Evidence map›Paper›PMID 36109679›Full record

ArticleNature methods2022

SVision: a deep learning approach to resolve complex structural variants.

Jiadong Lin, Songbo Wang, Peter A Audano, Deyu Meng, Jacob I Flores, Walter Kosters, Xiaofei Yang, Peng Jia, Tobias Marschall, Christine R Beck and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.

0numbers the graph read from it
0cells of the map it votes in
64citing 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

64 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. [Applications and Challenges of Deep Learning in Human Genome Research].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2026
    Review
  5. Review
  6. Article
  7. DNA Replication Errors Drive Genome-Wide Small Inverted Triplication Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  8. Review
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Review
  17. Review
  18. Review
  19. Article
  20. Article

4 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Jiadong Lin *MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.ORCID http://orcid.org/0000-0002-8116-5901
Songbo Wang *MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.ORCID http://orcid.org/0000-0003-4482-8128
Peter A AudanoThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0002-5187-0415
Deyu MengMOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
Jacob I FloresThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Walter KostersLeiden Institute of Advanced Computer Science, Faculty of Science, Leiden University, Leiden, the Netherlands.ORCID http://orcid.org/0000-0001-8860-0390
Xiaofei YangMOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.ORCID http://orcid.org/0000-0002-5118-7755
Peng JiaMOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
Tobias MarschallHeinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Dusseldorf, Germany.ORCID http://orcid.org/0000-0002-9376-1030
Christine R BeckThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0001-7821-8489
Kai YeMOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China. kaiye@xjtu.edu.cn.ORCID http://orcid.org/0000-0002-2851-6741

Funding

Shared Resource ManagementP30CA034196 · NCI · JACKSON LABORATORY · PI William Carl Skarnes · 1985 to 2026
$61.9M
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
Repetitive sequences drive genome variation and plasticityR35GM133600 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Christine R Beck · 2019 to 2026
$3.0M
NCI NIH HHS P30 CA034196NHGRI NIH HHS U24 HG007497NIGMS NIH HHS R35 GM133600
6 · The paper itself

Abstract

Complex structural variants (CSVs) encompass multiple breakpoints and are often missed or misinterpreted. We developed SVision, a deep-learning-based multi-object-recognition framework, to automatically detect and haracterize CSVs from long-read sequencing data. SVision outperforms current callers at identifying the internal structure of complex events and has revealed 80 high-quality CSVs with 25 distinct structures from an individual genome. SVision directly detects CSVs without matching known structures, allowing sensitive detection of both common and previously uncharacterized complex rearrangements.

Indexed as

Deep LearningGenomeHigh-Throughput Nucleotide SequencingSequence Analysis, DNA

Identifiers

PMID36109679
PMCPMC9985066

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.