ArticleGenome research2012
nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Novel gene-intergenic fusion involving ubiquitin E3 ligase UBE3C causes distal hereditary motor neuropathy.Brain : a journal of neurology · 2023Article
- Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants.Genomics, proteomics & bioinformatics · 2022Article
- Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data.GigaScience · 2021Article
- ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data.NAR genomics and bioinformatics · 2021Article
- Integrative reconstruction of cancer genome karyotypes using InfoGenomeR.Nature communications · 2021Article
- LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.BMC genomics · 2020Article
- Overview of research on fusion genes in prostate cancer.Translational cancer research · 2020Review
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.Genome biology · 2019Article
- Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.Nature communications · 2019Article
- NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors.BMC bioinformatics · 2019Article
- SeqOthello: querying RNA-seq experiments at scale.Genome biology · 2018Article
- Computational identification of micro-structural variations and their proteogenomic consequences in cancer.Bioinformatics (Oxford, England) · 2018Article
- Identifying simultaneous rearrangements in cancer genomes.Bioinformatics (Oxford, England) · 2018Article
- Reconstructing cancer karyotypes from short read data: the half empty and half full glass.BMC bioinformatics · 2017Article
- Scalable whole-genome single-cell library preparation without preamplification.Nature methods · 2017Article
- Computational approaches for the identification of cancer genes and pathways.Wiley interdisciplinary reviews. Systems biology and medicine · 2017Review
- Identification of complex genomic rearrangements in cancers using CouGaR.Genome research · 2017Article
- Computational Methods for Characterizing Cancer Mutational Heterogeneity.Frontiers in genetics · 2017Review
- Identifying fusion transcripts using next generation sequencing.Wiley interdisciplinary reviews. RNA · 2016Review
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Authors and funding
6 authors.
Funding
Abstract
Complex genomic rearrangements (CGRs) are emerging as a new feature of cancer genomes. CGRs are characterized by multiple genomic breakpoints and thus have the potential to simultaneously affect multiple genes, fusing some genes and interrupting other genes. Analysis of high-throughput whole-genome shotgun sequencing (WGSS) is beginning to facilitate the discovery and characterization of CGRs, but further development of computational methods is required. We have developed an algorithmic method for identifying CGRs in WGSS data based on shortest alternating paths in breakpoint graphs. Aiming for a method with the highest possible sensitivity, we use breakpoint graphs built from all WGSS data, including sequences with ambiguous genomic origin. Since the majority of cell function is encoded by the transcriptome, we target our search to find CGRs that underlie fusion transcripts predicted from matched high-throughput cDNA sequencing (RNA-seq). We have applied our method, nFuse, to the discovery of CGRs in publicly available data from the well-studied breast cancer cell line HCC1954 and primary prostate tumor sample 963. We first establish the sensitivity and specificity of the nFuse breakpoint prediction and scoring method using breakpoints previously discovered in HCC1954. We then validate five out of six CGRs in HCC1954 and two out of two CGRs in 963. We show examples of gene fusions that would be difficult to discover using methods that do not account for the existence of CGRs, including one important event that was missed in a previous study of the HCC1954 genome. Finally, we illustrate how CGRs may be used to infer the gene expression history of a tumor.
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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.