ArticleGenome research2017
GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 246 papers.
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Who cites it
246 citing papers in PubMed.
- Trial
- Safety, infectivity and immunogenicity of a genetically attenuated blood-stage malaria vaccine.BMC medicine · 2021Trial
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- Article
- Optimizing GRIDSS for clinical use: A targeted NGS filtering strategy for germline structural variant detection.European journal of human genetics : EJHG · 2026Article
- Dual plasmepsin IX and X inhibitors are refractory to development of resistance.PLoS pathogens · 2026Article
- Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregation.Cell reports · 2026Article
- Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.Nature communications · 2026Article
- HNRNPU mutations redirect cell cycle control to E2F in MYC-driven lymphomas.Blood advances · 2026Article
- Integration of Machine Learning-Based Pathogenicity Prediction and Phenotype Matching Improves Variant Prioritization in Rare Clinical Testing.Current issues in molecular biology · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Multi-modal data integration reveals functionally credible predictive biomarkers in ovarian cancer.Genome medicine · 2026Article
- Benchmarking of real-time, field-deployable whole-genome sequencing ofMicrobial genomics · 2026Article
- High-fidelity rare structural variant detection with HiFiRE3 reduced representation via restriction enzyme ends.bioRxiv : the preprint server for biology · 2026Article
- Effects of ethanol and acetaldehyde on multi-organ genomic mutation landscapes.Cell biology and toxicology · 2026Article
- Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma.Nature communications · 2026Article
- TriosCompass: a snakemake workflow for integrated detection of SNVs, indels, STRs, and structural de novo variants in parent-child trios.Bioinformatics (Oxford, England) · 2026Article
- GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.PLoS computational biology · 2026Article
- Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.G3 (Bethesda, Md.) · 2026Article
- Microglandular adenosis, triple negative breast carcinoma and DNA repair defects.Journal of clinical pathology · 2026Article
186 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis.
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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.