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

Active Publication Date: 2019-04-16
ZHENYUE BIOTECHNOLOGY JIANGSU CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, the RNA fusion detection method

Method used

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

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Experimental program
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Example Embodiment

[0174] Example 1

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

[0176] It can be done using commercially available kits.

[0177] 1RNA quality control

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

[0179] 1.2 RNA was diluted to less than 5ng / ul, and the integrity of RNA was assessed by Agilent RNA Pico 6000, and its RIN value and DV200 (%) were recorded.

[0180] 2DNA quality control

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

[0182] 2. RNA library construction

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

[0184] 2.1 rRNA removal and fragmentation

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

[0186] 2.1.1 RNA sample and probe hybridization

[0187] A DNA probe specific for the resulting rRNA is added ...

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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.

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. ...

Claims

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Application Information

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IPC IPC(8): G16B20/50C12Q1/6886
CPCC12Q1/6886C12Q2600/156
Inventor 张亚晰于佳宁宋雪颜林林林小静陈维之杜波何骥
Owner ZHENYUE BIOTECHNOLOGY JIANGSU CO LTD
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