{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:48:56Z","timestamp":1792784936384,"version":"4.5.0"},"reference-count":114,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"services and facilities of the Ko\u00e7 University Research Center for Translational Medicine","id":[{"id":"https:\/\/ror.org\/03j1wrb54","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Wolf Chair for Neurodevelopmental Psychiatry, a joint Hospital-University Named Chair between the University of Toronto, UHN, and the UHN Foundation","id":[{"id":"https:\/\/ror.org\/03dbr7087","id-type":"ROR","asserted-by":"crossref"}]},{"name":"honoraria for educative activities by the International Movement Disorder Society and Merz Pharmaceuticals","id":[{"id":"https:\/\/ror.org\/03m80tg69","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Global Parkinson's Genetics Program (GP2) funded by the Aligning Science Across Parkinson's initiative and implemented by The Michael J. Fox Foundation","id":[{"id":"https:\/\/ror.org\/03arq3225","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["TR 1714\/4-1"],"award-info":[{"award-number":["TR 1714\/4-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Parkinsons Dis."],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    In this study, we designed a gene panel based on Nanopore long-read sequencing using adaptive sampling, targeting\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u2009564 genes associated with Parkinson\u2019s disease (PD) and repeat expansion disorders. We investigated its diagnostic utility in\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200918 patients with (1) pathogenic variants in\n                    <jats:italic>LRRK2<\/jats:italic>\n                    ,\n                    <jats:italic>PRKN<\/jats:italic>\n                    ,\n                    <jats:italic>SNCA<\/jats:italic>\n                    , and\n                    <jats:italic>RAB32<\/jats:italic>\n                    (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20097); (2) idiopathic PD or FTD negative for known genetic causes (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20093); (3) repeat expansions in\n                    <jats:italic>ATXN1<\/jats:italic>\n                    ,\n                    <jats:italic>ATXN2<\/jats:italic>\n                    ,\n                    <jats:italic>ATXN3<\/jats:italic>\n                    ,\n                    <jats:italic>C9orf72<\/jats:italic>\n                    ,\n                    <jats:italic>DAB1<\/jats:italic>\n                    ,\n                    <jats:italic>FGF14<\/jats:italic>\n                    ,\n                    <jats:italic>HTT<\/jats:italic>\n                    , and\n                    <jats:italic>TAF1<\/jats:italic>\n                    -SVA (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20098). Three individuals were multiplexed per flow cell, achieving a mean coverage of 24X (SD\u2009=\u2009\u00b1\u20099X) per sample. Ultimately, 17\/20 (85%; Clopper\u2013Pearson 95% CI: 62\u201397%) expected pathogenic variants were identified; i.e., an\n                    <jats:italic>SNCA<\/jats:italic>\n                    triplication and two repeat expansions in\n                    <jats:italic>C9orf72<\/jats:italic>\n                    and\n                    <jats:italic>TAF1<\/jats:italic>\n                    -SVA were missed. Additional variants in\n                    <jats:italic>STXBP2<\/jats:italic>\n                    ,\n                    <jats:italic>AP4S1<\/jats:italic>\n                    ,\n                    <jats:italic>RARS2<\/jats:italic>\n                    ,\n                    <jats:italic>ALS2<\/jats:italic>\n                    , and\n                    <jats:italic>CNBP<\/jats:italic>\n                    were identified in five patients. Adaptive sampling is a versatile genetic diagnostic tool in neurodegenerative disorders, while enabling cost-effective multiplexing. Further validation and improvements in bioinformatic analysis are needed.\n                  <\/jats:p>","DOI":"10.1038\/s41531-026-01585-4","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T17:37:09Z","timestamp":1790271429000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Unified long-read panel for Parkinson\u2019s and repeat expansion disorders"],"prefix":"10.1038","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-9594-3673","authenticated-orcid":false,"given":"Andr\u00e9","family":"Fienemann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia C.","family":"Prietzsche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"La\u03b2","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Much","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susen","family":"Schaake","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theresa","family":"L\u00fcth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolin","family":"Gabbert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Zimprich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4688-8482","authenticated-orcid":false,"given":"Elisabeth","family":"St\u00f6gmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theresa","family":"K\u00f6nig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christos","family":"Ganos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1818-9839","authenticated-orcid":false,"given":"Tu\u011f\u00e7e","family":"G\u00fcl-Demirkale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6977-2517","authenticated-orcid":false,"given":"A. Nazl\u0131","family":"Ba\u015fak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5317-7369","authenticated-orcid":false,"given":"Roland Dominic G.","family":"Jamora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raymond L.","family":"Rosales","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8322-4226","authenticated-orcid":false,"given":"Gerard","family":"Saranza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cid Czarina E.","family":"Diesta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meret","family":"M\u00f6ller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max","family":"Borsche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-6313-7395","authenticated-orcid":false,"given":"Teresa","family":"Kleinz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3967-0282","authenticated-orcid":false,"given":"Alexander","family":"Balck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5969-6899","authenticated-orcid":false,"given":"Norbert","family":"Br\u00fcggemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3496-7194","authenticated-orcid":false,"given":"Philip","family":"Seibler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Klein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne","family":"Trinh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"key":"1585_CR1","doi-asserted-by":"publisher","first-page":"e080952","DOI":"10.1136\/bmj-2024-080952","volume":"388","author":"D Su","year":"2025","unstructured":"Su, D. et al. Projections for prevalence of Parkinson\u2019s disease and its driving factors in 195 countries and territories to 2050: modelling study of Global Burden of Disease Study 2021. BMJ 388, e080952 (2025).","journal-title":"BMJ"},{"key":"1585_CR2","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1016\/S1474-4422(24)00038-3","volume":"23","author":"Collaborators GBDNSD","year":"2024","unstructured":"Collaborators GBDNSD Global, regional, and national burden of disorders affecting the nervous system, 1990-2021: a systematic analysis for the Global Burden of Disease Study 2021. Lancet Neurol. 23, 344\u2013381 (2024).","journal-title":"Lancet Neurol."},{"key":"1585_CR3","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2021.776847","volume":"9","author":"Z Ou","year":"2021","unstructured":"Ou, Z. et al. Global trends in the incidence, prevalence, and years lived with disability of Parkinson\u2019s disease in 204 countries\/territories from 1990 to 2019. Front. Public Health 9, 776847 (2021).","journal-title":"Front. Public Health"},{"key":"1585_CR4","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1093\/bmb\/ldad035","volume":"149","author":"L Trevisan","year":"2024","unstructured":"Trevisan, L. et al. Genetics in Parkinson\u2019s disease, state-of-the-art and future perspectives. Br. Med. Bull. 149, 60\u201371 (2024).","journal-title":"Br. Med. Bull."},{"key":"1585_CR5","doi-asserted-by":"publisher","first-page":"1384","DOI":"10.1002\/mds.29500","volume":"38","author":"G Pal","year":"2023","unstructured":"Pal, G. et al. Genetic testing in Parkinson\u2019s disease. Mov. Disord. 38, 1384\u20131396 (2023).","journal-title":"Mov. Disord."},{"key":"1585_CR6","doi-asserted-by":"publisher","first-page":"1591","DOI":"10.1002\/mds.26424","volume":"30","author":"RB Postuma","year":"2015","unstructured":"Postuma, R. B. et al. MDS clinical diagnostic criteria for Parkinson\u2019s disease. Mov. Disord. 30, 1591\u20131601 (2015).","journal-title":"Mov. Disord."},{"key":"1585_CR7","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1016\/S1474-4422(23)00109-6","volume":"22","author":"A Siderowf","year":"2023","unstructured":"Siderowf, A. et al. Assessment of heterogeneity among participants in the Parkinson\u2019s progression markers initiative cohort using alpha-synuclein seed amplification: a cross-sectional study. Lancet Neurol. 22, 407\u2013417 (2023).","journal-title":"Lancet Neurol."},{"key":"1585_CR8","doi-asserted-by":"publisher","first-page":"7102","DOI":"10.1007\/s00415-024-12687-5","volume":"271","author":"F Hopfner","year":"2024","unstructured":"Hopfner, F., Hoglinger, G., German Parkinson\u2019s Guidelines, G. & Trenkwalder, C. Definition and diagnosis of Parkinson\u2019s disease: guideline \u201cParkinson\u2019s disease\u201d of the German Society of Neurology. J. Neurol. 271, 7102\u20137119 (2024).","journal-title":"J. Neurol."},{"key":"1585_CR9","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/S1474-4422(21)00030-2","volume":"20","author":"E Tolosa","year":"2021","unstructured":"Tolosa, E., Garrido, A., Scholz, S. W. & Poewe, W. Challenges in the diagnosis of Parkinson\u2019s disease. Lancet Neurol. 20, 385\u2013397 (2021).","journal-title":"Lancet Neurol."},{"key":"1585_CR10","doi-asserted-by":"publisher","first-page":"2652","DOI":"10.1093\/brain\/awae188","volume":"147","author":"A Westenberger","year":"2024","unstructured":"Westenberger, A. et al. Relevance of genetic testing in the gene-targeted trial era: the Rostock Parkinson\u2019s disease study. Brain 147, 2652\u20132667 (2024).","journal-title":"Brain"},{"key":"1585_CR11","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/S1474-4422(23)00404-0","volume":"23","author":"GU Hoglinger","year":"2024","unstructured":"Hoglinger, G. U. et al. A biological classification of Parkinson\u2019s disease: the SynNeurGe research diagnostic criteria. Lancet Neurol. 23, 191\u2013204 (2024).","journal-title":"Lancet Neurol."},{"key":"1585_CR12","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1007\/s00702-023-02612-x","volume":"130","author":"T Gasser","year":"2023","unstructured":"Gasser, T. Genetic testing for Parkinson\u2019s disease in clinical practice. J. Neural Transm. 130, 777\u2013782 (2023).","journal-title":"J. Neural Transm."},{"key":"1585_CR13","doi-asserted-by":"publisher","DOI":"10.1007\/s11910-021-01100-7","volume":"21","author":"L Cook","year":"2021","unstructured":"Cook, L., Schulze, J., Naito, A. & Alcalay, R. N. The role of genetic testing for Parkinson\u2019s disease. Curr. Neurol. Neurosci. Rep. 21, 17 (2021).","journal-title":"Curr. Neurol. Neurosci. Rep."},{"key":"1585_CR14","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.parkreldis.2021.10.001","volume":"92","author":"L Cook","year":"2021","unstructured":"Cook, L. et al. The commercial genetic testing landscape for Parkinson\u2019s disease. Park. Relat. Disord. 92, 107\u2013111 (2021).","journal-title":"Park. Relat. Disord."},{"key":"1585_CR15","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1007\/s00415-021-10461-5","volume":"269","author":"A Crook","year":"2022","unstructured":"Crook, A., Jacobs, C., Newton-John, T., O\u2019Shea, R. & McEwen, A. Genetic counseling and testing practices for late-onset neurodegenerative disease: a systematic review. J. Neurol. 269, 676\u2013692 (2022).","journal-title":"J. Neurol."},{"key":"1585_CR16","doi-asserted-by":"publisher","first-page":"426","DOI":"10.3389\/fgene.2019.00426","volume":"10","author":"T Mantere","year":"2019","unstructured":"Mantere, T., Kersten, S. & Hoischen, A. Long-read sequencing emerging in medical genetics. Front. Genet. 10, 426 (2019).","journal-title":"Front. Genet."},{"key":"1585_CR17","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nature24286","volume":"550","author":"J Shendure","year":"2017","unstructured":"Shendure, J. et al. DNA sequencing at 40: past, present and future. Nature 550, 345\u2013353 (2017).","journal-title":"Nature"},{"key":"1585_CR18","doi-asserted-by":"crossref","unstructured":"de Boer E. N. et al. Nanopore long-read sequencing as a first-tier diagnostic test to detect repeat expansions in neurological disorders. Int. J. Mol. Sci. 26, 2850 (2025).","DOI":"10.3390\/ijms26072850"},{"key":"1585_CR19","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1016\/j.ajhg.2021.03.011","volume":"108","author":"C Depienne","year":"2021","unstructured":"Depienne, C. & Mandel, J. L. 30 years of repeat expansion disorders: what have we learned and what are the remaining challenges? Am. J. Hum. Genet. 108, 764\u2013785 (2021).","journal-title":"Am. J. Hum. Genet."},{"key":"1585_CR20","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1002\/mds.30208","volume":"40","author":"T Wirth","year":"2025","unstructured":"Wirth, T., Kumar, K. R. & Zech, M. Long-read sequencing: the third generation of diagnostic testing for dystonia. Mov. Disord. 40, 1009\u20131019 (2025).","journal-title":"Mov. Disord."},{"key":"1585_CR21","first-page":"123","volume":"42","author":"R Owusu","year":"2023","unstructured":"Owusu, R. & Savarese, M. Long-read sequencing improves diagnostic rate in neuromuscular disorders. Acta Myol. 42, 123\u2013128 (2023).","journal-title":"Acta Myol."},{"key":"1585_CR22","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1016\/j.tig.2018.05.008","volume":"34","author":"EL van Dijk","year":"2018","unstructured":"van Dijk, E. L., Jaszczyszyn, Y., Naquin, D. & Thermes, C. The third revolution in sequencing technology. Trends Genet. 34, 666\u2013681 (2018).","journal-title":"Trends Genet."},{"key":"1585_CR23","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1002\/acn3.70008","volume":"12","author":"LI Rudaks","year":"2025","unstructured":"Rudaks, L. I. et al. Targeted long-read sequencing as a single assay improves the diagnosis of spastic-ataxia disorders. Ann. Clin. Transl. Neurol. 12, 832\u2013841 (2025).","journal-title":"Ann. Clin. Transl. Neurol."},{"key":"1585_CR24","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abm5386","volume":"8","author":"I Stevanovski","year":"2022","unstructured":"Stevanovski, I. et al. Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing. Sci. Adv. 8, eabm5386 (2022).","journal-title":"Sci. Adv."},{"key":"1585_CR25","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.70138","volume":"15","author":"S Chevrier","year":"2025","unstructured":"Chevrier, S., Richard, C., Mille, M., Bertrand, D. & Boidot, R. Nanopore adaptive sampling accurately detects nucleotide variants and improves the characterization of large-scale rearrangement for the diagnosis of cancer predisposition. Clin. Transl. Med. 15, e70138 (2025).","journal-title":"Clin. Transl. Med."},{"key":"1585_CR26","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-024-10902-1","volume":"25","author":"J Trinh","year":"2024","unstructured":"Trinh, J. et al. Optical genome mapping of structural variants in Parkinson\u2019s disease-related induced pluripotent stem cells. BMC Genom. 25, 980 (2024).","journal-title":"BMC Genom."},{"key":"1585_CR27","doi-asserted-by":"publisher","DOI":"10.3389\/fped.2021.633996","volume":"9","author":"VM Dantas","year":"2021","unstructured":"Dantas, V. M. et al. Germline compound heterozygous variants identified in the STXBP2 gene leading to a familial hemophagocytic lymphohistiocytosis type 5: a case report. Front. Pediatr. 9, 633996 (2021).","journal-title":"Front. Pediatr."},{"key":"1585_CR28","first-page":"e17674","volume":"98","author":"X Tang","year":"2019","unstructured":"Tang, X., Guo, X., Li, Q. & Huang, Z. Familial hemophagocytic lymphohistiocytosis type 5 in a Chinese Tibetan patient caused by a novel compound heterozygous mutation in STXBP2. SciMed Cent. 98, e17674 (2019).","journal-title":"SciMed Cent."},{"key":"1585_CR29","doi-asserted-by":"publisher","first-page":"1580","DOI":"10.1111\/ene.13085","volume":"23","author":"A Tessa","year":"2016","unstructured":"Tessa, A. et al. Identification of mutations in AP4S1\/SPG52 through next generation sequencing in three families. Eur. J. Neurol. 23, 1580\u20131587 (2016).","journal-title":"Eur. J. Neurol."},{"key":"1585_CR30","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1097\/NEN.0000000000000209","volume":"74","author":"NZ Lax","year":"2015","unstructured":"Lax, N. Z. et al. Neuropathologic characterization of pontocerebellar hypoplasia type 6 associated with cardiomyopathy and hydrops fetalis and severe multisystem respiratory chain deficiency due to novel RARS2 mutations. J. Neuropathol. Exp. Neurol. 74, 688\u2013703 (2015).","journal-title":"J. Neuropathol. Exp. Neurol."},{"key":"1585_CR31","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/ng1001-166","volume":"29","author":"S Hadano","year":"2001","unstructured":"Hadano, S. et al. A gene encoding a putative GTPase regulator is mutated in familial amyotrophic lateral sclerosis 2. Nat. Genet. 29, 166\u2013173 (2001).","journal-title":"Nat. Genet."},{"key":"1585_CR32","doi-asserted-by":"publisher","DOI":"10.1212\/NXG.0000000000200220","volume":"11","author":"M Wendlandt","year":"2025","unstructured":"Wendlandt, M. et al. Updated structure of CNBP repeat expansions in patients with myotonic dystrophy type 2 and its implication for standard diagnostics. Neurol. Genet. 11, e200220 (2025).","journal-title":"Neurol. Genet."},{"key":"1585_CR33","doi-asserted-by":"publisher","first-page":"864","DOI":"10.1126\/science.1062125","volume":"293","author":"CL Liquori","year":"2001","unstructured":"Liquori, C. L. et al. Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science 293, 864\u2013867 (2001).","journal-title":"Science"},{"key":"1585_CR34","doi-asserted-by":"publisher","first-page":"1887","DOI":"10.1093\/brain\/awad436","volume":"147","author":"R Curro","year":"2024","unstructured":"Curro, R. et al. Role of the repeat expansion size in predicting age of onset and severity in RFC1 disease. Brain 147, 1887\u20131898 (2024).","journal-title":"Brain"},{"key":"1585_CR35","doi-asserted-by":"publisher","first-page":"2029","DOI":"10.1101\/gr.278070.123","volume":"33","author":"WT Harvey","year":"2023","unstructured":"Harvey, W. T. et al. Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall. Genome Res. 33, 2029\u20132040 (2023).","journal-title":"Genome Res."},{"key":"1585_CR36","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1101\/gr.279634.124","volume":"35","author":"H Rafehi","year":"2025","unstructured":"Rafehi, H. et al. A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia. Genome Res 35, 769\u2013785 (2025).","journal-title":"Genome Res"},{"key":"1585_CR37","doi-asserted-by":"crossref","unstructured":"Mosbruger T. L. et al. Haplotypic resolution of the challenging genomic regions of MHC and KIR using a combination of targeted sequencing and a novel assembly pipeline. Nucleic Acids Res. 53, gkaf441 (2025).","DOI":"10.1093\/nar\/gkaf441"},{"key":"1585_CR38","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1159\/000502487","volume":"46","author":"S Klasberg","year":"2019","unstructured":"Klasberg, S., Surendranath, V., Lange, V. & Schofl, G. Bioinformatics strategies, challenges, and opportunities for next generation sequencing-based HLA genotyping. Transfus. Med Hemother. 46, 312\u2013325 (2019).","journal-title":"Transfus. Med Hemother."},{"key":"1585_CR39","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/s00438-024-02158-x","volume":"299","author":"Y Ji","year":"2024","unstructured":"Ji, Y., Zhao, J., Gong, J., Sedlazeck, F. J. & Fan, S. Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations. Mol. Genet. Genom. 299, 65 (2024).","journal-title":"Mol. Genet. Genom."},{"key":"1585_CR40","doi-asserted-by":"publisher","first-page":"1018","DOI":"10.1038\/s41587-022-01580-z","volume":"41","author":"L Weilguny","year":"2023","unstructured":"Weilguny, L. et al. Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design. Nat. Biotechnol. 41, 1018\u20131025 (2023).","journal-title":"Nat. Biotechnol."},{"key":"1585_CR41","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1038\/s41587-020-00746-x","volume":"39","author":"A Payne","year":"2021","unstructured":"Payne, A. et al. Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nat. Biotechnol. 39, 442\u2013450 (2021).","journal-title":"Nat. Biotechnol."},{"key":"1585_CR42","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1101\/gr.279168.124","volume":"34","author":"SV Iyer","year":"2024","unstructured":"Iyer, S. V., Goodwin, S. & McCombie, W. R. Leveraging the power of long reads for targeted sequencing. Genome Res. 34, 1701\u20131718 (2024).","journal-title":"Genome Res."},{"key":"1585_CR43","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqz027","volume":"2","author":"W De Coster","year":"2020","unstructured":"De Coster, W., Strazisar, M. & De Rijk, P. Critical length in long-read resequencing. NAR Genom. Bioinform. 2, lqz027 (2020).","journal-title":"NAR Genom. Bioinform."},{"key":"1585_CR44","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1038\/33416","volume":"392","author":"T Kitada","year":"1998","unstructured":"Kitada, T. et al. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature 392, 605\u2013608 (1998).","journal-title":"Nature"},{"key":"1585_CR45","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/S1474-4422(24)00121-2","volume":"23","author":"EK Gustavsson","year":"2024","unstructured":"Gustavsson, E. K. et al. RAB32 Ser71Arg in autosomal dominant Parkinson\u2019s disease: linkage, association, and functional analyses. Lancet Neurol. 23, 603\u2013614 (2024).","journal-title":"Lancet Neurol."},{"key":"1585_CR46","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1016\/j.neuron.2004.11.005","volume":"44","author":"A Zimprich","year":"2004","unstructured":"Zimprich, A. et al. Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology. Neuron 44, 601\u2013607 (2004).","journal-title":"Neuron"},{"key":"1585_CR47","doi-asserted-by":"publisher","first-page":"2201","DOI":"10.1002\/mds.28225","volume":"35","author":"A Greuel","year":"2020","unstructured":"Greuel, A. et al. GBA variants in Parkinson\u2019s disease: clinical, metabolomic, and multimodal neuroimaging phenotypes. Mov. Disord. 35, 2201\u20132210 (2020).","journal-title":"Mov. Disord."},{"key":"1585_CR48","doi-asserted-by":"crossref","unstructured":"Moustakli, E. et al. Long-read sequencing and structural variant detection: unlocking the hidden genome in rare genetic disorders. Diagnostics 15, 1803 (2025).","DOI":"10.3390\/diagnostics15141803"},{"key":"1585_CR49","doi-asserted-by":"crossref","unstructured":"Santos, R. et al. Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing. Int. J. Mol. Sci. 26, 4492 (2025).","DOI":"10.3390\/ijms26104492"},{"key":"1585_CR50","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1126\/science.1090278","volume":"302","author":"AB Singleton","year":"2003","unstructured":"Singleton, A. B. et al. alpha-Synuclein locus triplication causes Parkinson\u2019s disease. Science 302, 841 (2003).","journal-title":"Science"},{"key":"1585_CR51","doi-asserted-by":"crossref","unstructured":"Nardone G. G. et al. A hitchhiker guide to structural variant calling: a comprehensive benchmark through different sequencing technologies. Biomedicines 13, 1949 (2025).","DOI":"10.3390\/biomedicines13081949"},{"key":"1585_CR52","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.jare.2022.10.012","volume":"50","author":"J Cuenca-Guardiola","year":"2023","unstructured":"Cuenca-Guardiola, J. et al. Improvement of large copy number variant detection by whole genome nanopore sequencing. J. Adv. Res. 50, 145\u2013158 (2023).","journal-title":"J. Adv. Res."},{"key":"1585_CR53","doi-asserted-by":"crossref","unstructured":"Fienemann, A. et al. Complementarity of long-reads and optical mapping in Parkinson\u2019s disease for structural variants. Ann. Clin. Transl. Neurol. 13, 1467\u20131481 (2026).","DOI":"10.1002\/acn3.70332"},{"key":"1585_CR54","doi-asserted-by":"crossref","unstructured":"Nakamichi, K. et al. Targeted long-read sequencing enriches disease-relevant genomic regions of interest to provide complete Mendelian disease diagnostics. JCI Insight. 9, e183902 (2024).","DOI":"10.1172\/jci.insight.183902"},{"key":"1585_CR55","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.695172","volume":"12","author":"SHN Munk","year":"2021","unstructured":"Munk, S. H. N., Voutsinos, V. & Oestergaard, V. H. Large intronic deletion of the fragile site gene PRKN dramatically lowers its fragility without impacting gene expression. Front Genet. 12, 695172 (2021).","journal-title":"Front Genet."},{"key":"1585_CR56","doi-asserted-by":"publisher","first-page":"8370","DOI":"10.1038\/sj.onc.1207072","volume":"22","author":"SR Denison","year":"2003","unstructured":"Denison, S. R. et al. Alterations in the common fragile site gene Parkin in ovarian and other cancers. Oncogene 22, 8370\u20138378 (2003).","journal-title":"Oncogene"},{"key":"1585_CR57","doi-asserted-by":"crossref","unstructured":"Paivandy, A. et al. Flexible and rapid validation of structural variation using adaptive sampling. Eur J Hum Genet. 34, 649\u2013657 (2026).","DOI":"10.1038\/s41431-026-02039-4"},{"key":"1585_CR58","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.ajhg.2022.11.015","volume":"110","author":"H Rafehi","year":"2023","unstructured":"Rafehi, H. et al. An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA50\/ATX-FGF14. Am. J. Hum. Genet. 110, 105\u2013119 (2023).","journal-title":"Am. J. Hum. Genet."},{"key":"1585_CR59","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/j.ajhg.2017.06.007","volume":"101","author":"AI Seixas","year":"2017","unstructured":"Seixas, A. I. et al. A pentanucleotide ATTTC repeat insertion in the non-coding region of DAB1, mapping to SCA37, causes spinocerebellar ataxia. Am. J. Hum. Genet. 101, 87\u2013103 (2017).","journal-title":"Am. J. Hum. Genet."},{"key":"1585_CR60","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/ng1196-285","volume":"14","author":"G Imbert","year":"1996","unstructured":"Imbert, G. et al. Cloning of the gene for spinocerebellar ataxia 2 reveals a locus with high sensitivity to expanded CAG\/glutamine repeats. Nat. Genet. 14, 285\u2013291 (1996).","journal-title":"Nat. Genet."},{"key":"1585_CR61","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1038\/ng1194-221","volume":"8","author":"Y Kawaguchi","year":"1994","unstructured":"Kawaguchi, Y. et al. CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Nat. Genet. 8, 221\u2013228 (1994).","journal-title":"Nat. Genet."},{"key":"1585_CR62","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1038\/ng0793-221","volume":"4","author":"HT Orr","year":"1993","unstructured":"Orr, H. T. et al. Expansion of an unstable trinucleotide CAG repeat in spinocerebellar ataxia type 1. Nat. Genet. 4, 221\u2013226 (1993).","journal-title":"Nat. Genet."},{"key":"1585_CR63","doi-asserted-by":"crossref","unstructured":"A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington\u2019s disease chromosomes. The Huntington\u2019s Disease Collaborative Research Group. Cell 72, 971\u2013983 (1993).","DOI":"10.1016\/0092-8674(93)90585-E"},{"key":"1585_CR64","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/j.neuron.2011.09.010","volume":"72","author":"AE Renton","year":"2011","unstructured":"Renton, A. E. et al. A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 72, 257\u2013268 (2011).","journal-title":"Neuron"},{"key":"1585_CR65","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.neuron.2011.09.011","volume":"72","author":"M DeJesus-Hernandez","year":"2011","unstructured":"DeJesus-Hernandez, M. et al. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72, 245\u2013256 (2011).","journal-title":"Neuron"},{"key":"1585_CR66","doi-asserted-by":"publisher","first-page":"E11020","DOI":"10.1073\/pnas.1712526114","volume":"114","author":"DC Bragg","year":"2017","unstructured":"Bragg, D. C. et al. Disease onset in X-linked dystonia-parkinsonism correlates with expansion of a hexameric repeat within an SVA retrotransposon in TAF1. Proc. Natl. Acad. Sci. USA. 114, E11020\u2013E11028 (2017).","journal-title":"Proc. Natl. Acad. Sci. USA."},{"key":"1585_CR67","doi-asserted-by":"publisher","DOI":"10.1038\/srep01016","volume":"2","author":"P Fratta","year":"2012","unstructured":"Fratta, P. et al. C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms RNA G-quadruplexes. Sci. Rep. 2, 1016 (2012).","journal-title":"Sci. Rep."},{"key":"1585_CR68","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/s13024-024-00790-0","volume":"19","author":"E Udine","year":"2024","unstructured":"Udine, E. et al. Targeted long-read sequencing to quantify methylation of the C9orf72 repeat expansion. Mol. Neurodegener. 19, 99 (2024).","journal-title":"Mol. Neurodegener."},{"key":"1585_CR69","doi-asserted-by":"publisher","first-page":"1082","DOI":"10.1093\/brain\/awab006","volume":"144","author":"M DeJesus-Hernandez","year":"2021","unstructured":"DeJesus-Hernandez, M. et al. Long-read targeted sequencing uncovers clinicopathological associations for C9orf72-linked diseases. Brain 144, 1082\u20131088 (2021).","journal-title":"Brain"},{"key":"1585_CR70","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s13024-018-0274-4","volume":"13","author":"MTW Ebbert","year":"2018","unstructured":"Ebbert, M. T. W. et al. Long-read sequencing across the C9orf72 \u2018GGGGCC\u2019 repeat expansion: implications for clinical use and genetic discovery efforts in human disease. Mol. Neurodegener. 13, 46 (2018).","journal-title":"Mol. Neurodegener."},{"key":"1585_CR71","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1002\/ana.25488","volume":"85","author":"A Westenberger","year":"2019","unstructured":"Westenberger, A. et al. A hexanucleotide repeat modifies expressivity of X-linked dystonia parkinsonism. Ann. Neurol. 85, 812\u2013822 (2019).","journal-title":"Ann. Neurol."},{"key":"1585_CR72","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1056\/NEJMoa2207406","volume":"388","author":"D Pellerin","year":"2023","unstructured":"Pellerin, D. et al. Deep intronic FGF14 GAA repeat expansion in late-onset cerebellar ataxia. N. Engl. J. Med. 388, 128\u2013141 (2023).","journal-title":"N. Engl. J. Med."},{"key":"1585_CR73","doi-asserted-by":"publisher","first-page":"S59","DOI":"10.3233\/JND-150088","volume":"2","author":"G Meola","year":"2015","unstructured":"Meola, G. & Cardani, R. Myotonic dystrophy type 2: an update on clinical aspects, genetic and pathomolecular mechanism. J. Neuromuscul. Dis. 2, S59\u2013S71 (2015).","journal-title":"J. Neuromuscul. Dis."},{"key":"1585_CR74","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-023-04243-y","volume":"21","author":"SU Greer","year":"2023","unstructured":"Greer, S. U. et al. Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic. J. Transl. Med. 21, 378 (2023).","journal-title":"J. Transl. Med."},{"key":"1585_CR75","doi-asserted-by":"publisher","DOI":"10.1016\/j.gim.2025.101568","volume":"27","author":"M Ehman","year":"2025","unstructured":"Ehman, M. et al. The cost and cost trajectory of genome sequencing and bioinformatics analysis for Indigenous children with suspected rare diseases. Genet. Med. 27, 101568 (2025).","journal-title":"Genet. Med."},{"key":"1585_CR76","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1038\/s41436-019-0618-7","volume":"22","author":"K Schwarze","year":"2020","unstructured":"Schwarze, K. et al. The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom. Genet. Med. 22, 85\u201394 (2020).","journal-title":"Genet. Med."},{"key":"1585_CR77","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1038\/s41431-017-0081-3","volume":"26","author":"P Marino","year":"2018","unstructured":"Marino, P. et al. Cost of cancer diagnosis using next-generation sequencing targeted gene panels in routine practice: a nationwide French study. Eur. J. Hum. Genet. 26, 314\u2013323 (2018).","journal-title":"Eur. J. Hum. Genet."},{"key":"1585_CR78","unstructured":"(NASHIP) NAoSHIP. Chapter 11.4 of the EBM (German Uniform Evaluation Standard) 2026. Available from: https:\/\/www.kbv.de\/documents\/praxis\/abrechnung\/ebm\/2026-2-ebm.pdf."},{"key":"1585_CR79","doi-asserted-by":"publisher","unstructured":"Leonard, H. L. & Global Parkinson\u2019s Genetics, P. Novel Parkinson\u2019s Disease Genetic Risk Factors Within and Across European Populations. medRxiv. https:\/\/doi.org\/10.1101\/2025.03.14.24319455 (2025).","DOI":"10.1101\/2025.03.14.24319455"},{"key":"1585_CR80","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1038\/s41588-023-01584-8","volume":"56","author":"JJ Kim","year":"2024","unstructured":"Kim, J. J. et al. Multi-ancestry genome-wide association meta-analysis of Parkinson\u2019s disease. Nat. Genet. 56, 27\u201336 (2024).","journal-title":"Nat. Genet."},{"key":"1585_CR81","doi-asserted-by":"crossref","unstructured":"Jia, F., Fellner, A. & Kumar K. R. Monogenic Parkinson\u2019s disease: genotype, phenotype, pathophysiology, and genetic testing. Genes 13, 471 (2022).","DOI":"10.3390\/genes13030471"},{"key":"1585_CR82","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1007\/s00415-023-12058-6","volume":"271","author":"L Dratch","year":"2024","unstructured":"Dratch, L. et al. Genetic testing in adults with neurologic disorders: indications, approach, and clinical impacts. J. Neurol. 271, 733\u2013747 (2024).","journal-title":"J. Neurol."},{"key":"1585_CR83","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1101\/gr.279975.124","volume":"35","author":"M Mahmoud","year":"2025","unstructured":"Mahmoud, M., Agustinho, D. P. & Sedlazeck, F. J. A Hitchhiker\u2019s Guide to long-read genomic analysis. Genome Res. 35, 545\u2013558 (2025).","journal-title":"Genome Res."},{"key":"1585_CR84","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1002\/mds.30151","volume":"40","author":"G Cogan","year":"2025","unstructured":"Cogan, G., Daida, K., Blauwendraat, C., Billingsley, K. & Brice, A. Exploration of neurodegenerative diseases using long-read sequencing and optical genome mapping technologies. Mov. Disord. 40, 996\u20131008 (2025).","journal-title":"Mov. Disord."},{"key":"1585_CR85","unstructured":"CeGaT GmbH. National Library of Medicine 2025. Available from: https:\/\/www.ncbi.nlm.nih.gov\/gtr\/all\/tests\/?term=Neurodegenerative+Diseases."},{"key":"1585_CR86","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1002\/mds.28982","volume":"37","author":"LM Lange","year":"2022","unstructured":"Lange, L. M. et al. Nomenclature of genetic movement disorders: recommendations of the International Parkinson and Movement Disorder Society Task Force - An update. Mov. Disord. 37, 905\u2013935 (2022).","journal-title":"Mov. Disord."},{"key":"1585_CR87","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1016\/S1474-4422(19)30320-5","volume":"18","author":"MA Nalls","year":"2019","unstructured":"Nalls, M. A. et al. Identification of novel risk loci, causal insights, and heritable risk for Parkinson\u2019s disease: a meta-analysis of genome-wide association studies. Lancet Neurol. 18, 1091\u20131102 (2019).","journal-title":"Lancet Neurol."},{"key":"1585_CR88","doi-asserted-by":"crossref","unstructured":"Kleinz, T. et al. RAB32-Linked Parkinson\u2019s disease: deep phenotyping, MDSgene literature review, and application of SynNeurGe criteria. Mov Disord. 40, 2746\u20132769 (2025).","DOI":"10.1002\/mds.70037"},{"key":"1585_CR89","doi-asserted-by":"publisher","first-page":"2427","DOI":"10.1002\/mds.29221","volume":"37","author":"A Rosenbohm","year":"2022","unstructured":"Rosenbohm, A. et al. Familial cerebellar ataxia and amyotrophic lateral sclerosis\/frontotemporal dementia with DAB1 and C9ORF72 repeat expansions: an 18-Year study. Mov. Disord. 37, 2427\u20132439 (2022).","journal-title":"Mov. Disord."},{"key":"1585_CR90","doi-asserted-by":"publisher","first-page":"4072","DOI":"10.1093\/brain\/awaf183","volume":"148","author":"J Lass","year":"2025","unstructured":"Lass, J. et al. FGF14 repeat length and mosaic interruptions: modifiers of spinocerebellar ataxia 27B? Brain 148, 4072\u20134083 (2025).","journal-title":"Brain"},{"key":"1585_CR91","doi-asserted-by":"publisher","first-page":"1023","DOI":"10.1007\/s00415-023-12050-0","volume":"271","author":"M Borsche","year":"2024","unstructured":"Borsche, M. et al. Bilateral vestibulopathy in RFC1-positive CANVAS is distinctly different compared to FGF14-linked spinocerebellar ataxia 27B. J. Neurol. 271, 1023\u20131027 (2024).","journal-title":"J. Neurol."},{"key":"1585_CR92","doi-asserted-by":"publisher","unstructured":"Wengh\u00f6fer, A. et al. On behalf of the CARD Long-read Team 2024. Processing frozen archival human DNA samples for large-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP v1. protocols.io https:\/\/doi.org\/10.17504\/protocols.io.5jyl82morl2w\/v1 (2024).","DOI":"10.17504\/protocols.io.5jyl82morl2w\/v1"},{"key":"1585_CR93","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"1585_CR94","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","volume":"35","author":"P Di Tommaso","year":"2017","unstructured":"Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316\u2013319 (2017).","journal-title":"Nat. Biotechnol."},{"key":"1585_CR95","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).","journal-title":"Bioinformatics"},{"key":"1585_CR96","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1038\/s43588-022-00387-x","volume":"2","author":"Z Zheng","year":"2022","unstructured":"Zheng, Z. et al. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nat. Comput Sci. 2, 797\u2013803 (2022).","journal-title":"Nat. Comput Sci."},{"key":"1585_CR97","doi-asserted-by":"publisher","first-page":"1616","DOI":"10.1038\/s41587-024-02141-2","volume":"42","author":"M Smolka","year":"2024","unstructured":"Smolka, M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat. Biotechnol. 42, 1616 (2024).","journal-title":"Nat. Biotechnol."},{"key":"1585_CR98","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02447-3","volume":"22","author":"R Chiu","year":"2021","unstructured":"Chiu, R., Rajan-Babu, I. S., Friedman, J. M. & Birol, I. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol. 22, 224 (2021).","journal-title":"Genome Biol."},{"key":"1585_CR99","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. 2590, 127\u2013138 (2023).","journal-title":"Methods Mol. Biol."},{"key":"1585_CR100","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https:\/\/www.r-project.org\/ (2025)."},{"key":"1585_CR101","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","volume":"4","author":"H Wickham","year":"2019","unstructured":"Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).","journal-title":"J. Open Source Softw."},{"key":"1585_CR102","unstructured":"Wickham, H. et al. dplyr: A Grammar of Data Manipulation. R package version 1.2.1. https:\/\/dplyr.tidyverse.org\/ (2026)."},{"key":"1585_CR103","unstructured":"Wickham, H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4. https:\/\/ggplot2.tidyverse.org\/ (2016)."},{"key":"1585_CR104","unstructured":"Barrett, T. et al. data.table: Extension of \u2018data.frame\u2018. R package version 1.18.99. https:\/\/r-datatable.com (2026)."},{"key":"1585_CR105","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani, P. 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 6, 80\u201392 (2012).","journal-title":"Fly"},{"key":"1585_CR106","doi-asserted-by":"publisher","first-page":"D1062","DOI":"10.1093\/nar\/gkx1153","volume":"46","author":"MJ Landrum","year":"2018","unstructured":"Landrum, M. J. et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 46, D1062\u2013D1067 (2018).","journal-title":"Nucleic Acids Res."},{"key":"1585_CR107","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-022-05008-y","volume":"23","author":"TJ Nicholas","year":"2022","unstructured":"Nicholas, T. J., Cormier, M. J. & Quinlan, A. R. Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate. BMC Bioinform. 23, 490 (2022).","journal-title":"BMC Bioinform."},{"key":"1585_CR108","doi-asserted-by":"publisher","first-page":"3572","DOI":"10.1093\/bioinformatics\/bty304","volume":"34","author":"V Geoffroy","year":"2018","unstructured":"Geoffroy, V. et al. AnnotSV: an integrated tool for structural variations annotation. Bioinformatics 34, 3572\u20133574 (2018).","journal-title":"Bioinformatics"},{"key":"1585_CR109","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/gim.2015.30","volume":"17","author":"S Richards","year":"2015","unstructured":"Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 17, 405\u2013424 (2015).","journal-title":"Genet. Med."},{"key":"1585_CR110","doi-asserted-by":"publisher","first-page":"4809","DOI":"10.1093\/bioinformatics\/btz484","volume":"35","author":"RS Harris","year":"2019","unstructured":"Harris, R. S., Cechova, M. & Makova, K. D. Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data. Bioinformatics 35, 4809\u20134811 (2019).","journal-title":"Bioinformatics"},{"key":"1585_CR111","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24\u201326 (2011).","journal-title":"Nat. Biotechnol."},{"key":"1585_CR112","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","volume":"27","author":"H Li","year":"2011","unstructured":"Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987\u20132993 (2011).","journal-title":"Bioinformatics"},{"key":"1585_CR113","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02107-y","volume":"21","author":"T Jiang","year":"2020","unstructured":"Jiang, T. et al. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 21, 189 (2020).","journal-title":"Genome Biol."},{"key":"1585_CR114","doi-asserted-by":"publisher","first-page":"2907","DOI":"10.1093\/bioinformatics\/btz041","volume":"35","author":"D Heller","year":"2019","unstructured":"Heller, D. & Vingron, M. SVIM: structural variant identification using mapped long reads. Bioinformatics 35, 2907\u20132915 (2019).","journal-title":"Bioinformatics"}],"container-title":["npj Parkinson's Disease"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41531-026-01585-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41531-026-01585-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41531-026-01585-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T19:04:38Z","timestamp":1790276678000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41531-026-01585-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,24]]},"references-count":114,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1585"],"URL":"https:\/\/doi.org\/10.1038\/s41531-026-01585-4","relation":{},"ISSN":["2373-8057"],"issn-type":[{"value":"2373-8057","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,24]]},"assertion":[{"value":"7 January 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 September 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare the following competing interests: RDGJ has received travel grants and speakers\u2019 honoraria from Royal Care Super Specialty Hospital, Darya-Varya Laboratoria, and the Philippine offices of AbbVie, Exeltis, HI-Eisai, Innogen, Medichem, Natrapharm, Sun, Torrent, and Vexxa. M.B. received honoraria from Bial Germany. N.B. received honoraria from AbbVie, Esteve, Ipsen, Merz, Takeda, Teva, and Zambon. J.T. has received travel funding to speak on behalf of O.N.T. C.K. has served as a medical advisor to Centogene, Takeda, and Biogen and received speakers\u2019 honoraria from Bial, as well as royalties from Oxford University Press and Springer Nature. The other authors do not have a competing interest.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"233"}}