ArticleNature biotechnology2026
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.
Abstract read
In one paragraph
Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- 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
- nf-core/pacsomatic: a scalable somatic analytic pipeline using PacBio HiFi data.Bioinformatics (Oxford, England) · 2026Article
- Take Five: harmonization in personalized cancer vaccines for cancer immunotherapy.Experimental & molecular medicine · 2026Review
- ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.Nature methods · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Long-read sequencing of single cell-derived melanoma sublines reveals divergent and parallel genomic and epigenomic evolutionary trajectories.Nature communications · 2026Article
- Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer.Nature communications · 2026Article
- Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect.Bioinformatics (Oxford, England) · 2026Article
- Structural variant calling using Sniffles2.Nature protocols · 2026Review
- 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
- Chromosome-arm-specific telomere length governs dual modes of structural genome evolution in IDH-mutant astrocytoma.bioRxiv : the preprint server for biology · 2026Article
- SVScope improves somatic structural variations detection via graph-genome optimization.Genome biology · 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
- cuteHap: Haplotype-Aware Structural Variant Detection in Phased Long-Read Sequencing Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Comprehensive detection of genetic and epigenetic alterations in cancer using long reads with TumorLens.medRxiv : the preprint server for health sciences · 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
Corrections and comments
- Update of
Authors and funding
41 authors.
Ayse G KeskusCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-3934-8587
Asher BryantCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.ORCID http://orcid.org/0009-0005-9132-782X
Tanveer AhmadCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
Byunggil YooChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.
Sergey AganezovOxford Nanopore Technologies, New York, NY, USA.
Anton GoretskyCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.ORCID http://orcid.org/0009-0007-6595-9318
Ataberk DonmezCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
Lisa A LansdonChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.
Isabel RodriguezDivision of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA.
Jimin ParkUniversity of California, Santa Cruz, Genomics Institute, Santa Cruz, CA, USA.
Yuelin LiuCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
Xiwen CuiCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
Joshua GardnerUniversity of California, Santa Cruz, Genomics Institute, Santa Cruz, CA, USA.
Brandy McNultyUniversity of California, Santa Cruz, Genomics Institute, Santa Cruz, CA, USA.
Samuel SaccoUniversity of California, Santa Cruz, Genomics Institute, Santa Cruz, CA, USA.
Jyoti ShettySequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Yongmei ZhaoSequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.ORCID http://orcid.org/0000-0003-0800-4658
Bao TranSequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Giuseppe NarzisiNew York Genome Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-1118-8849
Adrienne HellandNew York Genome Center, New York, NY, USA.
Daniel E CookGoogle, Inc., Mountain View, CA, USA.
Pi-Chuan ChangGoogle, Inc., Mountain View, CA, USA.ORCID http://orcid.org/0000-0003-3021-6446
Alexey KolesnikovGoogle, Inc., Mountain View, CA, USA.
Andrew CarrollGoogle, Inc., Mountain View, CA, USA.ORCID http://orcid.org/0000-0002-4824-6689
Erin K MolloyDepartment of Computer Science, University of Maryland, College Park, MD, USA.
Chengpeng BiChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.
Adam WalterChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.
Margaret GibsonChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.
Irina PushelChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.ORCID http://orcid.org/0000-0002-0862-1923
Erin GuestChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.
Tomi PastinenChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.ORCID http://orcid.org/0000-0003-4016-5021
Kishwar ShafinDivision of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA.ORCID http://orcid.org/0000-0001-5252-3434
Karen H MigaUniversity of California, Santa Cruz, Genomics Institute, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0002-3670-4507
Salem MalikicCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-4215-5655
Chi-Ping DayCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.ORCID http://orcid.org/0000-0001-5200-2372
Nicolas RobineNew York Genome Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-5698-8183
Cenk SahinalpCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-2170-2808
Michael DeanDivision of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA.
Midhat S FarooqiChildren's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.
Benedict PatenUniversity of California, Santa Cruz, Genomics Institute, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0001-8863-3539
Mikhail KolmogorovCancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. mikhail.kolmogorov@nih.gov.ORCID http://orcid.org/0000-0002-5489-9045
Funding
The AnVIL Data Ecosystem DACReS SupplementU24HG010262 · NHGRI · BROAD INSTITUTE, INC. · PI Robert J Carroll, Jonathan Lawson · 2018 to 2026
$40.5MThe WashU-UCSC-EBI Human Genome Reference Center."U41HG010972 · NHGRI · WASHINGTON UNIVERSITY · PI Ira M Hall, Heng Li · 2019 to 2026
$24.9MDockstore: The Community Platform for Reproducible Biomedical Workflows and ApplicationsU24HG011853 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Jonathan Lawson, Benedict Paten · 2021 to 2026
$5.7MTelomere-to-telomere assemblies of human genomesR01HG011274 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Karen Hayden Miga · 2020 to 2026
$4.5MComputational tools for uniform processing and integration of human reference atlas data [2 of 5]OT2OD033761 · OD · CARNEGIE-MELLON UNIVERSITY · PI PATEN, BENEDICT, RUFFALO, MATTHEW · 2022 to 2025
$4.2MEnabling Comparative PangenomicsR01HG010485 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI HAUSSLER, DAVID H, MARTIN, FERGAL JAMES · 2020 to 2023
$2.6MTools for comprehensive variant characterization using the pangenomeU01HG013748 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI LI, HENG, MARSCHALL, TOBIAS · 2024 to 2024
$1.7MAdvanced development of Lancet, an emerging tool for complex variant calling in cancer genomicsU01CA253405 · NCI · NEW YORK GENOME CENTER · PI NARZISI, GIUSEPPE · 2021 to 2023
$1.5MNCI NIH HHS U01 CA253405NHGRI NIH HHS R01 HG010485NHGRI NIH HHS R01 HG011274NHGRI NIH HHS U01 HG013748NHGRI NIH HHS U24 HG010262NHGRI NIH HHS U24 HG011853NHGRI NIH HHS U41 HG010972NIH HHS OT2 OD033761U.S. Department of Health & Human Services | National Institutes of Health (NIH) OT2OD033761U.S. Department of Health & Human Services | National Institutes of Health (NIH) U01CA253405U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) Intramural fundingU.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) Intramural Research Program of the Center for Cancer ResearchU.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01HG010485U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01HG011274U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U01HG013748U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U24HG010262U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U24HG011853U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U41HG010972
Abstract
For the detection of somatic structural variation (SV) in cancer genomes, long-read sequencing is advantageous over short-read sequencing with respect to mappability and variant phasing. However, most current long-read SV detection methods are not developed for the analysis of tumor genomes characterized by complex rearrangements and heterogeneity. Here, we present Severus, a breakpoint graph-based algorithm for somatic SV calling from long-read cancer sequencing. Severus works with matching normal samples, supports unbalanced cancer karyotypes, can characterize complex multibreak SV patterns and produces haplotype-specific calls. On a comprehensive multitechnology cell line panel, Severus consistently outperforms other long-read and short-read methods in terms of SV detection F1 score (harmonic mean of the precision and recall). We also illustrate that compared to long-read methods, short-read sequencing systematically misses certain classes of somatic SVs, such as insertions or clustered rearrangements. We apply Severus to several clinical cases of pediatric leukemia/lymphoma, revealing clinically relevant cryptic rearrangements missed by standard genomic panels.
Indexed as
Gene RearrangementGenomic Structural VariationHigh-Throughput Nucleotide SequencingNeoplasmsSequence Analysis, DNASoftwareAlgorithmsCell Line, TumorGenome, HumanHumans
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
Read underepoch 390
Registered trials
None linked
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.