Treffer: Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data.
Title:
Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data.
Authors:
Su Y; Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.; Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China.; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA., Yu Z; Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.; Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China., Jin S; Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.; Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China., Ai Z; Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China., Yuan R; Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China., Chen X; Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.; Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China., Xue Z; Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.; Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China., Guo Y; Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.; Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China., Chen D; Center for Reproductive Medicine of the Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.; Centre for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China., Liang H; Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China., Liu Z; Zhejiang University-Angel Align Inc. R&D Center for Intelligent Healthcare, Zhejiang University-University of Illinois at Urbana-Champaign Institute (ZJU-UIUC Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China., Liu W; Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China. wanluliu@intl.zju.edu.cn.; Centre of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, 314400, Zhejiang, China. wanluliu@intl.zju.edu.cn.; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314100, China. wanluliu@intl.zju.edu.cn.; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, 310058, Zhejiang, China. wanluliu@intl.zju.edu.cn.
Source:
Nature communications [Nat Commun] 2024 May 10; Vol. 15 (1), pp. 3972. Date of Electronic Publication: 2024 May 10.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
Imprint Name(s):
Original Publication: [London] : Nature Pub. Group
MeSH Terms:
References:
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Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89. (PMID: 26542840)
Nat Biotechnol. 2013 Nov;31(11):1009-14. (PMID: 24108091)
Nat Methods. 2017 Apr;14(4):417-419. (PMID: 28263959)
Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278)
Nat Commun. 2021 Jan 4;12(1):2. (PMID: 33397972)
Nucleic Acids Res. 2023 Jan 25;51(2):e11. (PMID: 36478271)
Sci Data. 2022 Mar 2;9(1):69. (PMID: 35236860)
Cell Death Differ. 2023 Jan;30(1):69-81. (PMID: 35933500)
Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i222-i231. (PMID: 37387174)
Nat Biotechnol. 2014 Sep;32(9):903-14. (PMID: 25150838)
NAR Genom Bioinform. 2022 Dec 01;4(4):lqac092. (PMID: 36465498)
Nat Biotechnol. 2011 Jan;29(1):24-6. (PMID: 21221095)
Bioinformatics. 2023 Jun 1;39(6):. (PMID: 37267159)
Nat Rev Genet. 2014 Feb;15(2):121-32. (PMID: 24434847)
Bioinformatics. 2018 Sep 15;34(18):3094-3100. (PMID: 29750242)
Genome Biol. 2015 Jul 23;16:150. (PMID: 26201343)
Nat Methods. 2023 Nov;20(11):1810-1821. (PMID: 37783886)
Genome Biol. 2008;9(3):R50. (PMID: 18321378)
Nat Ecol Evol. 2022 Mar;6(3):273-287. (PMID: 34969986)
Nat Commun. 2024 May 10;15(1):3972. (PMID: 38730241)
Nat Methods. 2011 Jun;8(6):469-77. (PMID: 21623353)
Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):E4821-30. (PMID: 24282307)
Nat Genet. 2008 Dec;40(12):1413-5. (PMID: 18978789)
Nat Rev Genet. 2020 Oct;21(10):597-614. (PMID: 32504078)
Nat Methods. 2018 Mar;15(3):201-206. (PMID: 29334379)
Bioinformatics. 2014 Apr 1;30(7):923-30. (PMID: 24227677)
Nat Rev Mol Cell Biol. 2017 Jul;18(7):437-451. (PMID: 28488700)
Eur J Immunol. 2022 Jul;52(7):1058-1068. (PMID: 35460072)
Genome Biol. 2021 Nov 11;22(1):310. (PMID: 34763716)
Nat Commun. 2022 Jan 24;13(1):463. (PMID: 35075135)
Nat Rev Genet. 2019 Jul;20(7):417-431. (PMID: 30867571)
Stem Cell Reports. 2019 Oct 8;13(4):612-626. (PMID: 31522974)
Bioinformatics. 2013 Jan 1;29(1):119-21. (PMID: 23129296)
Nat Rev Mol Cell Biol. 2023 Apr;24(4):242-254. (PMID: 36229538)
BMC Genomics. 2022 Jul 22;23(1):530. (PMID: 35869428)
BMC Genomics. 2020 Oct 30;21(1):751. (PMID: 33126848)
Nat Commun. 2021 Jul 9;12(1):4203. (PMID: 34244519)
Bioinformatics. 2019 Nov 1;35(21):4469-4471. (PMID: 30989184)
Nat Methods. 2016 Sep;13(9):792-8. (PMID: 27502218)
Sci Adv. 2023 Jan 20;9(3):eabq5072. (PMID: 36662851)
Genome Res. 2020 Feb;30(2):287-298. (PMID: 32024662)
Nat Methods. 2024 May;21(5):793-797. (PMID: 38509328)
Genome Res. 2011 Mar;21(3):487-93. (PMID: 21209072)
Cell Stem Cell. 2016 Oct 6;19(4):502-515. (PMID: 27424783)
Nat Commun. 2023 Sep 23;14(1):5935. (PMID: 37741817)
Diabetes. 2021 Oct;70(10):2299-2312. (PMID: 34554924)
Nature. 2014 Nov 20;515(7527):355-64. (PMID: 25409824)
Nature. 2008 Nov 27;456(7221):470-6. (PMID: 18978772)
Bioinformatics. 2021 May 5;37(5):589-595. (PMID: 32976553)
BMC Bioinformatics. 2014 May 09;15:135. (PMID: 24885830)
Nat Biotechnol. 2015 Mar;33(3):290-5. (PMID: 25690850)
Genome Biol. 2019 Jun 20;20(1):125. (PMID: 31221194)
Nat Methods. 2024 Jul;21(7):1349-1363. (PMID: 38849569)
NAR Genom Bioinform. 2021 Apr 26;3(2):lqab028. (PMID: 33937765)
BMC Genomics. 2022 Jan 10;23(1):42. (PMID: 35012468)
Cell Rep. 2022 Aug 23;40(8):111240. (PMID: 36001968)
Nat Methods. 2019 Sep;16(9):879-886. (PMID: 31384046)
Nature. 2022 Dec;612(7941):725-731. (PMID: 36517592)
Nat Biotechnol. 2021 Nov;39(11):1348-1365. (PMID: 34750572)
Funct Integr Genomics. 2020 Jul;20(4):523-536. (PMID: 31955296)
Cell Stem Cell. 2019 May 2;24(5):724-735.e5. (PMID: 31006620)
Genome Biol. 2019 Dec 16;20(1):278. (PMID: 31842956)
Mol Immunol. 2021 May;133:53-62. (PMID: 33631555)
Nat Biotechnol. 2008 Oct;26(10):1146-53. (PMID: 18846088)
Bioinformatics. 2013 Jan 1;29(1):15-21. (PMID: 23104886)
F1000Res. 2020 Apr 28;9:304. (PMID: 32489650)
Nat Commun. 2020 Mar 18;11(1):1438. (PMID: 32188845)
Nat Biotechnol. 2023 Jul;41(7):915-918. (PMID: 36593406)
Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89. (PMID: 26542840)
Nat Biotechnol. 2013 Nov;31(11):1009-14. (PMID: 24108091)
Nat Methods. 2017 Apr;14(4):417-419. (PMID: 28263959)
Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278)
Nat Commun. 2021 Jan 4;12(1):2. (PMID: 33397972)
Nucleic Acids Res. 2023 Jan 25;51(2):e11. (PMID: 36478271)
Sci Data. 2022 Mar 2;9(1):69. (PMID: 35236860)
Cell Death Differ. 2023 Jan;30(1):69-81. (PMID: 35933500)
Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i222-i231. (PMID: 37387174)
Grant Information:
32170551 National Natural Science Foundation of China (National Science Foundation of China); 32270835 National Natural Science Foundation of China (National Science Foundation of China); 32250610202 National Natural Science Foundation of China (National Science Foundation of China)
Substance Nomenclature:
0 (RNA, Messenger)
0 (RNA Isoforms)
0 (Protein Isoforms)
0 (RNA Isoforms)
0 (Protein Isoforms)
Entry Date(s):
Date Created: 20240510 Date Completed: 20240510 Latest Revision: 20250104
Update Code:
20260130
PubMed Central ID:
PMC11087464
DOI:
10.1038/s41467-024-48117-3
PMID:
38730241
Database:
MEDLINE
Weitere Informationen
The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.
(© 2024. The Author(s).)