{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T23:00:03Z","timestamp":1793833203323,"version":"4.6.1"},"reference-count":59,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2024,4,29]],"date-time":"2024-04-29T00:00:00Z","timestamp":1714348800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,4,29]],"date-time":"2024-04-29T00:00:00Z","timestamp":1714348800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Genet"],"published-print":{"date-parts":[[2024,6]]},"DOI":"10.1038\/s41588-024-01719-5","type":"journal-article","created":{"date-parts":[[2024,4,29]],"date-time":"2024-04-29T06:01:59Z","timestamp":1714370519000},"page":"1080-1089","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":60,"title":["A GGC-repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy"],"prefix":"10.1038","volume":"56","author":[{"given":"Karla P.","family":"Figueroa","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9009-5458","authenticated-orcid":false,"given":"Caspar","family":"Gross","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9890-1960","authenticated-orcid":false,"given":"Elena","family":"Buena-Atienza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharan","family":"Paul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mandi","family":"Gandelman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naseebullah","family":"Kakar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6552-8362","authenticated-orcid":false,"given":"Marc","family":"Sturm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Casadei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0466-582X","authenticated-orcid":false,"given":"Jakob","family":"Admard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joohyun","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Z\u00fchlke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yorck","family":"Hellenbroich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jelena","family":"Pozojevic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4905-3093","authenticated-orcid":false,"given":"Saranya","family":"Balachandran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5273-5277","authenticated-orcid":false,"given":"Kristian","family":"H\u00e4ndler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3767-6376","authenticated-orcid":false,"given":"Simone","family":"Zittel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dagmar","family":"Timmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0654-836X","authenticated-orcid":false,"given":"Friedrich","family":"Erdlenbruch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Herrmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Feindt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1618-9269","authenticated-orcid":false,"given":"Martin","family":"Zenker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2805-4652","authenticated-orcid":false,"given":"Thomas","family":"Klopstock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5225-2443","authenticated-orcid":false,"given":"Claudia","family":"Dufke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel R.","family":"Scoles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnulf","family":"Koeppen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0583-4683","authenticated-orcid":false,"given":"Malte","family":"Spielmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7011-1369","authenticated-orcid":false,"given":"Olaf","family":"Riess","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Ossowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6033-4836","authenticated-orcid":false,"given":"Tobias B.","family":"Haack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0883-7879","authenticated-orcid":false,"given":"Stefan M.","family":"Pulst","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,4,29]]},"reference":[{"key":"1719_CR1","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/s12311-008-0028-x","volume":"7","author":"S Tsuji","year":"2008","unstructured":"Tsuji, S., Onodera, O., Goto, J., Nishizawa, M. & Study Group on Ataxic Diseases. Sporadic ataxias in Japan\u2014a population-based epidemiological study. Cerebellum 7, 189\u2013197 (2008).","journal-title":"Cerebellum"},{"key":"1719_CR2","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1007\/s00415-018-9076-4","volume":"266","author":"R Sullivan","year":"2019","unstructured":"Sullivan, R., Yau, W. Y., O\u2019Connor, E. & Houlden, H. Spinocerebellar ataxia: an update. J. Neurol. 266, 533\u2013544 (2019).","journal-title":"J. Neurol."},{"key":"1719_CR3","first-page":"392","volume":"59","author":"K Flanigan","year":"1996","unstructured":"Flanigan, K. et al. Autosomal dominant spinocerebellar ataxia with sensory axonal neuropathy (SCA4): clinical description and genetic localization to chromosome 16q22.1. Am. J. Hum. Genet. 59, 392\u2013399 (1996).","journal-title":"Am. J. Hum. Genet."},{"key":"1719_CR4","doi-asserted-by":"crossref","first-page":"eabj6965","DOI":"10.1126\/science.abj6965","volume":"376","author":"MR Vollger","year":"2022","unstructured":"Vollger, M. R. et al. Segmental duplications and their variation in a complete human genome. Science 376, eabj6965 (2022).","journal-title":"Science"},{"key":"1719_CR5","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1136\/jmg-2023-109470","volume":"61","author":"N Weisschuh","year":"2024","unstructured":"Weisschuh, N. et al. Diagnostic genome sequencing improves diagnostic yield: a prospective single-centre study in 1000 patients with inherited eye diseases. J. Med. Genet. 61, 186\u2013195 (2024).","journal-title":"J. Med. Genet."},{"key":"1719_CR6","doi-asserted-by":"publisher","unstructured":"Dolzhenko, E. et al. Resolving the unsolved: comprehensive assessment of tandem repeats at scale. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.05.12.540470 (2023).","DOI":"10.1101\/2023.05.12.540470"},{"key":"1719_CR7","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.ajhg.2023.11.008","volume":"111","author":"J Wallenius","year":"2024","unstructured":"Wallenius, J. et al. Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: a poly-glycine disease. Am. J. Hum. Genet. 111, 82\u201395 (2024).","journal-title":"Am. J. Hum. Genet."},{"key":"1719_CR8","doi-asserted-by":"publisher","unstructured":"Paucar, M. et al. Spinocerebellar ataxia type 4 is caused by a GGC expansion in the ZFHX3 gene and is associated with prominent dysautonomia and motor neuron signs. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2023.10.03.23296230 (2023).","DOI":"10.1101\/2023.10.03.23296230"},{"key":"1719_CR9","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1002\/mds.29704","volume":"39","author":"Z Chen","year":"2024","unstructured":"Chen, Z. et al. Adaptive long-read sequencing reveals GGC repeat expansion in ZFHX3 associated with spinocerebellar ataxia type 4. Mov. Disord. 39, 486\u2013497 (2024).","journal-title":"Mov. Disord."},{"key":"1719_CR10","doi-asserted-by":"publisher","unstructured":"Del Roc\u00edo P\u00e9rez Baca, M. et al. A novel neurodevelopmental syndrome caused by loss-of-function of the zinc finger homeobox 3 (ZFHX3) gene. Preprint at medRxiv https:\/\/doi.org\/10.1101\/2023.05.22.23289895 (2023).","DOI":"10.1101\/2023.05.22.23289895"},{"key":"1719_CR11","doi-asserted-by":"crossref","first-page":"e3001450","DOI":"10.1371\/journal.pbio.3001450","volume":"19","author":"A Sagner","year":"2021","unstructured":"Sagner, A. et al. A shared transcriptional code orchestrates temporal patterning of the central nervous system. PLoS Biol. 19, e3001450 (2021).","journal-title":"PLoS Biol."},{"key":"1719_CR12","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/s10038-022-01116-y","volume":"68","author":"H Ishiura","year":"2023","unstructured":"Ishiura, H., Tsuji, S. & Toda, T. Recent advances in CGG repeat diseases and a proposal of fragile X-associated tremor\/ataxia syndrome, neuronal intranuclear inclusion disease, and oculophryngodistal myopathy (FNOP) spectrum disorder. J. Hum. Genet. 68, 169\u2013174 (2023).","journal-title":"J. Hum. Genet."},{"key":"1719_CR13","doi-asserted-by":"crossref","first-page":"843014","DOI":"10.3389\/fgene.2022.843014","volume":"13","author":"M Boivin","year":"2022","unstructured":"Boivin, M. & Charlet-Berguerand, N. Trinucleotide CGG repeat diseases: an expanding field of polyglycine proteins? Front. Genet. 13, 843014 (2022).","journal-title":"Front. Genet."},{"key":"1719_CR14","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s40478-022-01383-y","volume":"10","author":"T Liufu","year":"2022","unstructured":"Liufu, T. et al. The polyG diseases: a new disease entity. Acta Neuropathol. Commun. 10, 79 (2022).","journal-title":"Acta Neuropathol. Commun."},{"key":"1719_CR15","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1016\/j.ajhg.2023.05.005","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 SCA27B\/ATX-FGF14. Am. J. Hum. Genet. 110, 1018 (2023).","journal-title":"Am. J. Hum. Genet."},{"key":"1719_CR16","doi-asserted-by":"crossref","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":"1719_CR17","doi-asserted-by":"crossref","first-page":"695","DOI":"10.3389\/fneur.2018.00695","volume":"9","author":"JL Famula","year":"2018","unstructured":"Famula, J. L. et al. Presence of middle cerebellar peduncle sign in FMR1 premutation carriers without tremor and ataxia. Front. Neurol. 9, 695 (2018).","journal-title":"Front. Neurol."},{"key":"1719_CR18","doi-asserted-by":"crossref","first-page":"2854","DOI":"10.1111\/ene.15905","volume":"30","author":"IV Podar","year":"2023","unstructured":"Podar, I. V. et al. First case of adult onset neuronal intranuclear inclusion disease with both typical radiological signs and NOTCH2NLC repeat expansions in a Caucasian individual. Eur. J. Neurol. 30, 2854\u20132858 (2023).","journal-title":"Eur. J. Neurol."},{"key":"1719_CR19","doi-asserted-by":"crossref","first-page":"3545","DOI":"10.1007\/s10072-023-06845-2","volume":"44","author":"M Liu","year":"2023","unstructured":"Liu, M. et al. A comprehensive study of clinicopathological and genetic features of neuronal intranuclear inclusion disease. Neurol. Sci. 44, 3545\u20133556 (2023).","journal-title":"Neurol. Sci."},{"key":"1719_CR20","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1007\/s00702-005-0362-9","volume":"113","author":"Y Hellenbroich","year":"2006","unstructured":"Hellenbroich, Y. et al. Spinocerebellar ataxia type 4 (SCA4): initial pathoanatomical study reveals widespread cerebellar and brainstem degeneration. J. Neural Transm. 113, 829\u2013843 (2006).","journal-title":"J. Neural Transm."},{"key":"1719_CR21","volume":"9","author":"S Paul","year":"2018","unstructured":"Paul, S., Dansithong, W., Figueroa, K. P., Scoles, D. R. & Pulst, S. M. Staufen1 links RNA stress granules and autophagy in a model of neurodegeneration. Nat. Commun. 9, 3648 (2018).","journal-title":"Nat. Commun."},{"key":"1719_CR22","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1002\/ana.26069","volume":"89","author":"S Paul","year":"2021","unstructured":"Paul, S. et al. Staufen1 in human neurodegeneration. Ann. Neurol. 89, 1114\u20131128 (2021).","journal-title":"Ann. Neurol."},{"key":"1719_CR23","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1002\/ana.26515","volume":"93","author":"S Paul","year":"2023","unstructured":"Paul, S. et al. Staufen impairs autophagy in neurodegeneration. Ann. Neurol. 93, 398\u2013416 (2023).","journal-title":"Ann. Neurol."},{"key":"1719_CR24","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/978-3-319-71779-1_8","volume":"1049","author":"DR Scoles","year":"2018","unstructured":"Scoles, D. R. & Pulst, S. M. Spinocerebellar ataxia type 2. Adv. Exp. Med. Biol. 1049, 175\u2013195 (2018).","journal-title":"Adv. Exp. Med. Biol."},{"key":"1719_CR25","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/79162","volume":"26","author":"DP Huynh","year":"2000","unstructured":"Huynh, D. P., Figueroa, K., Hoang, N. & Pulst, S. M. Nuclear localization or inclusion body formation of ataxin-2 are not necessary for SCA2 pathogenesis in mouse or human. Nat. Genet. 26, 44\u201350 (2000).","journal-title":"Nat. Genet."},{"key":"1719_CR26","doi-asserted-by":"crossref","first-page":"542","DOI":"10.4161\/auto.4600","volume":"3","author":"N Mizushima","year":"2007","unstructured":"Mizushima, N. & Yoshimori, T. How to interpret LC3 immunoblotting. Autophagy 3, 542\u2013545 (2007).","journal-title":"Autophagy"},{"key":"1719_CR27","doi-asserted-by":"crossref","first-page":"e202200169","DOI":"10.1002\/hlca.202200169","volume":"106","author":"AC Hill","year":"2023","unstructured":"Hill, A. C. & Hall, J. The MOE modification of RNA: origins and widescale impact on the oligonucleotide therapeutics field. Helv. Chim. Acta 106, e202200169 (2023).","journal-title":"Helv. Chim. Acta"},{"key":"1719_CR28","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/nature22038","volume":"544","author":"LA Becker","year":"2017","unstructured":"Becker, L. A. et al. Therapeutic reduction of ataxin-2 extends lifespan and reduces pathology in TDP-43 mice. Nature 544, 367\u2013371 (2017).","journal-title":"Nature"},{"key":"1719_CR29","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/nature22044","volume":"544","author":"DR Scoles","year":"2017","unstructured":"Scoles, D. R. et al. Antisense oligonucleotide therapy for spinocerebellar ataxia type 2. Nature 544, 362\u2013366 (2017).","journal-title":"Nature"},{"key":"1719_CR30","doi-asserted-by":"crossref","first-page":"104515","DOI":"10.1016\/j.nbd.2019.104515","volume":"130","author":"CM Rodriguez","year":"2019","unstructured":"Rodriguez, C. M. & Todd, P. K. New pathologic mechanisms in nucleotide repeat expansion disorders. Neurobiol. Dis. 130, 104515 (2019).","journal-title":"Neurobiol. Dis."},{"key":"1719_CR31","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1186\/s40478-019-0782-7","volume":"7","author":"A Krans","year":"2019","unstructured":"Krans, A., Skariah, G., Zhang, Y., Bayly, B. & Todd, P. K. Neuropathology of RAN translation proteins in fragile X-associated tremor\/ataxia syndrome. Acta Neuropathol. Commun. 7, 152 (2019).","journal-title":"Acta Neuropathol. Commun."},{"key":"1719_CR32","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1016\/j.neuron.2016.12.016","volume":"93","author":"C Sellier","year":"2017","unstructured":"Sellier, C. et al. Translation of expanded CGG repeats into FMRpolyG is pathogenic and may contribute to fragile X tremor ataxia syndrome. Neuron 93, 331\u2013347 (2017).","journal-title":"Neuron"},{"key":"1719_CR33","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1007\/s00401-021-02375-3","volume":"142","author":"S Zhong","year":"2021","unstructured":"Zhong, S. et al. Upstream open reading frame with NOTCH2NLC GGC expansion generates polyglycine aggregates and disrupts nucleocytoplasmic transport: implications for polyglycine diseases. Acta Neuropathol. 142, 1003\u20131023 (2021).","journal-title":"Acta Neuropathol."},{"key":"1719_CR34","doi-asserted-by":"crossref","first-page":"1825","DOI":"10.1016\/j.neuron.2021.03.038","volume":"109","author":"M Boivin","year":"2021","unstructured":"Boivin, M. et al. Translation of GGC repeat expansions into a toxic polyglycine protein in NIID defines a novel class of human genetic disorders: the polyG diseases. Neuron 109, 1825\u20131835 (2021).","journal-title":"Neuron"},{"key":"1719_CR35","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1038\/s41588-019-0459-y","volume":"51","author":"J Sone","year":"2019","unstructured":"Sone, J. et al. Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease. Nat. Genet. 51, 1215\u20131221 (2019).","journal-title":"Nat. Genet."},{"key":"1719_CR36","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1038\/s41588-019-0458-z","volume":"51","author":"H Ishiura","year":"2019","unstructured":"Ishiura, H. et al. Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease. Nat. Genet. 51, 1222\u20131232 (2019).","journal-title":"Nat. Genet."},{"key":"1719_CR37","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.ajhg.2019.05.013","volume":"105","author":"Y Tian","year":"2019","unstructured":"Tian, Y. et al. Expansion of human-specific GGC repeat in neuronal intranuclear inclusion disease-related disorders. Am. J. Hum. Genet. 105, 166\u2013176 (2019).","journal-title":"Am. J. Hum. Genet."},{"key":"1719_CR38","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","volume":"581","author":"KJ Karczewski","year":"2020","unstructured":"Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434\u2013443 (2020).","journal-title":"Nature"},{"key":"1719_CR39","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","volume":"18","author":"H Cheng","year":"2021","unstructured":"Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170\u2013175 (2021).","journal-title":"Nat. Methods"},{"key":"1719_CR40","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-14998-3","volume":"11","author":"TR Ranallo-Benavidez","year":"2020","unstructured":"Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 11, 1432 (2020).","journal-title":"Nat. Commun."},{"key":"1719_CR41","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1038\/s41592-023-01993-x","volume":"20","author":"M Kolmogorov","year":"2023","unstructured":"Kolmogorov, M. et al. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nat. Methods 20, 1483\u20131492 (2023).","journal-title":"Nat. Methods"},{"key":"1719_CR42","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.4235","volume":"36","author":"R Poplin","year":"2018","unstructured":"Poplin, R. et al. A universal SNP and small-indel variant caller using deep neural networks. Nat. Biotechnol. 36, 983\u2013987 (2018).","journal-title":"Nat. Biotechnol."},{"key":"1719_CR43","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14061","volume":"8","author":"DC Jeffares","year":"2017","unstructured":"Jeffares, D. C. et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat. Commun. 8, 14061 (2017).","journal-title":"Nat. Commun."},{"key":"1719_CR44","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540\u2013546 (2019).","journal-title":"Nat. Biotechnol."},{"key":"1719_CR45","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-02024-y","author":"M Smolka","year":"2024","unstructured":"Smolka, M. et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat. Biotechnol. https:\/\/doi.org\/10.1038\/s41587-023-02024-y (2024).","journal-title":"Nat. Biotechnol."},{"key":"1719_CR46","doi-asserted-by":"crossref","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":"1719_CR47","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1038\/s41592-021-01299-w","volume":"18","author":"K Shafin","year":"2021","unstructured":"Shafin, K. et al. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nat. Methods 18, 1322\u20131332 (2021).","journal-title":"Nat. Methods"},{"key":"1719_CR48","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"1719_CR49","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkz114","volume":"47","author":"Y Liao","year":"2019","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res. 47, e47 (2019).","journal-title":"Nucleic Acids Res."},{"key":"1719_CR50","doi-asserted-by":"crossref","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":"1719_CR51","doi-asserted-by":"crossref","first-page":"4754","DOI":"10.1093\/bioinformatics\/btz431","volume":"35","author":"E Dolzhenko","year":"2019","unstructured":"Dolzhenko, E. et al. ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. Bioinformatics 35, 4754\u20134756 (2019).","journal-title":"Bioinformatics"},{"key":"1719_CR52","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.cell.2007.11.019","volume":"131","author":"K Takahashi","year":"2007","unstructured":"Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861\u2013872 (2007).","journal-title":"Cell"},{"key":"1719_CR53","doi-asserted-by":"crossref","first-page":"3081","DOI":"10.1038\/nprot.2007.418","volume":"2","author":"K Takahashi","year":"2007","unstructured":"Takahashi, K., Okita, K., Nakagawa, M. & Yamanaka, S. Induction of pluripotent stem cells from fibroblast cultures. Nat. Protoc. 2, 3081\u20133089 (2007).","journal-title":"Nat. Protoc."},{"key":"1719_CR54","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/nmeth.1591","volume":"8","author":"K Okita","year":"2011","unstructured":"Okita, K. et al. A more efficient method to generate integration-free human iPS cells. Nat. Methods 8, 409\u2013412 (2011).","journal-title":"Nat. Methods"},{"key":"1719_CR55","doi-asserted-by":"crossref","first-page":"7060","DOI":"10.1074\/jbc.RA119.012131","volume":"295","author":"C Fu","year":"2020","unstructured":"Fu, C. et al. The transcription factor ZFHX3 is crucial for the angiogenic function of hypoxia-inducible factor 1\u03b1 in liver cancer cells. J. Biol. Chem. 295, 7060\u20137074 (2020).","journal-title":"J. Biol. Chem."},{"key":"1719_CR56","doi-asserted-by":"crossref","first-page":"32801","DOI":"10.1074\/jbc.M110.128330","volume":"285","author":"XY Dong","year":"2010","unstructured":"Dong, X. Y. et al. ATBF1 inhibits estrogen receptor (ER) function by selectively competing with AIB1 for binding to the ER in ER-positive breast cancer cells. J. Biol. Chem. 285, 32801\u201332809 (2010).","journal-title":"J. Biol. Chem."},{"key":"1719_CR57","doi-asserted-by":"publisher","unstructured":"Sturm, M. megSAP 2022_08. Zenodo https:\/\/doi.org\/10.5281\/zenodo.10817663 (2022).","DOI":"10.5281\/zenodo.10817663"},{"key":"1719_CR58","doi-asserted-by":"publisher","unstructured":"Gro\u00df, C. & Admard, J. megLR 1.0.0. Zenodo https:\/\/doi.org\/10.5281\/zenodo.10820153 (2023).","DOI":"10.5281\/zenodo.10820153"},{"key":"1719_CR59","doi-asserted-by":"publisher","unstructured":"Gro\u00df, C. expander. Zenodo https:\/\/doi.org\/10.5281\/zenodo.10820172 (2021).","DOI":"10.5281\/zenodo.10820172"}],"container-title":["Nature Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01719-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01719-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01719-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,19]],"date-time":"2024-07-19T10:31:43Z","timestamp":1721385103000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01719-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,29]]},"references-count":59,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,6]]}},"alternative-id":["1719"],"URL":"https:\/\/doi.org\/10.1038\/s41588-024-01719-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.10.26.23297560","asserted-by":"object"}]},"ISSN":["1061-4036","1546-1718"],"issn-type":[{"value":"1061-4036","type":"print"},{"value":"1546-1718","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,29]]},"assertion":[{"value":"3 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 March 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 April 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}