Abstract
We developed an innovative hybrid sequencing approach, IDP-fusion, to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. IDP-fusion is the first method to study gene fusion events by integrating Third Generation Sequencing long reads and Second Generation Sequencing short reads. We applied IDP-fusion to PacBio data and Illumina data from the MCF-7 breast cancer cells. Compared with the existing tools, IDP-fusion detects fusion genes at higher precision and a very low false positive rate. The results show that IDP-fusion will be useful for unraveling the complexity of multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes.
Highlights
A fusion gene is an aberrant gene formed by the concatenation of two separate genes
By inputting both Pacific Biosciences (PacBio) long reads and Illumina short reads to the error correction tool LSC [20], 7,425,797 errorcorrected PacBio long reads were output, 6,855,328 of which were mapped to the human genome
The corrected long reads and short reads were input into IDPfusion for detection of fusion genes, fusion sites and fusion isoforms, which are discussed in order below
Summary
A fusion gene is an aberrant gene formed by the concatenation of two separate genes. Gene fusion events are caused by genome translocation, interstitial deletion or chromosomal inversion. An oncogene can be upregulated by fusion with a gene containing a strong promoter [3]. A fusion gene can be translated to a fusion protein that contains chimeric domains from two genes. Such a chimeric domain combination is likely to result in aberrant fusion protein activity or loss of function of endogenous proteins. The classic example of a fusion gene with oncogenic activity is BCR–ABL1 in leukemia [4]. Because of the uniqueness of these fusion genes, they could serve as tumor-specific drug targets. There are likely many more fusion genes that remain to be detected and characterized [5]. The lack of a reliable and comprehensive fusion gene detection approach is a main obstacle in fusion gene research
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