ReviewBriefings in bioinformatics2021
Detection of somatic structural variants from short-read next-generation sequencing data.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 70 citations in OpenAlex.
- Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Molecular residual disease assessment in colorectal and bladder cancer by somatic structural variant analysis of cell-free DNA whole-genome sequencing data.Journal of translational medicine · 2026Article
- Article
- MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.BMC bioinformatics · 2025Article
- PSVRP: a pig structural variant reference panel for complex trait genomics and precision breeding.BMC genomics · 2025Article
- The continued promise of genomic technologies and software in neurogenetics.Journal of neuromuscular diseases · 2025Review
- OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis.Bioinformatics (Oxford, England) · 2025Article
- Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes.bioRxiv : the preprint server for biology · 2025Article
- MRDadaptis: self-adaptive parameter configuration enhances minimal residual disease detection in heterogeneous ctDNA samples.Briefings in bioinformatics · 2025Article
- Scaling for African Inclusion in High-Throughput Whole Cancer Genome Bioinformatic Workflows.Cancers · 2025Review
- Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations.Genome biology and evolution · 2025Article
- hDNApipe: streamlining human genome analysis and interpretation with an intuitive and user-friendly interface.NAR genomics and bioinformatics · 2025Article
- Unraveling MECP2 structural variants in previously elusive Rett syndrome cases through IGV interpretation.NPJ genomic medicine · 2025Article
- Rare pathogenic structural variants show potential to enhance prostate cancer germline testing for African men.Nature communications · 2025Article
- Unveiling the Genetic Landscape of Coronary Artery Disease Through Common and Rare Structural Variants.Journal of the American Heart Association · 2025Article
- Detection of Complex Genomic Rearrangements Using Short-Read Whole Genome Sequencing in C. elegans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Comparisons of performances of structural variants detection algorithms in solitary or combination strategy.PloS one · 2025Article
- Comprehensive evaluation and guidance of structural variation detection tools in chicken whole genome sequence data.BMC genomics · 2024Article
- Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing.Nature communications · 2024Article
- Investigating copy number variants in schizophrenia pedigrees using a new consensus pipeline called PECAN.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Somatic structural variants (SVs), which are variants that typically impact >50 nucleotides, play a significant role in cancer development and evolution but are notoriously more difficult to detect than small variants from short-read next-generation sequencing (NGS) data. This is due to a combination of challenges attributed to the purity of tumour samples, tumour heterogeneity, limitations of short-read information from NGS and sequence alignment ambiguities. In spite of active development of SV detection tools (callers) over the past few years, each method has inherent advantages and limitations. In this review, we highlight some of the important factors affecting somatic SV detection and compared the performance of seven commonly used SV callers. In particular, we focus on the extent of change in sensitivity and precision for detecting different SV types and size ranges from samples with differing variant allele frequencies and sequencing depths of coverage. We highlight the reasons for why some SV callers perform well in some settings but not others, allowing our evaluation findings to be extended beyond the seven SV callers examined in this paper. As the importance of large SVs become increasingly recognized in cancer genomics, this paper provides a timely review on some of the most impactful factors influencing somatic SV detection that should be considered when choosing SV callers.
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Registered trials
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.