Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data.

Humans Alternative Splicing RNA, Messenger / genetics Algorithms Sequence Analysis, RNA / methods RNA Isoforms / genetics Software Computational Biology / methods High-Throughput Nucleotide Sequencing / methods Protein Isoforms / genetics

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
10 May 2024
Historique:
received: 18 10 2022
accepted: 19 04 2024
medline: 11 5 2024
pubmed: 11 5 2024
entrez: 10 5 2024
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-024-48117-3 PMID: 38730241
pubmed: 38730241
doi: 10.1038/s41467-024-48117-3
pii: 10.1038/s41467-024-48117-3
doi:

Substances chimiques

RNA, Messenger 0
RNA Isoforms 0
Protein Isoforms 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

3972

Subventions

Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32170551
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32270835
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32250610202

Informations de copyright

© 2024. The Author(s).

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Auteurs

Yaqi 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.

Zhejian 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.

Siqian 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.

Zhipeng Ai (Z)

Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China.

Ruihong 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.

Xinyi 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.

Ziwei 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.

Yixin 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.

Di 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.

Hongqing Liang (H)

Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310006, Zhejiang, China.
ORCID: 0000-0002-5494-2197

Zuozhu 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.

Wanlu 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.
ORCID: 0000-0001-5963-2908

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Maturation post-transcriptionnelle des ARN › Épissage des ARN › Épissage alternatif › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN messager › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › Isoformes d'ARN › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Comprehensive assessment of mRNA isoform...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Isoformes de protéines › Comprehensive assessment of mRNA isoform...