Fusion genes and their discovery using high throughput sequencing

Cancer Lett. 2013 Nov 1;340(2):192-200. doi: 10.1016/j.canlet.2013.01.011. Epub 2013 Jan 29.


Fusion genes are hybrid genes that combine parts of two or more original genes. They can form as a result of chromosomal rearrangements or abnormal transcription, and have been shown to act as drivers of malignant transformation and progression in many human cancers. The biological significance of fusion genes together with their specificity to cancer cells has made them into excellent targets for molecular therapy. Fusion genes are also used as diagnostic and prognostic markers to confirm cancer diagnosis and monitor response to molecular therapies. High-throughput sequencing has enabled the systematic discovery of fusion genes in a wide variety of cancer types. In this review, we describe the history of fusion genes in cancer and the ways in which fusion genes form and affect cellular function. We also describe computational methodologies for detecting fusion genes from high-throughput sequencing experiments, and the most common sources of error that lead to false discovery of fusion genes.

Keywords: Cancer; Fusion gene; High throughput sequencing.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Biomarkers, Tumor / genetics*
  • Computational Biology
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Gene Fusion*
  • Genetic Predisposition to Disease
  • Genetic Testing
  • Genome, Human*
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Neoplasms / diagnosis
  • Neoplasms / genetics*
  • Neoplasms / therapy
  • Phenotype
  • Precision Medicine
  • Predictive Value of Tests
  • Prognosis
  • Reproducibility of Results
  • Sequence Analysis, DNA*


  • Biomarkers, Tumor