ArticleBMC genomics2013
Identification of gene fusions from human lung cancer mass spectrometry data.
Article in BMC genomics, 2013. 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.
- Fusion genes in cancers: Biogenesis, functions, and therapeutic implications.Genes & diseases · 2025Review
- Identification of gene fusion events inNAR genomics and bioinformatics · 2020Article
- ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection.BMC medical genomics · 2020Article
- FusionPro, a Versatile Proteogenomic Tool for Identification of Novel Fusion Transcripts and Their Potential Translation Products in Cancer Cells.Molecular & cellular proteomics : MCP · 2019Article
- Bronchoalveolar Lavage Proteomics in Patients with Suspected Lung Cancer.Scientific reports · 2017Article
- Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification.BMC genomics · 2016Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.Scientific reports · 2015Article
- A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.PloS one · 2015Article
- The Structural Characterization of Tumor Fusion Genes and Proteins.Computational and mathematical methods in medicine · 2015Article
- Article
- Onco-proteogenomics: cancer proteomics joins forces with genomics.Nature methods · 2014Article
- Interdisciplinary dialogue for education, collaboration, and innovation: intelligent Biology and Medicine in and beyond 2013.BMC genomics · 2013Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTandem mass spectrometry (MS/MS) technology has been applied to identify proteins, as an ultimate approach to confirm the original genome annotation. To be able to identify gene fusion proteins, a special database containing peptides that cross over gene fusion breakpoints is needed.
methodsIt is impractical to construct a database that includes all possible fusion peptides originated from potential breakpoints. Focusing on 6259 reported and predicted gene fusion pairs from ChimerDB 2.0 and Cancer Gene Census, we for the first time created a database CanProFu that comprehensively annotates fusion peptides formed by exon-exon linkage between these pairing genes.
resultsApplying this database to mass spectrometry datasets of 40 human non-small cell lung cancer (NSCLC) samples and 39 normal lung samples with stringent searching criteria, we were able to identify 19 unique fusion peptides characterizing gene fusion events. Among them 11 gene fusion events were only found in NSCLC samples. And also, 4 alternative splicing events were characterized in cancerous or normal lung samples.
conclusionsThe database and workflow in this work can be flexibly applied to other MS/MS based human cancer experiments to detect gene fusions as potential disease biomarkers or drug targets.
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