Method for detecting fusion gene based on transcriptome sequencing data

Abstract

The invention relates to a method for detecting a fusion gene based on transcriptome sequencing data. The method comprises the following steps of S1: performing second-generation transcriptome sequencing and third-generation transcriptome sequencing on a sample to obtain second-generation transcriptome sequencing data and third-generation transcriptome sequencing data; S2: comparing the third-generation transcriptome sequencing data with a reference genome, identifying FLNC reads possibly subjected to gene fusion and gene pairs possibly participating in fusion, extracting a sequence of the FLNC reads possibly subjected to the gene fusion, and judging a fusion position; and S3: comparing the second-generation transcriptome sequencing data with the FLNC reads possibly subjected to the gene fusion, obtained in the step S2, and identifying the gene pairs fused indeed according to logarithms of discordant paired-end reads and the number of junction reads in a comparison result and the number of the FLNC reads possibly subjected to the gene fusion. According to the method, the fusion gene is detected in combination with third-generation transcriptome sequencing and second-generation transcriptome sequencing, so that a result of detecting the fusion gene in combination with second-generation and third-generation sequencing support evidences is more reliable.

Description

technical field [0001] The present invention relates to the field of transcriptome analysis, more particularly, to a method for detecting fusion genes based on transcriptome sequencing data. Background technique [0002] Gene rearrangement is a phenomenon that often occurs between genetic materials in organisms. Gene rearrangement often leads to fusion genes of one or more genes or gene fragments that are not originally under a cistron, and are transcribed as a cistron , which will lead to the activation, inactivation or new function of certain genes. The occurrence of many diseases is accompanied by the phenomenon of fusion genes. For example, leukemia is often accompanied by fusion genes such as bcr / abl, AML1 / ETO, CBFβ / MYH11, PML / RARα, etc. Fusion genes are also found in various solid tumors, non-small cell lung cancer EML4-ALK in prostate cancer, SLC45A3-ELK4 in prostate cancer, PAX3-FOXO1 in rhabdomyosarcoma, etc. Scientific research has found that some fusion genes ar...

AI Technical Summary

Problems solved by technology

Compared with the short-read long read sequence of the second-generation sequencing, the long-read long read sequence of the third-generation sequencing can more effectively reduce the false positive caused by the alignment error during the alignment process, but this type of false positive cannot be completely avoided

At the same time, the third-generation transcriptome sequencing will also randomly generate some chimeric reads formed by random connection of fragments from different genes during the library construction process, resulting in false positive fusions