Device for detecting blood disease fusion gene

A fusion gene and blood disease technology, applied in the field of biology, can solve problems such as instability, undetectable fusion type, difficulty in sample storage and transportation, etc.

Pending Publication Date: 2020-05-19
北京橡鑫生物科技有限公司 +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

First, multiplex PCR or gel electrophoresis techniques can only detect known fusion types that have been designed, but cannot detect fusion types without

Method used

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  • Device for detecting blood disease fusion gene
  • Device for detecting blood disease fusion gene
  • Device for detecting blood disease fusion gene

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0048] Sample: Known sample, clinically detected positive for BCR-ABL1 fusion.

[0049] Use the device of the present invention (execution command reference figure 1 shown):

[0050] 1. The input data is the raw data of next-generation sequencing off-machine, and the data format is fastq.

[0051] 1) Preprocess the original off-machine data, including removing adapters and low-quality data (sequences with N content > 5 or bases below Q15 in the sequence > 40%).

[0052] 2) Compare and sort the processed original off-machine data with the reference genome, and obtain the comparison results, and the data format is bam.

[0053] 3) Identify the duplication reads of the bam file and remove the duplication reads.

[0054] 2. Identify candidate k-mers that may contain breakpoints on the processed alignment data.

[0055] Carry out k-mers recognition in the way of pattern growth, assuming a sequence M of length N is given, k-mer refers to a sequence of length k, this sequence is ...

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Abstract

The invention discloses a device for detecting a blood disease fusion gene. The device comprises a sequencing module used for obtaining sequencing data of a tumor sample through next-generation sequencing; a data preprocessing module used for preprocessing the sequencing data obtained in the sequencing module; a candidate k-mers identification module used for identifying candidate k-mers possiblycomprising breakpoints in the sequencing data processed by the data preprocessing module; a local assembly comparison recognition fusion mode module used for extracting reads where a candidate k-mersset of the tumor sample is located and paired reads, and carrying out local assembly to obtain contigs; a fusion gene credibility prediction module used for predicting the fusion gene credibility; anda fusion result annotation module used for annotating the breakpoints obtained in the fusion gene credibility prediction module. By applying the technical scheme provided by the invention, various fusion variation types of multiple genes can be accurately identified.

Description

technical field [0001] The invention relates to the technical field of biology, in particular to a device for detecting blood disease fusion genes. Background technique [0002] The human genome consists of 23 pairs of chromosomes, including 22 pairs of somatic chromosomes, one X chromosome and one Y chromosome. The genome contains a total of about 3 billion DNA base pairs, including about 25,000 genes. function. Fusion gene refers to the splicing of two non-adjacent genes in the genome under the influence of natural or foreign environmental factors to form a new gene fragment. The occurrence of fusion genes often leads to sequence abnormality or protein function abnormality, which in turn leads to or promotes the occurrence and development of tumors. Many human diseases may be caused by gene fusion, including some genetic diseases, cancer and hematological tumors. Some gene fusions are important clinical features and prognostic factors of hematological tumors. [0003] I...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B40/00
CPCG16B30/10G16B40/00
Inventor 张萌萌郭璟楼峰曹善柏
Owner 北京橡鑫生物科技有限公司
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