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DNA homologous recombination anomaly detection method and application thereof

A detection method and homologous recombination technology, applied in the field of medical molecular biology, can solve problems such as genome instability, and achieve the effects of reducing sequencing costs, high capture efficiency, and good capture stability and uniformity

Active Publication Date: 2021-01-15
北京迈基诺基因科技股份有限公司
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

In addition, mutations in other HRR-related genes, such as PALB2, CDK12, RAD51, CHEK2, ATM, etc., or methylation of the BRCA1 gene promoter, as well as other unspecified reasons, can cause HRD and lead to genome instability

Method used

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  • DNA homologous recombination anomaly detection method and application thereof
  • DNA homologous recombination anomaly detection method and application thereof
  • DNA homologous recombination anomaly detection method and application thereof

Examples

Experimental program
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Effect test

Embodiment 1

[0036] Example 1. Establishment of detection method for abnormal DNA homologous recombination

[0037] 1. Probe design

[0038] (1) SNP screening

[0039] Screen 50,000 SNP sites from 301 Chinese populations including the Beijing Han population (CHB), the Southern Han population (CHS), and the Dai population in Xishuangbanna (CDX) in the Thousand Genomes database according to the following rules (see the table below for some points) 1):

[0040] A. Eliminate Y chromosome and mitochondrial SNPs, and filter SNPs with minor allele frequency (MAF) less than 5%;

[0041] B. Filter SNPs that deviate significantly from the Hardy-Weinberg equilibrium;

[0042] C. Filter Insertion and Deletion;

[0043] D. SNPs that do not contain repeat regions within 75 bp upstream and downstream of the screening site;

[0044] E. Screen for SNPs within 75 bp upstream and downstream of the site that have no homology to other regions of the human genome;

[0045] F. The interval is 30KB, and th...

Embodiment 2

[0104] Embodiment 2, using the method of embodiment 1 to detect the HRD of 11 routine ovarian cancer patients

[0105] Using the method of Example 1, the HRD of 11 patients with ovarian cancer (all with the informed consent of the patients) were detected. The test results show that the reagent and method of Example 1 have a high capture rate for the target region, the average effective sequencing READ amount of the target region reaches 20Mb, and the average sequencing depth of the target region is above 3000X (see Table 2).

[0106] Table 2, utilize the method of the present invention to the quality control data result that 11 routine ovarian cancer patients detect

[0107]

[0108] By analyzing the BRCA gene mutations and HRD characteristic genomic scar events in 11 patients with ovarian cancer, such as loss of heterozygosity (Loss of Heterozygosity), Telomeric Allelic Imbalance, and Large- scale State Transitions), etc., respectively, according to the influence range of...

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Abstract

The invention provides a DNA homologous recombination anomaly detection method. The method comprises the following steps of (1) screening SNP sites; (2) designing a capture probe for the screened SNPsites; (3) carrying out genome DNA extraction and library construction; (4) carrying out library targeted enrichment; and (5) carrying out high-throughput sequencing, analyzing sequencing data, and using Kolmogorov-Smirnov test or scorHRD when the HRD state is judged.

Description

technical field [0001] The invention belongs to the field of medical molecular biology, and in particular relates to a method for detecting abnormality of DNA homologous recombination and its application. Background technique [0002] There are two main methods of DNA repair, one of which is accurate homologous recombination repair (Homologous Recombination Repair, HRR), and the other is error-prone non-homologous chromosome bonding repair (Non-Homologous End-Joining , NHEJ). The first repair method is common in DNA single-strand breaks, and the second repair is common in double-strand DNA breaks. HRR is a complex signaling pathway involving multiple steps, the key proteins of which are BRCA1 and BRCA2. Homologous Recombination Deficiency (HRD) will be caused if the mutation of BRCA gene leads to the loss of function of BRCA1 and BRCA2 proteins. In addition, mutations in other HRR-related genes, such as PALB2, CDK12, RAD51, CHEK2, ATM, etc., or methylation of the BRCA1 ge...

Claims

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Application Information

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IPC IPC(8): C12Q1/6858G16B20/20G16B25/20
CPCC12Q1/6858G16B20/20G16B25/20C12Q2531/113C12Q2535/122C12Q2537/165
Inventor 伍建姬晓雯王海丽刘娜韩路任丽娜
Owner 北京迈基诺基因科技股份有限公司
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