ArticleNature methods2018
Picky comprehensively detects high-resolution structural variants in nanopore long reads.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 126 citations in OpenAlex.
- Review
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- DNA Replication Errors Drive Genome-Wide Small Inverted Triplication Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- NanoVar: a comprehensive workflow for structural variant detection to uncover the genome's hidden patterns.Nature protocols · 2026Review
- Sequential sequencing reveals the architecture and complexity of genomic variants in patients with Alport syndrome.Nature communications · 2026Article
- SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies.Genome biology · 2025Article
- Review
- Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs.iScience · 2025Article
- Current research status of third-generation sequencing technology in thalassemia detection.Frontiers in pediatrics · 2025Review
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology.BMC genomics · 2024Article
- FindCSV: a long-read based method for detecting complex structural variations.BMC bioinformatics · 2024Article
- Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data.Genome biology · 2024Article
- The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research.Viruses · 2024Review
- Whole genome sequencing analysis on antibiotic-resistantJournal of veterinary science · 2024Article
- Regulation and function of transposable elements in cancer genomes.Cellular and molecular life sciences : CMLS · 2024Review
- Article
- Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv.Nucleic acids research · 2023Article
- A survey of algorithms for the detection of genomic structural variants from long-read sequencing data.Nature methods · 2023Review
- SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data.BMC bioinformatics · 2023Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( https://github.com/TheJacksonLaboratory/Picky ), to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation. Examination of genome-wide breakpoints at nucleotide resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with the propensity for interchromosomal connectivity and was found to be enriched in promoters and transcribed regions of the genome. Furthermore, we observed an over-representation of reciprocal translocations from chromosomal double-crossovers through phased SVs. We demonstrate that Picky analysis is an effective tool for comprehensive detection of SVs in cancer genomes from long-read data.
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