Evidence map›Paper›PMID 41068563›Full record

ArticleBMC genomics2025

Complex structural variant visualization with SVTopo.

Jonathan R Belyeu, William J Rowell, Juniper A Lake, James Matthew Holt, Zev Kronenberg, Christopher T Saunders, Michael A Eberle

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

7 authors.

Jonathan R BelyeuComputational Biology, PacBio, 305 O'Brien Drive, Menlo Park, CA, 94025, USA. jbelyeu@pacb.com.
William J RowellComputational Biology, PacBio, 305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Juniper A LakeComputational Biology, PacBio, 305 O'Brien Drive, Menlo Park, CA, 94025, USA.
James Matthew HoltComputational Biology, PacBio, 305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Zev KronenbergComputational Biology, PacBio, 305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Christopher T SaundersComputational Biology, PacBio, 305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Michael A EberleComputational Biology, PacBio, 305 O'Brien Drive, Menlo Park, CA, 94025, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundStructural variants are genomic variants that impact at least 50 nucleotides. Structural variants can play major roles in diversity and human health. Many structural variants are difficult to interpret and understand with existing visualization tools, especially when comprised of inverted sequences or multiple breakend pairs.

resultsWe present SVTopo, a tool to visualize germline structural variants with supporting evidence from high-accuracy long reads in easily understood figures. We include examples of 101 visually complex structural variants from seven unrelated human genomes, manually assigned to ten categories. These demonstrate a broad spectrum of rearrangement and showcase the frequency of complex structural variants in human genomes.

conclusionsSVTopo shows breakpoint evidence in ways that aid reasoning about the impact of multi-breakpoint rearrangements. The images created aid human reasoning about the result of structural variation on gene and regulatory regions.

Indexed as

GenomicsGenomic Structural VariationSoftwareGenome, HumanHumansComplex SVGenome visualizationLong-read sequencingStructural variant

Identifiers

PMID41068563
PMCPMC12512824

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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.