ArticleBMC medical genomics2015
OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing.
Article in BMC medical genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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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.
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Who cites it
6 citing papers in PubMed, 12 citations in OpenAlex.
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- PANOPLY: Omics-Guided Drug Prioritization Method Tailored to an Individual Patient.JCO clinical cancer informatics · 2018Article
- The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine.Journal of molecular biology · 2018Review
- Metastatic triple-negative breast cancer patient withCold Spring Harbor molecular case studies · 2017Article
- Identification of breast cancer candidate genes using gene co-expression and protein-protein interaction information.Oncotarget · 2016Article
- Omics Pipe: a community-based framework for reproducible multi-omics data analysis.Bioinformatics (Oxford, England) · 2015Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundBreast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient. Next generation sequencing of RNA (RNA-Seq) is a suitable method to detect targets for individualized treatment. Challenges that arise are i) preprocessing and analyzing RNA-Seq data in the n-of-1 setting, ii) extracting clinically relevant and actionable targets from complex data, iii) integrating drug databases, and iv) reporting results to clinicians in a timely and understandable manner.
resultsTo address these challenges, we present OncoRep, an RNA-Seq based n-of-1 reporting tool for breast cancer patients. It reports molecular classification, altered genes and pathways, gene fusions, clinically actionable mutations and drug recommendations. It visualizes the data in an approachable html-based interactive report and a PDF clinical report, providing the clinician and tumor board with a tool to guide the treatment decision making process.
conclusionsOncoRep is free and open-source ( https://bitbucket.org/sulab/oncorep/ ), thereby offering a platform for future development and innovation by the community.
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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.