Method and device for detecting gene fusion mutation, storage medium, processor and method for normalizing transcription group data expression quantity

A technology of fusion mutation and gene fusion, which is applied in the fields of genomics, proteomics, biochemical equipment and methods, etc., and can solve problems such as false positives

CN109637587AActive Publication Date: 2019-04-16ZHENYUE BIOTECHNOLOGY JIANGSU CO LTD
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Patent Information

Authority / Receiving Office
CN · China
Current Assignee / Owner
Publication Date
2019-04-16

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Abstract

The invention discloses a method and device for detecting gene fusion mutation, a storage medium, a processor and a method for standardizing the transcription group data expression quantity so as to reduce the false positivity of detection. The method comprises the following steps of: detecting whether a sample to be detected accords with a known fusion mutation type from a transcript level; if not, detecting whether the sample to be detected has potential fusion, wherein the potential fusion comprises at least one of the following: unknown fusion exists on the transcript level of a protooncogene; the protooncogene has structural fusion at the genome level; if so, detecting whether the potential fusion is sense fusion or not, and if so, detecting whether the expression level of the protooncogene is abnormal in the following two aspects: over-expression of a functional area of the protooncogene; significant differences in the expression quantities of the protooncogene in 5'and 3'ends. If yes, judging to be positive, otherwise judging to be negative. The method integrates multi-dimensional fusion characteristics to reduce false positives of detection results.
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Description

technical field

[0001] The present application relates to the field of gene mutation detection, in particular, to a method, device, storage medium, processor, and method for standardizing the expression level of transcriptome data for detecting gene fusion mutations. Background technique

[0002] Gene fusion mutation is a common chromosomal variation, which refers to the formation of new genes due to chromosomal mutations such as chromosomal translocation, intermediate deletion, or chromosome inversion of two genes or fragments of multiple genes. The fusion of a strong promoter and a downstream functional gene will cause abnormal expression of the downstream gene. According to functional classification, the downstream functional genes of fusion genes found in tumors can be divided into the following categories: kinases, transcription factors, metabolic enzymes, Wnt signaling pathways, TGFβ, chromatin modifying genes, etc. All of these genes have proto-oncogene properties. ...

Examples

Embodiment 1

[0175] 1. Co-extraction of DNA / RNA

[0176] It can be done with commercial kits on the market.

[0177] 1RNA quality control

[0178] 1.1 The concentration of extracted RNA was first determined by Qubit RNA HS.

[0179] 1.2 Dilute the RNA to below 5ng / ul, use Agilent RNA Pico 6000 to evaluate the integrity of the RNA, and record the RIN value and DV200 (%).

[0180] 2 DNA quality control

[0181] 2.1 Concentration measurement: Quantification of extracted DNA using Qubit

[0182] 2. RNA library construction

[0183] The initial amount of library construction is 100ng total RNA, and the rRNA is removed first, and then the remaining total RNA is used for library construction. The details are as follows:

[0184] 2.1 rRNA removal and fragmentation

[0185] The removal of rRNA uses a more conventional probe binding method, as follows:

[0186] 2.1.1 Hybridization of RNA samples with probes

[0187] A DNA probe that specifically results in rRNA is added to the RNA.

[0188...