{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T19:01:41Z","timestamp":1780513301306,"version":"3.54.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,9,26]],"date-time":"2024-09-26T00:00:00Z","timestamp":1727308800000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31870079"],"award-info":[{"award-number":["31870079"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021QY2004"],"award-info":[{"award-number":["2021QY2004"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Short-tandem repeats (STRs) are the type of genetic markers extensively utilized in biomedical and forensic applications. Due to sequencing noise in nanopore sequencing, accurate analysis methods are lacking. We developed NASTRA, an innovative tool for Nanopore Autosomal Short Tandem Repeat Analysis, which overcomes traditional database-based methods\u2019 limitations and provides a precise germline analysis of STR genetic markers without the need for allele sequence reference. Demonstrating high accuracy in cell line authentication testing and paternity testing, NASTRA significantly surpasses existing methods in both speed and accuracy. This advancement makes it a promising solution for rapid cell line authentication and kinship testing, highlighting the potential of nanopore sequencing for in-field applications.<\/jats:p>","DOI":"10.1093\/bib\/bbae472","type":"journal-article","created":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T08:53:51Z","timestamp":1725958431000},"source":"Crossref","is-referenced-by-count":6,"title":["NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3621-1024","authenticated-orcid":false,"given":"Zilin","family":"Ren","sequence":"first","affiliation":[{"name":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , No. 573 Yujinxiang Street, Jingyue District, Changchun 130012,","place":["China"]},{"name":"School of Information Science and Technology, Northeast Normal University , No. 2555 Jingyue Street, Jingyue District, Changchun 130117,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiarong","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Forensic Medicine, Shanxi Medical University , No. 55 Wenhua Street, Yuci District, Taiyuan 030001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yixiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , No. 573 Yujinxiang Street, Jingyue District, Changchun 130012,","place":["China"]},{"name":"School of Information Science and Technology, Northeast Normal University , No. 2555 Jingyue Street, Jingyue District, Changchun 130117,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Forensic Medicine, Shanxi Medical University , No. 55 Wenhua Street, Yuci District, Taiyuan 030001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pingping","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, Northeast Normal University , No. 2555 Jingyue Street, Jingyue District, Changchun 130117,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiguo","family":"Xue","sequence":"additional","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences, No. 27 Taiping Road, Haidian District, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1911-7922","authenticated-orcid":false,"given":"Xiaochen","family":"Bo","sequence":"additional","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences, No. 27 Taiping Road, Haidian District, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Zhou","sequence":"additional","affiliation":[{"name":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , No. 573 Yujinxiang Street, Jingyue District, Changchun 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiangwei","family":"Yan","sequence":"additional","affiliation":[{"name":"School of Forensic Medicine, Shanxi Medical University , No. 55 Wenhua Street, Yuci District, Taiyuan 030001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Ni","sequence":"additional","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences, No. 27 Taiping Road, Haidian District, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,9,25]]},"reference":[{"key":"2024092601344415000_ref1","doi-asserted-by":"publisher","first-page":"1682","DOI":"10.1002\/(SICI)1522-2683(19990101)20:8%3c1682::AID-ELPS1682%3e3.0.CO;2-Z","article-title":"The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems","volume":"20","author":"Chakraborty","year":"1999","journal-title":"Electrophoresis"},{"key":"2024092601344415000_ref2","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1111\/j.1556-4029.2006.00046.x","article-title":"Genetics and genomics of core short tandem repeat loci used in human identity testing","volume":"51","author":"Butler","year":"2006","journal-title":"J Forensic Sci"},{"key":"2024092601344415000_ref3","doi-asserted-by":"publisher","first-page":"8012","DOI":"10.1073\/pnas.121616198","article-title":"Short tandem repeat profiling provides an international reference standard for human cell lines","volume":"98","author":"Masters","year":"2001","journal-title":"Proc Natl Acad Sci"},{"key":"2024092601344415000_ref4","first-page":"103","article-title":"Short tandem repeat DNA typing provides an international reference standard for authentication of human cell lines","volume":"22","author":"Dirks","year":"2005","journal-title":"ALTEX"},{"key":"2024092601344415000_ref5","first-page":"149","article-title":"Efficient DNA fingerprinting method for the identification of cross-culture contamination of cell lines","volume":"12","author":"Matsuo","year":"1999","journal-title":"Hum Cell"},{"key":"2024092601344415000_ref6","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.fsigen.2008.02.002","article-title":"Resolving relationship tests that show ambiguous STR results using autosomal SNPs as supplementary markers","volume":"2","author":"Phillips","year":"2008","journal-title":"Forensic Sci Int Genet"},{"key":"2024092601344415000_ref7","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/nrg2952","article-title":"Improving human forensics through advances in genetics, genomics and molecular biology","volume":"12","author":"Kayser","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2024092601344415000_ref8","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1093\/nar\/29.1.320","article-title":"STRBase: a short tandem repeat DNA database for the human identity testing community","volume":"29","author":"Ruitberg","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2024092601344415000_ref9","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/nmeth.3403","article-title":"Reproducibility: changing the policies and culture of cell line authentication","volume":"12","author":"Freedman","year":"2015","journal-title":"Nat Methods"},{"key":"2024092601344415000_ref10","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1038\/nature14397","article-title":"A resource for cell line authentication, annotation and quality control","volume":"520","author":"Yu","year":"2015","journal-title":"Nature"},{"key":"2024092601344415000_ref11","doi-asserted-by":"publisher","first-page":"25","DOI":"10.7171\/jbt.18-2902-002","article-title":"The Cellosaurus, a cell-line knowledge resource","volume":"29","author":"Bairoch","year":"2018","journal-title":"J Biomol Tech"},{"key":"2024092601344415000_ref12","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1002\/ijc.24999","article-title":"Cell line cross-contamination initiative: an interactive reference database of STR profiles covering common cancer cell lines","volume":"126","author":"Dirks","year":"2010","journal-title":"Int J Cancer"},{"key":"2024092601344415000_ref13","doi-asserted-by":"publisher","first-page":"D925","DOI":"10.1093\/nar\/gkn730","article-title":"Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines","volume":"37","author":"Romano","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2024092601344415000_ref14","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1002\/ijc.32639","article-title":"CLASTR: the Cellosaurus STR similarity search tool\u2014a precious help for cell line authentication","volume":"146","author":"Robin","year":"2020","journal-title":"Int J Cancer"},{"key":"2024092601344415000_ref15","doi-asserted-by":"publisher","DOI":"10.1016\/j.fsigen.2021.102621","article-title":"Nanopore sequencing of a forensic combined STR and SNP multiplex","volume":"56","author":"Tytgat","year":"2022","journal-title":"Forensic Sci Int Genet"},{"key":"2024092601344415000_ref16","doi-asserted-by":"publisher","DOI":"10.1002\/wfs2.1323","article-title":"A review of the potential of the MinIONTM single-molecule sequencing system for forensic applications","volume":"1","author":"Plesivkova","year":"2019","journal-title":"WIREs Forensic Science"},{"key":"2024092601344415000_ref17","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.27798","article-title":"Rapid re-identification of human samples using portable DNA sequencing","volume":"6","author":"Zaaijer","year":"2017","journal-title":"Elife"},{"key":"2024092601344415000_ref18","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1038\/nature22401","article-title":"Establishment and cryptic transmission of Zika virus in Brazil and the Americas","volume":"546","author":"Faria","year":"2017","journal-title":"Nature"},{"key":"2024092601344415000_ref19","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1038\/nature16996","article-title":"Real-time, portable genome sequencing for Ebola surveillance","volume":"530","author":"Quick","year":"2016","journal-title":"Nature"},{"key":"2024092601344415000_ref20","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.3390\/ijerph16071097","article-title":"Metagenomic profiling of microbial pathogens in the little Bighorn River, Montana","volume":"16","author":"Hamner","year":"2019","journal-title":"Int J Environ Res Public Health"},{"key":"2024092601344415000_ref21","doi-asserted-by":"publisher","first-page":"632","DOI":"10.3390\/genes10090632","article-title":"Tree lab: portable genomics for early detection of plant viruses and pests in sub-Saharan Africa","volume":"10","author":"Boykin","year":"2019","journal-title":"Genes"},{"key":"2024092601344415000_ref22","doi-asserted-by":"publisher","first-page":"381","DOI":"10.3390\/genes11040381","article-title":"Nanopore sequencing of a forensic STR multiplex reveals loci suitable for single-contributor STR profiling","volume":"11","author":"Tytgat","year":"2020","journal-title":"Genes (Basel)"},{"key":"2024092601344415000_ref23","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/s10038-019-0688-z","article-title":"Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study","volume":"65","author":"Asogawa","year":"2020","journal-title":"J Hum Genet"},{"key":"2024092601344415000_ref24","doi-asserted-by":"publisher","DOI":"10.1016\/j.fsigen.2021.102629","article-title":"Accurate profiling of forensic autosomal STRs using the Oxford nanopore technologies MinION device","volume":"56","author":"Hall","year":"2022","journal-title":"Forensic Sci Int Genet"},{"key":"2024092601344415000_ref25","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1186\/s13073-017-0456-7","article-title":"Interrogating the \u2018unsequenceable\u2019 genomic trinucleotide repeat disorders by long-read sequencing","volume":"9","author":"Liu","year":"2017","journal-title":"Genome Med"},{"key":"2024092601344415000_ref26","doi-asserted-by":"publisher","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":"2024092601344415000_ref27","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/s13059-022-02670-6","article-title":"DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing","volume":"23","author":"Fang","year":"2022","journal-title":"Genome Biol"},{"key":"2024092601344415000_ref28","doi-asserted-by":"publisher","first-page":"1685","DOI":"10.1007\/s00414-021-02604-0","article-title":"Forensic nanopore sequencing of STRs and SNPs using Verogen\u2019s ForenSeq DNA signature prep kit and MinION","volume":"135","author":"Ren","year":"2021","journal-title":"Int J Leg Med"},{"key":"2024092601344415000_ref29","doi-asserted-by":"publisher","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":"2024092601344415000_ref30","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1016\/j.fsigen.2015.06.005","article-title":"STR allele sequence variation: current knowledge and future issues","volume":"18","author":"Gettings","year":"2015","journal-title":"Forensic Sci Int Genet"},{"key":"2024092601344415000_ref31","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/j.fsisyn.2020.06.001","article-title":"The development of forensic science standards in China","volume":"2","author":"Zhai","year":"2020","journal-title":"Forensic Sci Int Synerg"},{"key":"2024092601344415000_ref32","doi-asserted-by":"publisher","first-page":"454","DOI":"10.3390\/genes12030454","article-title":"Noninvasive prenatal paternity testing with a combination of well-established SNP and STR markers using massively parallel sequencing","volume":"12","author":"Shen","year":"2021","journal-title":"Genes (Basel)"},{"key":"2024092601344415000_ref33","doi-asserted-by":"publisher","DOI":"10.1016\/j.fsigen.2019.102158","article-title":"Development and comprehensive evaluation of a noninvasive prenatal paternity testing method through a scaled trial","volume":"43","author":"Chang","year":"2019","journal-title":"Forensic Sci Int Genet"},{"key":"2024092601344415000_ref34","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1186\/s12859-016-0930-z","article-title":"Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments","volume":"17","author":"Daily","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2024092601344415000_ref35","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2024092601344415000_ref36","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","author":"Li","year":"2021","journal-title":"Bioinformatics"},{"key":"2024092601344415000_ref37","doi-asserted-by":"crossref","first-page":"baaa055","DOI":"10.1093\/database\/baaa055","article-title":"CNSA: a data repository for archiving omics data","volume":"2020","author":"Guo","year":"2020","journal-title":"Database (Oxford)"},{"key":"2024092601344415000_ref38","doi-asserted-by":"publisher","first-page":"799","DOI":"10.16288\/j.yczz.20-080","article-title":"CNGBdb: China National GeneBank DataBase","volume":"42","author":"Chen","year":"2020","journal-title":"Yi Chuan"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/6\/bbae472\/59335346\/bbae472.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/6\/bbae472\/59335346\/bbae472.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,25]],"date-time":"2024-09-25T21:35:01Z","timestamp":1727300101000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae472\/7774877"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,23]]},"references-count":38,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,9,23]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae472","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.11.04.565630","asserted-by":"object"}]},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,11]]},"published":{"date-parts":[[2024,9,23]]},"article-number":"bbae472"}}