ArticleNature genetics2023
Most large structural variants in cancer genomes can be detected without long reads.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 36 citations in OpenAlex.
- Article
- The ageing holobiont: crosstalk between telomere dynamics, oxidative stress and the gut microbiome.Biological reviews of the Cambridge Philosophical Society · 2026Review
- HOROSCOPE: Decoding human centromere architecture from short reads usingbioRxiv : the preprint server for biology · 2026Article
- Whole genome resequencing reveals the genetic basis of stature in short-statured Indian cattle.Scientific reports · 2026Article
- Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies.Scientific reports · 2026Article
- A complete human pancreatic cancer genome.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally Diverse Cohort.bioRxiv : the preprint server for biology · 2026Article
- Harnessing Proteogenomics to Advance Precision Oncology: From Melanoma and Hepatocellular Carcinoma Perspective.Current oncology reports · 2026Review
- Proof-of-concept study for the detection of somatic structural variant driver alterations using HiFi long-read sequencing in a pediatric leukemia cohort.NPJ genomic medicine · 2026Article
- Novel driver gene MDC1 confers homologous recombination repair deficiency and genomic instability in chemoresistant relapsing ovarian cancer.Journal of translational medicine · 2026Article
- High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq.Nucleic acids research · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- Complex de novo structural variants are an underestimated cause of rare disorders.Nature communications · 2025Article
- Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders.Diagnostics (Basel, Switzerland) · 2025Review
- SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.Nature methods · 2025Article
- Flexible, production-scale, human whole genome sequencing on a benchtop sequencer.BMC genomics · 2025Article
- Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T.Genome research · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
Corrections and comments
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Authors and funding
20 authors at 3 institutions in 1 country.
Funding
Abstract
Short-read sequencing is the workhorse of cancer genomics yet is thought to miss many structural variants (SVs), particularly large chromosomal alterations. To characterize missing SVs in short-read whole genomes, we analyzed 'loose ends'-local violations of mass balance between adjacent DNA segments. In the landscape of loose ends across 1,330 high-purity cancer whole genomes, most large (>10-kb) clonal SVs were fully resolved by short reads in the 87% of the human genome where copy number could be reliably measured. Some loose ends represent neotelomeres, which we propose as a hallmark of the alternative lengthening of telomeres phenotype. These pan-cancer findings were confirmed by long-molecule profiles of 38 breast cancer and melanoma cases. Our results indicate that aberrant homologous recombination is unlikely to drive the majority of large cancer SVs. Furthermore, analysis of mass balance in short-read whole genome data provides a surprisingly complete picture of cancer chromosomal structure.
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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.