humbert","sequence":"additional","affiliation":[{"name":"Aix-Marseille Univ-INSERM, Marseille Medical Genetics , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laur\u00e8ne","family":"G\u00e9rard","sequence":"additional","affiliation":[{"name":"Service de G\u00e9n\u00e9tique M\u00e9dicale, H\u00f4pitaux Universitaires de Marseille, H\u00f4pital Timone Adulte, Biog\u00e9nop\u00f4le , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathalie","family":"Eudes","sequence":"additional","affiliation":[{"name":"Aix-Marseille Univ-INSERM, Marseille Medical Genetics , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amire","family":"Assoumani","sequence":"additional","affiliation":[{"name":"Service de G\u00e9n\u00e9tique M\u00e9dicale, H\u00f4pitaux Universitaires de Marseille, H\u00f4pital Timone Adulte, Biog\u00e9nop\u00f4le , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Bertaux","sequence":"additional","affiliation":[{"name":"Service de G\u00e9n\u00e9tique M\u00e9dicale, H\u00f4pitaux Universitaires de Marseille, H\u00f4pital Timone Adulte, Biog\u00e9nop\u00f4le , Marseille 13005 ,","place":["France"]},{"name":"Centre de ressources Biologiques, H\u00f4pitaux Universitaires de Marseille, H\u00f4pital Timone Adulte, Biog\u00e9nop\u00f4le , Marseille 13005 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"Verebi","sequence":"additional","affiliation":[{"name":"Service de M\u00e9decine G\u00e9nomique, Maladies de Systeme et D\u2019Organe-F\u00e9d\u00e9ration de G\u00e9n\u00e9tique et de M\u00e9decine G\u00e9nomique, DMU BioPhyGen, APHP Centre-Universit\u00e9 Paris Cite-H\u00f4pital Cochin , Paris 75014 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliette","family":"Nectoux","sequence":"additional","affiliation":[{"name":"Service de M\u00e9decine G\u00e9nomique, Maladies de Systeme et D\u2019Organe-F\u00e9d\u00e9ration de G\u00e9n\u00e9tique et de M\u00e9decine G\u00e9nomique, DMU BioPhyGen, APHP Centre-Universit\u00e9 Paris Cite-H\u00f4pital Cochin , Paris 75014 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Grenoble Alpes, Inserm, CHU Grenoble Alpes, GIN , Grenoble 38000 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6654-8090","authenticated-orcid":false,"given":"C\u00e9line","family":"Tard","sequence":"additional","affiliation":[{"name":"Inserm, CHU Lille, U1172 \u2013 LilNCog \u2013 Lille Neuroscience & Cognition, University of Lille , Lille F-59000 ,","place":["France"]},{"name":"Centre de r\u00e9f\u00e9rence des maladies neuromusculaires Nord\/Est\/Ile-de-France, Service de neurologie, CHU de Lille , Lille 59000 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2535-2198","authenticated-orcid":false,"given":"M\u00e9lanie","family":"Fradin","sequence":"additional","affiliation":[{"name":"Service de g\u00e9n\u00e9tique M\u00e9dicale CHU Rennes, Rennes, Centre de Comp\u00e9tences Maladies Neuromusculaires de Rennes , Rennes 35000 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sample","volume":"75","author":"Mostacciuolo","year":"2009","journal-title":"Clin Genet"},{"key":"2026050508310893800_awag029-B4","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s13023-014-0218-1","article-title":"Low penetrance in facioscapulohumeral muscular dystrophy type 1 with large pathological D4Z4 alleles: A cross-sectional multicenter study","volume":"10","author":"Salort-Campana","year":"2015","journal-title":"Orphanet J Rare Dis"},{"key":"2026050508310893800_awag029-B5","first-page":"411","article-title":"Genetic linkage map of facioscapulohumeral muscular dystrophy and five polymorphic loci on chromosome 4q35-qter","volume":"51","author":"Wijmenga","year":"1992","journal-title":"Am J Hum Genet"},{"key":"2026050508310893800_awag029-B6","first-page":"396","article-title":"Regional mapping of facioscapulohumeral muscular dystrophy gene on 4q35: Combined analysis of an international consortium","volume":"51","author":"Sarfarazi","year":"1992","journal-title":"Am J Hum Genet"},{"key":"2026050508310893800_awag029-B7","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1006\/geno.1994.1006","article-title":"Pulsed-field gel electrophoresis of the D4F104S1 locus reveals the size and the parental origin of the facioscapulohumeral muscular dystrophy (FSHD)-associated deletions","volume":"19","author":"Wijmenga","year":"1994","journal-title":"Genomics"},{"key":"2026050508310893800_awag029-B8","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1093\/hmg\/2.12.2037","article-title":"FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit","volume":"2","author":"van Deutekom","year":"1993","journal-title":"Hum Mol Genet"},{"key":"2026050508310893800_awag029-B9","doi-asserted-by":"crossref","first-page":"e372","DOI":"10.1212\/NXG.0000000000000372","article-title":"Methylation hotspots evidenced by deep sequencing in patients with facioscapulohumeral dystrophy and mosaicism","volume":"5","author":"Roche","year":"2019","journal-title":"Neurol Genet"},{"key":"2026050508310893800_awag029-B10","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1002\/ana.20625","article-title":"Variable hypomethylation of D4Z4 in facioscapulohumeral muscular dystrophy","volume":"58","author":"van Overveld","year":"2005","journal-title":"Ann Neurol"},{"key":"2026050508310893800_awag029-B11","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1126\/science.1189044","article-title":"A unifying genetic model for facioscapulohumeral muscular dystrophy","volume":"329","author":"Lemmers","year":"2010","journal-title":"Science"},{"key":"2026050508310893800_awag029-B12","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/S0378-1119(99)00267-X","article-title":"Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FSHD identifies a putative gene within each 3.3 kb 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patients","volume":"2","author":"Matsumura","year":"2002","journal-title":"BMC Neurol"},{"key":"2026050508310893800_awag029-B16","first-page":"100323","article-title":"Prevalence and disease progression of genetically-confirmed facioscapulohumeral muscular dystrophy type 1 (FSHD1) in China between 2001 and 2020: A nationwide population-based study","volume":"18","author":"Wang","year":"2022","journal-title":"Lancet Reg Health West Pac"},{"key":"2026050508310893800_awag029-B17","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1159\/000472291","article-title":"Physical mapping evidence for a duplicated region on chromosome 10qter showing high homology with the facioscapulohumeral muscular dystrophy locus on chromosome 4qter","volume":"3","author":"Deidda","year":"1995","journal-title":"Eur J Hum Genet"},{"key":"2026050508310893800_awag029-B18","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1002\/ana.10057","article-title":"Complete allele information in the diagnosis of facioscapulohumeral muscular dystrophy by triple DNA analysis","volume":"50","author":"Lemmers","year":"2001","journal-title":"Ann Neurol"},{"key":"2026050508310893800_awag029-B19","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1136\/jmedgenet-2020-107041","article-title":"Chromosome 10q-linked FSHD identifies DUX4 as principal disease gene","volume":"59","author":"Lemmers","year":"2022","journal-title":"J Med Genet"},{"key":"2026050508310893800_awag029-B20","doi-asserted-by":"crossref","first-page":"1370","DOI":"10.1038\/ng.2454","article-title":"Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2","volume":"44","author":"Lemmers","year":"2012","journal-title":"Nat Genet"},{"key":"2026050508310893800_awag029-B21","doi-asserted-by":"crossref","first-page":"e2441","DOI":"10.1212\/WNL.0000000000009617","article-title":"Homozygous nonsense variant in LRIF1 associated with facioscapulohumeral 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