ArticleCell genomics2023
Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.
Article in Cell genomics, 2023. 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, 42 citations in OpenAlex.
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Long-read sequencing of single cell-derived melanoma sublines reveals divergent and parallel genomic and epigenomic evolutionary trajectories.Nature communications · 2026Article
- GEAR Genomics: a user-friendly, open-source web platform enabling interactive genomic analysis for molecular biologists.Nucleic acids research · 2026Article
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (bioRxiv : the preprint server for biology · 2026Article
- Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies.Scientific reports · 2026Article
- Leveraging a spectrum of cytogenomics methods for profiling complex karyotypes in chronic lymphocytic leukemia.Human genomics · 2026Article
- 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
- Mitotic microhomology-mediated break-induced replication promotes chromoanasynthesis.Nature communications · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Exploratory analysis of the molecular and genomic landscape of upper tract urothelial carcinoma using long-read sequencing.BMC cancer · 2025Article
- Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories.bioRxiv : the preprint server for biology · 2025Article
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- Loss of CFHR5 function reduces the risk for age-related macular degeneration.Nature communications · 2025Article
- GW: ultra-fast chromosome-scale visualization of genomics data.Nature methods · 2025Article
- SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.Nature methods · 2025Article
- Chromoanagenesis in Osteosarcoma.Biomolecules · 2025Review
- The impact of long-read sequencing on human population-scale genomics.Genome research · 2025Review
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
Abstract
Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assembled complex rearrangements, including a 1.55-Mbp chromothripsis event, and we uncover a complex SV pattern termed templated insertion (TI) thread, characterized by short (mostly <1 kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50 kbp in size. TI threads occur in 3% of cancers, with a prevalence up to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read-based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in cancer-driver genes. Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements.
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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.