{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T11:58:48Z","timestamp":1787918328896,"version":"build-2784847793"},"reference-count":157,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,16]],"date-time":"2024-12-16T00:00:00Z","timestamp":1734307200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Research Council, Advanced Grant","award":["742436"],"award-info":[{"award-number":["742436"]}]},{"name":"NSC-Reconstruct Consortium, European Union's Horizon 2020 Research and Innovation Program","award":["874758"],"award-info":[{"award-number":["874758"]}]},{"name":"C.H.D.I. Foundation","award":["JSC A11103"],"award-info":[{"award-number":["JSC A11103"]}]},{"name":"Leslie Gehry Prize for Innovation in Science from the Hereditary Disease Foundation"},{"DOI":"10.13039\/501100002426","name":"Fondazione Telethon","doi-asserted-by":"publisher","award":["GMR23T1059"],"award-info":[{"award-number":["GMR23T1059"]}],"id":[{"id":"10.13039\/501100002426","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002426","name":"Fondazione Telethon","doi-asserted-by":"publisher","award":["GMR23T1216"],"award-info":[{"award-number":["GMR23T1216"]}],"id":[{"id":"10.13039\/501100002426","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministero dell'Istruzione, dell'Universit\u00e0 e della Ricerca","award":["2022LBENTH"],"award-info":[{"award-number":["2022LBENTH"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The accurate characterization of triplet repeats, especially the overrepresented CAG repeats, is increasingly relevant for several reasons. First, germline expansion of CAG repeats above a gene-specific threshold causes multiple neurodegenerative disorders; for instance, Huntington\u2019s disease (HD) is triggered by &amp;gt;36 CAG repeats in the huntingtin (HTT) gene. Second, extreme expansions up to 800 CAG repeats have been found in specific cell types affected by the disease. Third, synonymous single nucleotide variants within the CAG repeat stretch influence the age of disease onset. Thus, new sequencing-based protocols that profile both the length and the exact nucleotide sequence of triplet repeats are crucial. Various strategies to enrich the target gene over the background, along with sequencing platforms and bioinformatic pipelines, are under development. This review discusses the concepts, challenges, and methodological opportunities for analyzing triplet repeats, using HD as a case study. Starting with traditional approaches, we will explore how sequencing-based methods have evolved to meet increasing scientific demands. We will also highlight experimental and bioinformatic challenges, aiming to provide a guide for accurate triplet repeat characterization for diagnostic and therapeutic purposes.<\/jats:p>","DOI":"10.1093\/nar\/gkae1155","type":"journal-article","created":{"date-parts":[[2024,12,16]],"date-time":"2024-12-16T10:08:16Z","timestamp":1734343696000},"source":"Crossref","is-referenced-by-count":12,"title":["Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington\u2019s disease"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1192-0684","authenticated-orcid":false,"given":"Simone","family":"Maestri","sequence":"first","affiliation":[{"name":"Department of Biosciences, University of Milan, Street Giovanni Celoria , 26, 20133, Milan,","place":["Italy"]},{"name":"INGM, Istituto Nazionale Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Street Francesco Sforza, 35, 20122, Milan,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6020-1287","authenticated-orcid":false,"given":"Davide","family":"Scalzo","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milan, Street Giovanni Celoria , 26, 20133, Milan,","place":["Italy"]},{"name":"INGM, Istituto Nazionale Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Street Francesco Sforza, 35, 20122, Milan,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6567-0660","authenticated-orcid":false,"given":"Gianluca","family":"Damaggio","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milan, Street Giovanni Celoria , 26, 20133, Milan,","place":["Italy"]},{"name":"INGM, Istituto Nazionale Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Street Francesco Sforza, 35, 20122, Milan,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4812-3809","authenticated-orcid":false,"given":"Martina","family":"Zobel","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milan, Street Giovanni Celoria , 26, 20133, Milan,","place":["Italy"]},{"name":"INGM, Istituto Nazionale Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Street Francesco Sforza, 35, 20122, Milan,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9793-9644","authenticated-orcid":false,"given":"Dario","family":"Besusso","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milan, Street Giovanni Celoria , 26, 20133, Milan,","place":["Italy"]},{"name":"INGM, Istituto Nazionale Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Street Francesco Sforza, 35, 20122, Milan,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0755-4917","authenticated-orcid":false,"given":"Elena","family":"Cattaneo","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milan, Street Giovanni Celoria , 26, 20133, Milan,","place":["Italy"]},{"name":"INGM, Istituto Nazionale Genetica Molecolare \u2018Romeo ed Enrica Invernizzi\u2019 , Street Francesco Sforza, 35, 20122, Milan,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,12,16]]},"reference":[{"key":"2025011110050469200_B1","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/nrg1348","article-title":"Microsatellites: simple sequences with complex evolution","volume":"5","author":"Ellegren","year":"2004","journal-title":"Nat. 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Neurol."},{"key":"2025011110050469200_B26","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1002\/ana.410410414","article-title":"Brain regional differences in the expansion of a CAG repeat in the spinocerebellar ataxias: dentatorubral-pallidoluysian atrophy, machado-joseph disease, and spinocerebellar ataxia type 1","volume":"41","author":"Hashida","year":"1997","journal-title":"Ann. Neurol."},{"key":"2025011110050469200_B27","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1002\/ana.410350116","article-title":"Myotonic dystrophy patients have larger CTG expansions in skeletal muscle than in leukocytes","volume":"35","author":"Thornton","year":"1994","journal-title":"Ann. 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Genet."},{"key":"2025011110050469200_B41","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1006\/mcpr.1993.1034","article-title":"A new polymerase chain reaction (PCR) assay for the trinucleotide repeat that is unstable and expanded on Huntington\u2019s disease chromosomes","volume":"7","author":"Warner","year":"1993","journal-title":"Mol. Cell. Probes"},{"key":"2025011110050469200_B42","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1093\/hmg\/3.1.65","article-title":"A CCG repeat polymorphism adjacent to the CAG repeat in the Huntington disease gene: implications for diagnostic accuracy and predictive testing","volume":"3","author":"Andrew","year":"1994","journal-title":"Hum. Mol. 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Sci."},{"key":"2025011110050469200_B64","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1161\/01.CIR.91.2.513","article-title":"Unstable triplet repeat diseases","volume":"91","author":"Monckton","year":"1995","journal-title":"Circulation"},{"key":"2025011110050469200_B65","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":"2025011110050469200_B66","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.fsigen.2015.11.005","article-title":"Sequence variation of 22 autosomal STR loci detected by next generation sequencing","volume":"21","author":"Gettings","year":"2016","journal-title":"Forensic Sci. Int. Genet."},{"key":"2025011110050469200_B67","doi-asserted-by":"crossref","first-page":"e418","DOI":"10.1016\/j.fsigss.2017.09.155","article-title":"Investigating the effects of different library preparation protocols on STR sequencing","volume":"6","author":"Riman","year":"2017","journal-title":"Forensic Sci. Int. Genet. Suppl. Ser."},{"key":"2025011110050469200_B68","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.3390\/biom13101546","article-title":"Optical genome mapping enables detection and accurate sizing of RFC1 repeat expansions","volume":"13","author":"Facchini","year":"2023","journal-title":"Biomolecules"},{"key":"2025011110050469200_B69","doi-asserted-by":"crossref","first-page":"e1094","DOI":"10.1002\/cpz1.1094","article-title":"Optical genome mapping for applications in repeat expansion disorders","volume":"4","author":"van\u00a0der\u00a0Sanden","year":"2024","journal-title":"Curr. Protoc."},{"key":"2025011110050469200_B70","doi-asserted-by":"crossref","first-page":"105328","DOI":"10.1016\/j.ebiom.2024.105328","article-title":"Tissue-specific TCF4 triplet repeat instability revealed by optical genome mapping","volume":"108","author":"Zarouchlioti","year":"2024","journal-title":"Ebiomedicine"},{"key":"2025011110050469200_B71","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1038\/d41586-023-00512-4","article-title":"Innovative technologies crowd the short-read sequencing market","volume":"614","author":"Eisenstein","year":"2023","journal-title":"Nature"},{"key":"2025011110050469200_B72","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1002\/cpmb.59","article-title":"Overview of next generation sequencing technologies","volume":"122","author":"Slatko","year":"2018","journal-title":"Curr. Protoc. Mol. 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Rep."},{"key":"2025011110050469200_B77","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1602\/neurorx.2.3.447","article-title":"The use of the R6 transgenic mouse models of Huntington\u2019s disease in attempts to develop novel therapeutic strategies","volume":"2","author":"Li","year":"2005","journal-title":"NeuroRx"},{"key":"2025011110050469200_B78","doi-asserted-by":"crossref","first-page":"e49838","DOI":"10.1371\/journal.pone.0049838","article-title":"Comprehensive behavioral and molecular characterization of a new knock-in mouse model of Huntington\u2019s disease: zQ175","volume":"7","author":"Menalled","year":"2012","journal-title":"PLoS One"},{"key":"2025011110050469200_B79","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s41592-022-01730-w","article-title":"Method of the year: long-read sequencing","volume":"20","author":"Marx","year":"2023","journal-title":"Nat. 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J."},{"key":"2025011110050469200_B92","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/btt647","article-title":"Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing","volume":"30","author":"Doi","year":"2014","journal-title":"Bioinformatics"},{"key":"2025011110050469200_B93","doi-asserted-by":"crossref","first-page":"e0175958","DOI":"10.1371\/journal.pone.0175958","article-title":"Inheritance patterns of ATCCT repeat interruptions in spinocerebellar ataxia type 10 (SCA10) expansions","volume":"12","author":"Landrian","year":"2017","journal-title":"PLoS One"},{"key":"2025011110050469200_B94","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1038\/s41431-018-0156-9","article-title":"De novorepeat interruptions are associated with reduced somatic instability and mild or absent clinical features in myotonic dystrophy type 1","volume":"26","author":"Cumming","year":"2018","journal-title":"Eur. J. Hum. Genet."},{"key":"2025011110050469200_B95","doi-asserted-by":"crossref","first-page":"2616","DOI":"10.3390\/ijms22052616","article-title":"Robust detection of somatic mosaicism and repeat interruptions by long-read targeted sequencing in myotonic dystrophy type 1","volume":"22","author":"Mangin","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"2025011110050469200_B96","first-page":"100146","article-title":"Haplotyping SNPs for allele-specific gene editing of the expanded huntingtin allele using long-read sequencing","volume":"4","author":"Fang","year":"2022","journal-title":"HGG Adv."},{"key":"2025011110050469200_B97","doi-asserted-by":"crossref","first-page":"102459","DOI":"10.1016\/j.fsigen.2020.102459","article-title":"Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers","volume":"51","author":"Woerner","year":"2021","journal-title":"Forensic Sci. Int. Genet."},{"key":"2025011110050469200_B98","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/s41592-020-01041-y","article-title":"High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing","volume":"18","author":"Karst","year":"2021","journal-title":"Nat. Methods"},{"key":"2025011110050469200_B99","doi-asserted-by":"crossref","first-page":"4025","DOI":"10.1038\/s41467-020-17800-6","article-title":"High throughput error corrected Nanopore single cell transcriptome sequencing","volume":"11","author":"Lebrigand","year":"2020","journal-title":"Nat. Commun."},{"key":"2025011110050469200_B100","doi-asserted-by":"crossref","first-page":"S47","DOI":"10.1016\/j.atherosclerosis.2023.06.202","article-title":"Nanopore sequencing with unique molecular identifiers preserves SNP haplotypes of the LPA KIV-2 copy number variation","volume":"379","author":"Amstler","year":"2023","journal-title":"Atherosclerosis"},{"key":"2025011110050469200_B101","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1186\/s13059-022-02778-9","article-title":"INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing","volume":"23","author":"Ivan\u010di\u0107","year":"2022","journal-title":"Genome Biol."},{"key":"2025011110050469200_B102","doi-asserted-by":"crossref","first-page":"6023","DOI":"10.1038\/s41467-020-19687-9","article-title":"UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution","volume":"11","author":"Zurek","year":"2020","journal-title":"Nat. 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Genet."},{"key":"2025011110050469200_B105","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s13059-019-1856-3","article-title":"NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION","volume":"20","author":"De\u00a0Roeck","year":"2019","journal-title":"Genome Biol."},{"key":"2025011110050469200_B106","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":"2025011110050469200_B107","doi-asserted-by":"crossref","DOI":"10.1101\/203919","article-title":"Amplification-free, CRISPR-Cas9 targeted enrichment and SMRT sequencing of repeat-expansion disease causative genomic regions","author":"Tsai","year":"2017"},{"key":"2025011110050469200_B108","doi-asserted-by":"crossref","first-page":"2092","DOI":"10.1038\/s41436-019-0453-x","article-title":"CRISPR\/Cas9-targeted enrichment and long-read sequencing of the Fuchs endothelial corneal dystrophy\u2013associated TCF4 triplet repeat","volume":"21","author":"Hafford-Tear","year":"2019","journal-title":"Genet. Med."},{"key":"2025011110050469200_B109","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/s13007-020-00661-x","article-title":"CRISPR-Cas9 enrichment and long read sequencing for fine mapping in plants","volume":"16","author":"L\u00f3pez-Girona","year":"2020","journal-title":"Plant Methods"},{"key":"2025011110050469200_B110","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.3390\/ijms24021076","article-title":"CRISPR\/Cas9-mediated enrichment coupled to nanopore sequencing provides a valuable tool for the precise reconstruction of large genomic target regions","volume":"24","author":"Lopatriello","year":"2023","journal-title":"Int. J. Mol. Sci."},{"key":"2025011110050469200_B111","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1038\/s41531-017-0029-x","article-title":"Parkinson\u2019s disease associated with pure ATXN10 repeat expansion","volume":"3","author":"Sch\u00fcle","year":"2017","journal-title":"NPJ Parkinsons Dis."},{"key":"2025011110050469200_B112","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s13024-018-0274-4","article-title":"Long-read sequencing across the C9orf72 \u2018GGGGCC\u2019 repeat expansion: implications for clinical use and genetic discovery efforts in human disease","volume":"13","author":"Ebbert","year":"2018","journal-title":"Mol. Neurodegener."},{"key":"2025011110050469200_B113","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1002\/humu.23580","article-title":"Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing","volume":"39","author":"H\u00f6ijer","year":"2018","journal-title":"Hum. Mutat."},{"key":"2025011110050469200_B114","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1093\/brain\/awab006","article-title":"Long-read targeted sequencing uncovers clinicopathological associations for C9orf72-linked diseases","volume":"144","author":"DeJesus-Hernandez","year":"2021","journal-title":"Brain"},{"key":"2025011110050469200_B115","doi-asserted-by":"crossref","first-page":"1478","DOI":"10.1038\/s41587-019-0293-x","article-title":"Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing","volume":"37","author":"Giesselmann","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"2025011110050469200_B116","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/s41587-020-0407-5","article-title":"Targeted nanopore sequencing with Cas9-guided adaptor ligation","volume":"38","author":"Gilpatrick","year":"2020","journal-title":"Nat. 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Adv."},{"key":"2025011110050469200_B123","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1038\/s41525-022-00331-y","article-title":"Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing","volume":"7","author":"Miyatake","year":"2022","journal-title":"NPJ Genom. Med."},{"key":"2025011110050469200_B124","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1038\/s41587-022-01580-z","article-title":"Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design","volume":"41","author":"Weilguny","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"2025011110050469200_B125","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1002\/mds.29704","article-title":"Adaptive long-read sequencing reveals GGC repeat expansion in ZFHX3 associated with spinocerebellar ataxia type 4","volume":"39","author":"Chen","year":"2024","journal-title":"Mov. Disord."},{"key":"2025011110050469200_B126","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1038\/s41593-022-01033-5","article-title":"Exome sequencing of individuals with Huntington\u2019s disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset","volume":"25","author":"McAllister","year":"2022","journal-title":"Nat. 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Bioinform."},{"key":"2025011110050469200_B129","doi-asserted-by":"crossref","first-page":"1971","DOI":"10.1093\/bib\/bbz099","article-title":"Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data","volume":"21","author":"Chiara","year":"2020","journal-title":"Brief. Bioinform."},{"key":"2025011110050469200_B130","doi-asserted-by":"crossref","first-page":"e90","DOI":"10.1093\/nar\/gkz501","article-title":"Profiling the genome-wide landscape of tandem repeat expansions","volume":"47","author":"Mousavi","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2025011110050469200_B131","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1101\/gr.135780.111","article-title":"lobSTR: a short tandem repeat profiler for personal genomes","volume":"22","author":"Gymrek","year":"2012","journal-title":"Genome Res."},{"key":"2025011110050469200_B132","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/nmeth.4267","article-title":"Genome-wide profiling of heritable and de novo STR variations","volume":"14","author":"Willems","year":"2017","journal-title":"Nat. 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Genet."},{"key":"2025011110050469200_B136","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-022-02826-4","article-title":"STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci","volume":"23","author":"Dashnow","year":"2022","journal-title":"Genome Biol."},{"key":"2025011110050469200_B137","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/s13073-017-0456-7","article-title":"Interrogating the \u201cunsequenceable\u201d genomic trinucleotide repeat disorders by long-read sequencing","volume":"9","author":"Liu","year":"2017","journal-title":"Genome Med."},{"key":"2025011110050469200_B138","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/s13059-019-1667-6","article-title":"Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads","volume":"20","author":"Mitsuhashi","year":"2019","journal-title":"Genome Biol."},{"key":"2025011110050469200_B139","doi-asserted-by":"crossref","first-page":"4809","DOI":"10.1093\/bioinformatics\/btz484","article-title":"Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data","volume":"35","author":"Harris","year":"2019","journal-title":"Bioinformatics"},{"key":"2025011110050469200_B140","doi-asserted-by":"crossref","unstructured":"Bolognini D., Magi A., Benes V., Korbel J.O., Rausch T. TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data. GigaScience. 2020; 9:giaa101","DOI":"10.1093\/gigascience\/giaa101"},{"key":"2025011110050469200_B141","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/s13059-021-02447-3","article-title":"Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences","volume":"22","author":"Chiu","year":"2021","journal-title":"Genome Biol."},{"key":"2025011110050469200_B142","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/978-1-0716-1036-7_9","article-title":"lamassemble: multiple alignment and consensus sequence of long reads","volume":"2231","author":"Frith","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"2025011110050469200_B143","doi-asserted-by":"crossref","first-page":"1093519","DOI":"10.3389\/fmolb.2023.1093519","article-title":"NanoSTR: a method for detection of target short tandem repeats based on nanopore sequencing data","volume":"10","author":"Lang","year":"2023","journal-title":"Front. Mol. Biosci."},{"key":"2025011110050469200_B144","doi-asserted-by":"crossref","DOI":"10.1101\/2024.05.01.24306681","article-title":"Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing","author":"Deynze","year":"2024"},{"key":"2025011110050469200_B145","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2025011110050469200_B146","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1038\/s41587-023-02057-3","article-title":"Characterization and visualization of tandem repeats at genome scale","volume":"42","author":"Dolzhenko","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"2025011110050469200_B147","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/s13059-022-02751-6","article-title":"Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres","volume":"23","author":"Tan","year":"2022","journal-title":"Genome Biol."},{"key":"2025011110050469200_B148","doi-asserted-by":"crossref","first-page":"btad388","DOI":"10.1093\/bioinformatics\/btad388","article-title":"WarpSTR: determining tandem repeat lengths using raw nanopore signals","volume":"39","author":"Sitar\u010d\u00edk","year":"2023","journal-title":"Bioinformatics"},{"key":"2025011110050469200_B149","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/s41588-019-0575-8","article-title":"A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo","volume":"52","author":"Nakamori","year":"2020","journal-title":"Nat. Genet."},{"key":"2025011110050469200_B150","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/s00439-024-02644-7","article-title":"Novel genotype\u2013phenotype correlations, differential cerebellar allele-specific methylation, and a common origin of the (ATTTC)n insertion in spinocerebellar ataxia type 37","volume":"143","author":"Sanchez-Flores","year":"2024","journal-title":"Hum. Genet."},{"key":"2025011110050469200_B151","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2025011110050469200_B152","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s40246-023-00522-3","article-title":"The application of long-read sequencing in clinical settings","volume":"17","author":"Oehler","year":"2023","journal-title":"Hum. 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