ArticlePeerJ2017
Prioritisation of structural variant calls in cancer genomes.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- HER2-positive neuroendocrine breast carcinoma: a case study uncoversPathologica · 2025Article
- Mucinous cystic neoplasms and simple mucinous cysts are two distinct precursors of pancreatic cancer: clinicopathological, genomic, and transcriptomic characterization.The Journal of pathology · 2025Article
- Neoadjuvant triplet immune checkpoint blockade in newly diagnosed glioblastoma.Nature medicine · 2025Article
- Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.Nucleic acids research · 2023Article
- A survey of algorithms for the detection of genomic structural variants from long-read sequencing data.Nature methods · 2023Review
- Integrative characterization of intraductal tubulopapillary neoplasm (ITPN) of the pancreas and associated invasive adenocarcinoma.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
- Juvenile polyposis diagnosed with an integrated histological, immunohistochemical and molecular approach identifying new SMAD4 pathogenic variants.Familial cancer · 2022Article
- "Pure" hepatoid tumors of the pancreas harboring CTNNB1 somatic mutations: a new entity among solid pseudopapillary neoplasms.Virchows Archiv : an international journal of pathology · 2022Article
- Histo-molecular characterization of pancreatic cancer with microsatellite instability: intra-tumor heterogeneity, B2M inactivation, and the importance of metastatic sites.Virchows Archiv : an international journal of pathology · 2022Article
- Article
- RAF1 rearrangements are common in pancreatic acinar cell carcinomas.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2020Article
- Mutational signatures in tumours induced by high and low energy radiation in Trp53 deficient mice.Nature communications · 2020Article
- Visualization tools for human structural variations identified by whole-genome sequencing.Journal of human genetics · 2020Review
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sensitivity of short read DNA-sequencing for gene fusion detection is improving, but is hampered by the significant amount of noise composed of uninteresting or false positive hits in the data. In this paper we describe a tiered prioritisation approach to extract high impact gene fusion events from existing structural variant calls. Using cell line and patient DNA sequence data we improve the annotation and interpretation of structural variant calls to best highlight likely cancer driving fusions. We also considerably improve on the automated visualisation of the high impact structural variants to highlight the effects of the variants on the resulting transcripts. The resulting framework greatly improves on readily detecting clinically actionable structural variants.
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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.