Technological Advances in the Detection of Novel Fusion Genes

Abstract

Since their first discovery in chronic myeloid leukaemia, fusion genes have been shown to play a central role in haematologic cancers. However, aberrations arising from this type of somatic mutations have been neglected in common solid tumours, largely because of limitations of current cytogenetic techniques. The recent discovery of recurrent gene fusions in prostate and lung cancer has led to a renewed interest in the identification of novel fusion genes in solid tumours. In this review, we discuss the technical challenges of studying gene fusions in solid tumours, appraise the application of newer molecular techniques and highlight emerging technologies, with the focus on next‐generation sequencing and chromogenic in situ hybridisation, that have greatly enhanced the speed and reliability of gene fusion discovery in malignant solid tumours.

Key Concepts:

  • A fusion gene is a gene hybrid formed from linking two physically separated genes.

  • A fusion gene can occur as a result of chromosomal rearrangements such as translocations, insertions, deletions and inversions, which lead to novel protein fusion products.

  • The detection of fusion genes is being recognised as a promising clinical tool for the diagnosis, staging classification, prognosis and treatment of cancer.

  • Gene fusions have been an underappreciated class of mutation in solid tumours.

  • The identification of gene fusions in solid tumours is technically challenging due to the complex and often chaotic karyotypic profiles of solid cancers.

  • Recent advances in genomics obtained from next generation sequencing, coupled with the emerging field of bioinformatics and ever‐advancing molecular techniques, have uncovered many novel oncogenic fusion genes in solid tumours that were unable to be detected by traditional cytogenetic methods.

  • Fluorescence In‐Situ Hybridisation (FISH) is recognised as the most effective diagnostic methods for the detection of gene fusions.

  • Transcriptome‐sequencing (also known as RNA‐sequencing), a recently introduced high‐throughput method of characterising ribonucleic acid (RNA) transcribed from the genome is rapidly emerging as the key method for the discovery of gene fusions.

  • Numerous challenges and unanswered issues remained with the discovery of novel gene fusions and their development as effective targeted cancer therapies or as clinical diagnostic and/or prognostic tools.

Keywords: fusion genes; genomic rearrangement; next‐generation sequencing; cancer genomics; chromogenic in‐situ hybridisation; fluorescence in‐situ hybridisation

Figure 1.

Fusion genes in cancer. Chromosomal aberrations (including translocation, insertion, deletion and inversion) can result in either fusion of an oncogene with another gene (a) or forced activation of an oncogene or down‐regulation of a tumour suppressor gene (b). P1 and P2 represent regulatory promoter elements for Gene 1 and 2, respectively. Arrows indicate locations of chromosomal breakpoints. The boxes represent exons whereas the lines between the boxes represent introns.

Figure 2.

Molecular and cytological techniques used in fusion gene discovery studies. (a) Exon‐walking quantitative real‐time PCR: an obvious over‐expression pattern from only the 3′ regions of the candidate gene suggests the presence of a genetic rearrangement. Arrows represent primer pairs. (b) 5′ RACE assay for the identification of unknown 5′ fusion partner. (c) Fusion‐specific RT‐PCR, where arrows represent forward and reverse primers set spanning the junction between the two fused genes. (d) FISH: Break‐apart (left) and fusion probe (right) strategies.

Figure 3.

Paired‐end sequencing versus single‐end sequencing. Paired‐end strategy (above) linked two reads as belonging to the same transcribed unit. With single‐end approach (below) individual reads are associated with independent genes, thus this method requires that the read spans the fusion junction.

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Further Reading

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Web Links

The Cancer Genome Atlas, http://cancergenome.nih.gov/

The Mitelman Database of Chromosome Aberrations in Cancer, http://cgap.nci.nih.gov/Chromosomes/Mitelman

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Leow, Pay Chin, Ku, Chee‐Seng, Soo, Ross, and Soong, Richie(Sep 2012) Technological Advances in the Detection of Novel Fusion Genes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023916]