ArticleGenome research2020
Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
What it found
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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.
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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.
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Who cites it
68 citing papers in PubMed, 107 citations in OpenAlex.
- Validation structures for sequence variants of uncertain significance in hereditary cancer.European journal of human genetics : EJHG · 2026Review
- Long-read, whole-genome sequencing and chemotherapy response of two patient-derived organoids from a TP53- and KRAS-mutant ovarian carcinoma.bioRxiv : the preprint server for biology · 2026Article
- VCboost: reducing false positives in long-read variant calling for single-nucleotide polymorphism and indel detection in challenging genomic regions.Briefings in bioinformatics · 2026Article
- Multiplatform comparisons and annotation of structural variants highlight the utility of the T2T reference genome in human diagnostics.GigaScience · 2026Article
- Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC.NPJ digital medicine · 2026Article
- VACmap: an accurate long-read aligner for unraveling complex genomic rearrangements.Nature communications · 2026Article
- Article
- Establishment of Breast Cancer Organoids: A Systematic Review and Meta-Analysis.International journal of breast cancer · 2026Article
- SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies.Genome biology · 2025Article
- Alternative splicing generates HER2 isoform diversity underlying antibody-drug conjugate resistance in breast cancer.Genome research · 2025Article
- Analytical validation of germline small variant detection using long-read HiFi genome sequencing.Genome research · 2025Article
- Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis.Genome research · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T.Genome research · 2025Article
- Review
- Single-Cell Sequencing: Genomic and Transcriptomic Approaches in Cancer Cell Biology.International journal of molecular sciences · 2025Review
- De novo and somatic structural variant discovery with SVision-pro.Nature biotechnology · 2025Article
- Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution.Nucleic acids research · 2025Article
- Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes.Cell genomics · 2024Article
- Detection of mosaic and population-level structural variants with Sniffles2.Nature biotechnology · 2024Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 4 institutions in 1 country.
Funding
Abstract
Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. We performed whole-genome sequencing of the SKBR3 breast cancer cell line and patient-derived tumor and normal organoids from two breast cancer patients using Illumina/10x Genomics, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT) sequencing. We then inferred SVs and large-scale allele-specific copy number variants (CNVs) using an ensemble of methods. Our findings show that long-read sequencing allows for substantially more accurate and sensitive SV detection, with between 90% and 95% of variants supported by each long-read technology also supported by the other. We also report high accuracy for long reads even at relatively low coverage (25×-30×). Furthermore, we integrated SV and CNV data into a unifying karyotype-graph structure to present a more accurate representation of the mutated cancer genomes. We find hundreds of variants within known cancer-related genes detectable only through long-read sequencing. These findings highlight the need for long-read sequencing of cancer genomes for the precise analysis of their genetic instability.
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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.