ArticleGenome research2017
Identification of complex genomic rearrangements in cancers using CouGaR.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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.
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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.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Chromoplexy: A Pathway to Genomic Complexity and Cancer Development.International journal of molecular sciences · 2025Review
- Chromoplexy.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Chromothripsis.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Whole-exome sequencing of Indian prostate cancer reveals a novel therapeutic target: POLQ.Journal of cancer research and clinical oncology · 2023Article
- HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery.Bioinformatics (Oxford, England) · 2022Article
- Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants.Genomics, proteomics & bioinformatics · 2022Article
- Decoding the heterogeneous landscape in the development prostate cancer.Oncology letters · 2021Review
- Integrative reconstruction of cancer genome karyotypes using InfoGenomeR.Nature communications · 2021Article
- How Chaotic Is Genome Chaos?Cancers · 2021Review
- Complex Variant Discovery Using Discordant Cluster Normalization.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.Cell · 2020Article
- Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.Genome research · 2020Article
- AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications.Nature communications · 2020Article
- Recovering rearranged cancer chromosomes from karyotype graphs.BMC bioinformatics · 2019Article
- Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.Nature communications · 2019Article
- Toward Recovering Allele-specific Cancer Genome Graphs.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer.Genome research · 2018Article
- Identifying simultaneous rearrangements in cancer genomes.Bioinformatics (Oxford, England) · 2018Article
- Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line.Frontiers in oncology · 2018Article
- Reconstructing cancer karyotypes from short read data: the half empty and half full glass.BMC bioinformatics · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
The genomic alterations associated with cancers are numerous and varied, involving both isolated and large-scale complex genomic rearrangements (CGRs). Although the underlying mechanisms are not well understood, CGRs have been implicated in tumorigenesis. Here, we introduce CouGaR, a novel method for characterizing the genomic structure of amplified CGRs, leveraging both depth of coverage (DOC) and discordant pair-end mapping techniques. We applied our method to whole-genome sequencing (WGS) samples from The Cancer Genome Atlas and identify amplified CGRs in at least 5.2% (10+ copies) to 17.8% (6+ copies) of the samples. Furthermore, ∼95% of these amplified CGRs contain genes previously implicated in tumorigenesis, indicating the importance and widespread occurrence of CGRs in cancers. Additionally, CouGaR identified the occurrence of 'chromoplexy' in nearly 63% of all prostate cancer samples and 30% of all bladder cancer samples. To further validate the accuracy of our method, we experimentally tested 17 predicted fusions in two pediatric glioma samples and validated 15 of these (88%) with precise resolution of the breakpoints via qPCR experiments and Sanger sequencing, with nearly perfect copy count concordance. Additionally, to further help display and understand the structure of CGRs, we have implemented CouGaR-viz, a generic stand-alone tool for visualization of the copy count of regions, breakpoints, and relevant genes.
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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.