Method and device for detecting chromosome joint deletion and storage medium

A chromosome and mutation detection technology, applied in the field of chromosome detection, can solve the problems of 1p/19q chromosome joint deletion, etc., and achieve the effect of improving the use efficiency

Inactive Publication Date: 2021-04-30
SHENZHEN HAPLOX BIOTECH
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Problems solved by technology

However, there is currently no method for analyzing the combined deletion of 1p / 19q chromosomes for high-throughput sequencing data

Method used

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  • Method and device for detecting chromosome joint deletion and storage medium
  • Method and device for detecting chromosome joint deletion and storage medium

Examples

Experimental program
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Effect test

Embodiment

[0070] In this example, the capture probes targeting the 1p and 19q regions are used to hybridize and capture genomic DNA, and then perform high-throughput sequencing; this example analyzes and detects chromosome loss of heterozygosity based on high-throughput capture sequencing. Specifically, this example Loss of heterozygosity on chromosome 1p and 19q was analyzed by combining point mutation frequency and copy number variation. Specific steps include:

[0071] The capture sequencing results of the short arm of chromosome 1 and the long arm of chromosome 19 of the tumor tissue sample and the corresponding normal control sample were respectively obtained, and the capture sequencing results of the tumor tissue sample and the normal control sample were compared to the reference genome and deduplication was obtained. The data after deduplication, and then perform the following operations:

[0072] a, Read the SNP result file generated by VarScan2 to obtain the variation informat...

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Abstract

The invention discloses a method and device for detecting chromosome joint deletion and a storage medium. The method comprises the following steps: performing SNP analysis on deduplicated data by adopting variation detection software to obtain variation information; reading dbSNP site information of which the crowd frequency is higher than 0.01 in a thousand-person genome database in 1p and 19q capture regions; acquiring copy number variation information in 1p and 19q regions by adopting copy number variation detection software; acquiring mutation frequency information of a normal control sample and mutation frequency of a tumor tissue sample; and analyzing 1p/19q joint deletion based on the point mutation frequency and the copy number change. 1p/19q chromosome joint deletion is analyzed through point mutation frequency and copy number change of high-throughput sequencing data; the blank of analyzing and detecting 1p/19q chromosome joint deletion by high-throughput sequencing data is filled; variation detection such as point mutation, insertion and deletion and fusion can be carried out; and the sequencing data use efficiency is improved.

Description

technical field [0001] The present application relates to the field of chromosome detection, in particular to a method, device and storage medium for detecting joint deletion of chromosomes. Background technique [0002] Gliomas are mainly divided into astrocytic tumors, oligodendrogliomatous cell tumors, oligoastrocytic tumors, ependymal tumors, and choroid plexus tumors according to their histomorphological differences. Among them, astrocytic tumors, oligodendrogliomas, and oligoastrocytic tumors all have a combined deletion of 1p / 19q, that is, the combined deletion of the short arm of chromosome 1 and the long arm of chromosome 19, or Chromosomal loss of heterozygosity. Studies have shown that the combined deletion rate of 1p / 19q in oligodendroglioma cell tumors is the highest, and its incidence can reach 50%-80%. 36%; the 1p / 19q chromosome joint deletion rate of astrocytic tumors is about 11%. [0003] Therefore, the detection of combined deletion of 1p / 19q chromosome...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B20/30G16B30/10G16B40/00
CPCG16B20/20G16B20/30G16B30/10G16B40/00
Inventor 许明炎陈亚如周衍庆陈实富
Owner SHENZHEN HAPLOX BIOTECH
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