Method and system for efficient and economical detection of fusion genes

Abstract

The invention relates to the field of biotechnology, and more specifically to a fusion gene detection method. The method for efficient and economical detection of fusion genes provided by the invention includes: (1) core gene screening: selecting a core genome combination participating in fusion according to the tumor type; (2) core gene hybrid capture probe design: conducting imbricated full coverage probe design on the core gene obtained in step (1); (3) sequencing library construction: extracting the genomic DNA or transcriptome RNA of the a to-be-detected sample, and constructing an initial library; (4) probe hybrid capture: subjecting the probe synthesized according to step (2) and the initial library obtained by step (3) to hybrid capture reaction; and (5) high-throughput sequencing:conducting high-throughput sequencing on the probe hybrid captured core gene participated fusion gene; and (6) bioinformatic analysis: screening the sequencing data to obtain the fusion gene detection result. The method is fast, efficient and comprehensive.

Description

technical field [0001] The invention relates to the field of biotechnology, more specifically, to a fusion gene detection method. Background technique [0002] Fusion gene refers to the process of fusion of all or part of the sequences of two genes into a new gene, which is the result of mutations such as chromosomal translocation, insertion, inversion, deletion, etc. Generate a new fusion gene, which will be carcinogenic. For example, in 1973, Janet Rowley of the University of Chicago confirmed that the formation mechanism of the Philadelphia chromosome comes from chromosomal translocation, and discovered the first fusion gene BCR-ABL1 in leukemia. Gene fusion is a common feature of tumors, which can promote the occurrence and development of tumors. In many tumor types, a large number of fusion genes have been widely found, for example, one in urothelial carcinoma of the bladder, breast cancer, glioblastoma multiforme, squamous cell carcinoma of the head and neck, clear c...

AI Technical Summary

Problems solved by technology

Although Southern Blotting and RT-PCR techniques can detect fusion genes more accurately, they have disadvantages such as low throughput and inability to check unknown fusion genes. For example, the KMT2A gene has been reported to have as many genes as AFF1, MLLT10, MLLT3, MLLT1 and ELL. 64 fusion methods, so Southern Blotting and RT-PCR techniques cannot meet the needs of today's large-scale clinical sample testing

[0004] Due to the advantages of high-throughput, next-generation sequencing technology can comprehensively sequence the genomic DNA and transcriptome RNA of tumor samples (ie, WGS, WTS), and then obtain the information of all fusion genes in tumor tissues, including DNA and RNA levels. However, the bioinformatics analysis of whole genome sequencing (WGS) and transcriptome sequencing (WTS) has problems such as complex and cumbersome analysis steps, long time-consuming, and high false positive rate of fusion genes.

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