fusioncancer-database of fusion genes related to human cancer

RNA-SEQ sequencing can be used for fusion gene discovery, in the past more than 10 years, the RNA-SEQ sequencing data has been increasing, the data of the fusion gene found is also increasing;

Fusioncancer is a database of human cancer-related fusion genes using RNA-SEQ data from the NCBI SRA database, using Tophat-fusion, Soap-fusion, Fusionmap, Chimerascan 4 prediction of fusion gene software;

The URL is as follows:

http://donglab.ecnu.edu.cn/databases/FusionCancer/

Click the Borwse DB button to first browse the records in the database

DataBase ID: For each fusion gene record, will give a unique ID, with FUSC beginning, followed by numbers;

Head gene: The first genes that produce fused genes

Head Breakpoint: The location of the junction of the fused gene on the first gene

Tail Gene: A second gene that produces fused genes

Tail Breakpoint: The location of the junction of the fusion gene on the second gene

Cancer type: The corresponding cancer type

SRA: Number of raw data in the SRA database

Detail: fusion of genetic details;

Take the first, for example, click on Fusion Detail, the details are as follows

In the detailed information interface, the software for predicting the fusion gene is also given in the breakpoint or exon region of the gene; The number of reads supported,

You can also get a sequence of fused genes by clicking the link at the bottom. For the above fusion gene, the transcription sequence is as follows:

For the fusion gene, the most direct result only detects the junction of two genes, breakpoint, in fact, is not able to directly determine the full-length sequence of the fusion transcript, this is a second-generation sequencing compared to three-phase sequencing a disadvantage;

The sequence given here is actually a combination of all the transcripts of two genes, and you can see that the breakpoints are the same.

Summarize:

For the detection of fusion genes, the second generation sequencing has the following drawbacks:

1) can only give the fusion gene, and the detected fusion gene has false positive;

2) There is no specific sequence of fusion transcripts, no direct evidence of fusion genes;

The three-generation sequencing has a congenital advantage in the detection of fusion genes due to its long-reading advantage;

Fusioncancer database can be regarded as the integration of the second generation sequencing in fusion gene detection, first used 4 software to predict, through the database, can be screened out 4 kinds of software predicted by the fusion gene, can reduce the false positive rate, followed by the possible fusion transcription sequence, The follow-up of RT-PCR verification;

fusioncancer-database of fusion genes related to human cancer