Evidence map›Paper›PMID 39301431›Full record

ArticleJournal of bioinformatics and systems biology : Open access2023

Novornabreak: Local Assembly for Novel Splice Junction and Fusion Transcript Detection from RNA-Seq Data.

Yukun Tan, Vakul Mohanty, Shaoheng Liang, Jinzhuang Dou, Jun Ma, Kun Hee Kim, Marc Jan Bonder, Xinghua Shi, Charles Lee, Human Genome Structural Variation Consortium and 2 more

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In one paragraph

Article in Journal of bioinformatics and systems biology : Open access, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

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4 · The record

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5 · Who and what money

Authors and funding

12 authors.

Yukun TanDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Vakul MohantyDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Shaoheng LiangDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Jinzhuang DouDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Jun MaDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Kun Hee KimDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Marc Jan BonderDivision of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
Xinghua ShiDepartment of Computer & Information Sciences, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA.
Charles LeeThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Human Genome Structural Variation Consortium
Zechen ChongDepartment of Genetics, the University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
Ken ChenDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.

Funding

Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Fabien Delerue · 1985 to 2026
$290.8M
Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human GenomesU24HG007497 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Evan Eichler, Jan Oliver Korbel · 2019 to 2026
$17.2M
Structural variation analysis with and without a reference genomeR35GM138212 · NIGMS · UNIVERSITY OF VIRGINIA · PI Zechen Chong · 2020 to 2026
$2.6M
Informatics for Functional Integration of Heterogeneous Cancer Genome and Transcriptome Sequencing DataU01CA247760 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI CHEN, KEN · 2020 to 2022
$1.2M
NCI NIH HHS P30 CA016672NCI NIH HHS U01 CA247760NHGRI NIH HHS U24 HG007497NIGMS NIH HHS R35 GM138212
6 · The paper itself

Abstract

We present novoRNABreak, a unified framework for cancer specific novel splice junction and fusion transcript detection in RNA-seq data obtained from human cancer samples. novoRNABreak is based on a local assembly model, which offers a tradeoff between the alignment-based and de novo whole transcriptome assembly (WTA) methods. This approach is accurate and sensitive in assembling novel junctions that are difficult to directly align or have multiple alignments. Additionally, it is more efficient due to the strategy that focuses on junctions rather than full length transcripts. The performance of novoRNABreak is demonstrated by a comprehensive set of experiments using synthetic data generated based on genome reference, as well as real RNA-seq data from breast cancer and prostate cancer samples. The results show that our tool has a better performance by fully utilizing unmapped reads and precisely identifying the junctions where short reads or small exons have multiple alignments. novoRNABreak is a fully-fledged program available on GitHub (https://github.com/KChen-lab/novoRNABreak).

Indexed as

cancer specificfusion transcriptslocal assembly modelnovel splice junctionsnovoRNABreakunified framework

Identifiers

PMID39301431
PMCPMC11412692

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.