ArticleCell genomics2022
A multi-platform reference for somatic structural variation detection.
Article in Cell genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- Improving Long-Read Somatic Structural Variant Calling with Pangenome and De Novo Personal Genome Assembly.Cancer research communications · 2026Article
- Comprehensive evaluation of structural variation detection for germline and somatic analysis with long-read sequencing data.Briefings in bioinformatics · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies.Scientific reports · 2026Article
- SVScope improves somatic structural variations detection via graph-genome optimization.Genome biology · 2026Article
- Leveraging a spectrum of cytogenomics methods for profiling complex karyotypes in chronic lymphocytic leukemia.Human genomics · 2026Article
- Reference-Guided Chromosome-by-Chromosome de novo Assembly at Scale Using Low-Coverage High-Fidelity Long-Reads with HiFiCCL.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions.bioRxiv : the preprint server for biology · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Article
- Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes.bioRxiv : the preprint server for biology · 2025Article
- Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly.bioRxiv : the preprint server for biology · 2025Article
- A telomere-to-telomere map of somatic mutation burden and functional impact in cancer.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive benchmarking of somatic mutation detection by the SMaHT Network.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking of low coverage sequencing workflows for precision genotyping in eggplant.BMC plant biology · 2025Article
- SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.Nature methods · 2025Article
- SVHunter: long-read-based structural variation detection through the transformer model.Briefings in bioinformatics · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality, gold-standard datasets that enable the benchmarking of experimental approaches and bioinformatic analysis pipelines. Here, we performed somatic SV analysis of the paired melanoma and normal lymphoblastoid COLO829 cell lines using four different sequencing technologies. Based on the evidence from multiple technologies combined with extensive experimental validation, we compiled a comprehensive set of carefully curated and validated somatic SVs, comprising all SV types. We demonstrate the utility of this resource by determining the SV detection performance as a function of tumor purity and sequence depth, highlighting the importance of assessing these parameters in cancer genomics projects. The truth somatic SV dataset as well as the underlying raw multi-platform sequencing data are freely available and are an important resource for community somatic benchmarking efforts.
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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 Socratic graph.