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Competence Center T\u00fcbingen","award":["OS 647\/1-1"],"award-info":[{"award-number":["OS 647\/1-1"]}]},{"name":"DFG-funded NGS Competence Center T\u00fcbingen","award":["458746698"],"award-info":[{"award-number":["458746698"]}]},{"name":"DFG-funded NGS Competence Center T\u00fcbingen","award":["GAP-101080997"],"award-info":[{"award-number":["GAP-101080997"]}]},{"name":"DFG-funded NGS Competence Center T\u00fcbingen","award":["INST 37\/1049-1"],"award-info":[{"award-number":["INST 37\/1049-1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Friedreich\u2019s ataxia (FRDA) is an autosomal recessive neurodegenerative disorder characterized by ataxia, sensory loss and pyramidal signs. While the majority of FRDA cases are caused by biallelic GAA trinucleotide repeat expansions in intron 1 of FXN, there is a subset of patients harboring a heterozygous pathogenic small variant compound-heterozygous with a GAA repeat expansion. We report on the diagnostic journey of a 21-year-old patient who was clinically suspected of having FRDA at the age of 12 years. Genetic testing included fragment analysis, gene panel analysis and exome sequencing, which only detected one pathogenic heterozygous missense variant (c.389 G&gt;T,p.Gly130Val) in FXN. Although conventional repeat analyses failed to detect GAA expansions in our patient, subsequent short-read genome sequencing (GS) indicated a potential GAA repeat expansion. This finding was confirmed by long-read GS, which in addition revealed a complex pattern of interruptions. Both large and small GAA expansions with divergent interruptions containing G, A, GA, GAG and\/or GAAG sequences were present within one allele, indicating mosaic sequence variations. Our findings underscore the complexity of repeat expansions which can exhibit both interruptions and somatic instability. We also highlight the utility of long-read GS in unraveling intricate genetic profiles, ultimately contributing to more accurate diagnoses in clinical practice.<\/jats:p>","DOI":"10.3390\/ijms26114969","type":"journal-article","created":{"date-parts":[[2025,5,22]],"date-time":"2025-05-22T07:04:28Z","timestamp":1747897468000},"page":"4969","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Long-Read Sequencing Identifies Mosaic Sequence Variations in Friedreich\u2019s Ataxia-GAA Repeats"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7996-5283","authenticated-orcid":false,"given":"Joohyun","family":"Park","sequence":"first","affiliation":[{"name":"Institute of Medical Genetics and Applied Genomics, University of T\u00fcbingen, 72076 T\u00fcbingen, 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Clinical Brain Research, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Buena-Atienza","sequence":"additional","affiliation":[{"name":"Institute of Medical Genetics and Applied Genomics, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"},{"name":"NGS Competence Center T\u00fcbingen, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-0399-7217","authenticated-orcid":false,"given":"Lara G.","family":"St\u00fchn","sequence":"additional","affiliation":[{"name":"Institute of Medical Genetics and Applied Genomics, University of T\u00fcbingen, 72076 T\u00fcbingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9009-5458","authenticated-orcid":false,"given":"Caspar","family":"Gross","sequence":"additional","affiliation":[{"name":"Institute of Medical Genetics and 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Engl. J. Med."},{"key":"ref_3","unstructured":"Adam, M.P., Feldman, J., Mirzaa, G.M., Pagon, R.A., Wallace, S.E., Bean, L.J.H., Gripp, K.W., and Amemiya, A. (2025). Friedreich Ataxia. GeneReviews((R)) 1993\u20132025, University of Washington. GeneReviews\u00ae [Internet]."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1034\/j.1600-0404.2003.00190.x","article-title":"Expanded GAA repeats and clinical variation in Friedreich\u2019s ataxia","volume":"109","author":"Mateo","year":"2004","journal-title":"Acta Neurol. Scand."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"4112","DOI":"10.1007\/s00415-023-11745-8","article-title":"Short-read genome sequencing allows \u201cen route\u201d diagnosis of patients with atypical Friedreich ataxia","volume":"270","author":"Fleszar","year":"2023","journal-title":"J. Neurol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/brain\/104.3.589","article-title":"Friedreich\u2019s ataxia: A clinical and genetic study of 90 families with an analysis of early diagnostic criteria and intrafamilial clustering of clinical features","volume":"104","author":"Harding","year":"1981","journal-title":"Brain"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1002\/mds.1210","article-title":"Sequence variation in GAA repeat expansions may cause differential phenotype display in Friedreich\u2019s ataxia","volume":"16","author":"McDaniel","year":"2001","journal-title":"Mov. Disord."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1002\/ana.24595","article-title":"Compound heterozygous FXN mutations and clinical outcome in friedreich ataxia","volume":"79","author":"Galea","year":"2016","journal-title":"Ann. Neurol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/s10048-019-00594-1","article-title":"The first biallelic missense mutation in the FXN gene in a consanguineous Turkish family with Charcot-Marie-Tooth-like phenotype","volume":"21","author":"Candayan","year":"2020","journal-title":"Neurogenetics"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1002\/ana.22671","article-title":"FXN methylation predicts expression and clinical outcome in Friedreich ataxia","volume":"71","author":"Carrodus","year":"2012","journal-title":"Ann. Neurol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Long, A., Napierala, J.S., Polak, U., Hauser, L., Koeppen, A.H., Lynch, D.R., and Napierala, M. (2017). Somatic instability of the expanded GAA repeats in Friedreich\u2019s ataxia. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0189990"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Nethisinghe, S., Kesavan, M., Ging, H., Labrum, R., Polke, J.M., Islam, S., Garcia-Moreno, H., Callaghan, M.F., Cavalcanti, F., and Pook, M.A. (2021). Interruptions of the FXN GAA Repeat Tract Delay the Age at Onset of Friedreich\u2019s Ataxia in a Location Dependent Manner. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22147507"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4754","DOI":"10.1093\/bioinformatics\/btz431","article-title":"ExpansionHunter: A sequence-graph-based tool to analyze variation in short tandem repeat regions","volume":"35","author":"Dolzhenko","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Al-Mahdawi, S., Ging, H., Bayot, A., Cavalcanti, F., La Cognata, V., Cavallaro, S., Giunti, P., and Pook, M.A. (2018). Large Interruptions of GAA Repeat Expansion Mutations in Friedreich Ataxia Are Very Rare. Front. Cell Neurosci., 12.","DOI":"10.3389\/fncel.2018.00443"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"fcad020","DOI":"10.1093\/braincomms\/fcad020","article-title":"Sequencing through hyperexpanded Friedreich\u2019s ataxia-GAA repeats by nanopore technology: Implications in genotype-phenotype correlation","volume":"5","author":"Uppili","year":"2023","journal-title":"Brain Commun."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1101\/gr.141705.112","article-title":"Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene","volume":"23","author":"Loomis","year":"2013","journal-title":"Genome Res."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Mangin, A., de Pontual, L., Tsai, Y.C., Monteil, L., Nizon, M., Boisseau, P., Mercier, S., Ziegle, J., Harting, J., and Heiner, C. (2021). Robust Detection of Somatic Mosaicism and Repeat Interruptions by Long-Read Targeted Sequencing in Myotonic Dystrophy Type 1. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22052616"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1093\/brain\/awac160","article-title":"Mosaic divergent repeat interruptions in XDP influence repeat stability and disease onset","volume":"146","author":"Trinh","year":"2023","journal-title":"Brain"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1016\/j.ajhg.2021.03.011","article-title":"30 years of repeat expansion disorders: What have we learned and what are the remaining challenges?","volume":"108","author":"Depienne","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Park, J., Sturm, M., Seibel-Kelemen, O., Ossowski, S., and Haack, T.B. (2024). Lessons Learned from Translating Genome Sequencing to Clinical Routine: Understanding the Accuracy of a Diagnostic Pipeline. Genes, 15.","DOI":"10.3390\/genes15010136"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1038\/s41588-024-01719-5","article-title":"A GGC-repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy","volume":"56","author":"Figueroa","year":"2024","journal-title":"Nat. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1816","DOI":"10.1093\/bioinformatics\/btac058","article-title":"LongPhase: An ultra-fast chromosome-scale phasing algorithm for small and large variants","volume":"38","author":"Lin","year":"2022","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1038\/s43588-022-00387-x","article-title":"Symphonizing pileup and full-alignment for deep learning-based long-read variant calling","volume":"2","author":"Zheng","year":"2022","journal-title":"Nat. Comput. Sci."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/11\/4969\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:38:09Z","timestamp":1760031489000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/11\/4969"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,22]]},"references-count":24,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2025,6]]}},"alternative-id":["ijms26114969"],"URL":"https:\/\/doi.org\/10.3390\/ijms26114969","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,22]]}}}