Method for detecting gene rearrangement, device, storage medium and processor

A technology of gene rearrangement and storage medium, applied in the fields of genomics, instruments, proteomics, etc., can solve the problem of difficulty in detecting the position of gene rearrangement breakpoints, and achieve the effect of low cost and high detection accuracy.

Active Publication Date: 2019-05-03
BEIJING USCI MEDICAL LAB CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] The main purpose of the present invention is to provide a method, device, storage medium and processor for detecting gene rearrangement, so as to solve the problem that it is difficult to detect the breakpoint position where gene rearrangement occurs in the prior art

Method used

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  • Method for detecting gene rearrangement, device, storage medium and processor
  • Method for detecting gene rearrangement, device, storage medium and processor
  • Method for detecting gene rearrangement, device, storage medium and processor

Examples

Experimental program
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Embodiment 1

[0062] Embodiment 1 detects the method for MLL-PTD gene rearrangement

[0063] 1. Samples and data

[0064] 1) Extract the patient's bone marrow or peripheral blood and store it in a collection tube.

[0065] 2) Extract the sample nucleic acid, and store the remaining samples at -80°C.

[0066] 3) Construct a sequencing library, and enrich the target region by hybridization capture method (the hybridization capture probes of the MLL gene are 36 exons of the gene, see Table 1 below for the specific sequence).

[0067] 4) The captured library is sequenced on the machine.

[0068] Table 1:

[0069]

[0070]

[0071]

[0072]

[0073]

[0074]

[0075] 2. Preprocessing of sequencing data

[0076] 1) Data quality control

[0077] Mainly to delete low-quality sequences, sequences containing more than 5 bases N were deleted; sequences with an average sequencing quality of 40 consecutive nucleotides lower than Q20 were also deleted.

[0078] 2) Alignment of MLL...

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Abstract

The invention provides a method for detecting gene rearrangement, a device, a storage medium and a processor. The method comprises the steps of acquiring a to-be-compared sequence of a to-be-tested sample; comparing the to-be-compared sequence with a reference genome, obtaining an abnormal comparison sequence, wherein the abnormal comparison sequence comprises the sequences with abnormal comparingpositions, the sequence with abnormal comparing directions, and the sequence incapable of comparing with the reference genome; determining the position of a candidate breakpoint according to the comparing position and the comparing direction of the abnormal comparison sequence in the reference genome; performing assembly by means of the sequence at the position which supports the candidate breakpoint in the to-be-compared sequence, and keeping the breakpoints same with the sequence information at the position of the candidate breakpoint in an assembling result as the breakpoints for gene rearrangement. The method, the device, the storage medium and the processor settle a problem of high difficulty in detecting the positions of the gene rearrangement in prior art.

Description

technical field [0001] The invention relates to the field of gene variation detection, in particular to a method, device, storage medium and processor for detecting gene rearrangement. Background technique [0002] In the prior art, nested RT-PCR is usually used to detect gene rearrangement, and the steps are as follows: based on the known target gene sequence, specific probes are prepared to detect gene rearrangement. The nested PCR reaction has two PCR amplifications, which reduces the possibility of amplifying multiple target sites (because there are few primers complementary to both sets of primers) and increases the sensitivity of detection; there are two pairs of PCR primers The pairing with the detection template increases the reliability of detection. Since the second set of primers is located within the first-round PCR product, it is extremely unlikely that the non-target fragment contains two sets of primer binding sites, so it is unlikely that the second set of p...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B20/30
Inventor 王彬安刘洋洋李富威王建伟伍启熹刘倩刘珂弟唐宇
Owner BEIJING USCI MEDICAL LAB CO LTD
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