ArticleNature cancer2022
Starfish infers signatures of complex genomic rearrangements across human cancers.
Article in Nature cancer, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 30 citations in OpenAlex.
- The landscape of structural variation in pediatric cancer.Cancer cell · 2026Article
- Integrated genomic and proteomic profiling reveals insights into chemoradiation resistance in cervical cancer.Molecular oncology · 2026Article
- Panorama of Chromosomal Instability in Lung Cancer.medRxiv : the preprint server for health sciences · 2025Article
- Sc-TUSV-Ext: Single-Cell Clonal Lineage Inference from Single Nucleotide Variants, Copy Number Alterations, and Structural Variants.Journal of computational biology : a journal of computational molecular cell biology · 2025Article
- CCRR: a user-friendly platform for analyzing complex chromosomal rearrangements in tumors.Bioinformatics (Oxford, England) · 2025Article
- The landscape of structural variation in pediatric cancer.bioRxiv : the preprint server for biology · 2025Article
- Chromoanagenesis and Beyond: Catastrophic Events Shaping the Genome.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Starfish: Deciphering Complex Genomic Rearrangement Signatures Across Human Cancers.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A review on trends in development and translation of omics signatures in cancer.Computational and structural biotechnology journal · 2024Review
- Transcription and DNA replication collisions lead to large tandem duplications and expose targetable therapeutic vulnerabilities in cancer.Nature cancer · 2024Article
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- Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach.Nature protocols · 2024Review
- Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements.Nature reviews. Genetics · 2024Review
- Accurate and sensitive mutational signature analysis with MuSiCal.Nature genetics · 2024Article
- Aneuploidy and complex genomic rearrangements in cancer evolution.Nature cancer · 2024Review
- Large tandem duplications in cancer result from transcription and DNA replication collisions.medRxiv : the preprint server for health sciences · 2024Article
- Boveri and beyond: Chromothripsis and genomic instability from mitotic errors.Molecular cell · 2024Review
- The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients.Nature communications · 2024Article
- ReConPlot: an R package for the visualization and interpretation of genomic rearrangements.Bioinformatics (Oxford, England) · 2023Article
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
Complex genomic rearrangements (CGRs) are common in cancer and are known to form via two aberrant cellular structures-micronuclei and chromatin bridges. However, which of these mechanisms is more relevant to CGR formation in cancer and whether there are other undiscovered mechanisms remain unknown. Here we developed a computational algorithm, 'Starfish', to analyze 2,014 CGRs from 2,428 whole-genome-sequenced (WGS) tumors and discovered six CGR signatures based on their copy number and breakpoint patterns. Extensive benchmarking showed that our CGR signatures are highly accurate and biologically meaningful. Three signatures can be attributed to known biological processes-micronuclei- and chromatin-bridge-induced chromothripsis and circular extrachromosomal DNA. Over half of the CGRs belong to the remaining three signatures, not reported previously. A unique signature, which we named 'hourglass chromothripsis', with localized breakpoints and a low amount of DNA loss, is abundant in prostate cancer. Hourglass chromothripsis is associated with mutant SPOP, which may induce genome instability.
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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.