Evidence map›Paper›PMID 42021344›Full record

ArticleGenome biology2026

SVScope improves somatic structural variations detection via graph-genome optimization.

Kailing Tu, Qilin Zhang, Yang Li, Yucong Li, Lanfang Yuan, Jing Wang, Jie Tang, Lin Xia, Wei Huang, Dan Xie

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Kailing Tu *Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
Qilin Zhang *Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
Yang LiLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
Yucong LiLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
Lanfang YuanLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
Jing WangLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
Jie TangLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
Lin XiaLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China.
Wei HuangSchool of Mathematics and Statistics, Key Laboratory for Applied Statistics of the Ministry of Education, Northeast Normal University, 5268 Renmin Street, Changchun, 130024, China. huangw482@nenu.edu.cn.
Dan XieLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17, Section 3, Renmin South Road, Chengdu, 610041, Sichuan, China. danxie@scu.edu.cn.

Funding

National Natural Science Foundation of China 11671073National Natural Science Foundation of China 32200508National Natural Science Foundation of China 32300522National Natural Science Foundation of China 82072582National Natural Science Foundation of China 82173383the 1·3·5 project for disciplines of excellence, West China Hospital, Sichuan University ZYYC23024the Science and Technology Department of Sichuan Province, China 2024NSFSC1187the Science and Technology Department of Sichuan Province, China 2025ZNSFSC1098
6 · The paper itself

Abstract

Somatic structural variations (SVs) are critical in cancer genomes, yet their detection from long-read sequencing remains challenging due to alignment errors in repetitive regions. We develop SVScope, leveraging full-length reads and local graph-genome optimization with a random forest strategy to improve somatic SV calling. We also provide ScopeVIZ, a companion pipeline for visualizing read clustering at breakpoints. Across seven benchmark cell lines sequenced with ONT and PacBio platforms, as well as simulated datasets, SVScope consistently outperforms state-of-the-art methods, achieving up to 23.64% improvement in F1-score. Using SVScope, we validate 32 somatic SVs, expanding the ground-truth dataset by 47.06%.

Indexed as

GenomicsGenomic Structural VariationNeoplasmsSoftwareAlgorithmsGenome, HumanHigh-Throughput Nucleotide SequencingHumansSequence Analysis, DNALocal graph genome optimizationLong-read sequencing (LRS)Somatic structural variation

Identifiers

PMID42021344
PMCPMC13238139

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LicenceCC BY-NC-ND
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Registered trials

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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.