Fusion genes and their discovery using high throughput sequencing

Abstract

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.

Figure 1

An illustration of the four basic types of chromosomal rearrangement and how they lead to the formation of fusion genes. Original genomic layout is shown at the top, layout after rearrangement is shown at the bottom. Scissors indicate genomic breakpoints. A discontinuity in the black line indicates separate chromosomes.

Figure 2

A read-through fusion transcript is formed when an RNA polymerase continues transcribing beyond the end of a gene and transcription continues to an adjacent downstream gene. Exon skipping due to missing splice sites can give rise to a fusion transcript encoding a functional chimeric protein. Boxes indicate exons, thicker boxes indicate coding sequence.

Figure 3

A chromosomal rearrangement with intergenic breakpoints can result in a fusion gene encoding a functional chimeric protein. Illustration depicts two example scenarios. Boxes indicate exons, thicker boxes indicate coding sequence.

Figure 4

Illustration of the typical workflow involved in fusion gene discovery. The process for mate trimming is shown as performed by the ChimeraScan algorithm [57].

Figure 5

An illustration of the “incomplete elongation” theory for the formation of PCR chimeras [61]. According to this theory, a PCR chimaera is formed when an incomplete elongation product (pink) of a PCR primer (red) hybridizes with an unrelated but partially homologous template (orange), followed by chimeric elongation.

Figure 6

Data showing inter-sample contamination in a batch of transcriptome sequenced samples from The Cancer Genome Atlas glioblastoma project. Batch #2 is contaminated with fusion transcripts from a single sample expressing high levels of the fusion. Y-axis represents the total number of mate pairs spanning the fusion junction. The top panel (FGFR3-TACC3) shows the number of reads overlapping the fusion junction. The middle and bottom panels show the number of reads aligned to FGFR3 and TACC3 transcript sequences.