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HRD score calculation method based on chip detection

A calculation method and chip detection technology, applied in biochemical equipment and methods, sequence analysis, microbial measurement/inspection, etc., can solve the problems of comprehensive scoring of homologous recombination defects and the inability to accurately judge the status of homologous recombination defects, etc. Achieve the effect of low cost, convenient and quick operation

Pending Publication Date: 2021-02-23
HENAN CANCER HOSPITAL
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Problems solved by technology

[0003] However, there is currently no comprehensive scoring method for homologous recombination deficiency (HRD), which cannot accurately determine the status of homologous recombination deficiency in the tested tumor samples

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  • HRD score calculation method based on chip detection
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Embodiment 1

[0033] The present invention provides such Figure 1-2 A method for calculating HRD scores based on chip detection is shown, and the specific operation steps are as follows:

[0034] 1): Take FFPE (Formalin-Fixed and Paraffin-Embedded, FFPE) samples from confirmed tumor patients to make H&E stained sections, observe the tumor cell content (TC%, Tumor Cell Percentage), and confirm that the tumor cell content is not less than 30%;

[0035] 2): Take the FFPE sample that has been screened for tumor cell content in step 1), and extract DNA (commercial FFPE sample DNA extraction kit can be used), the extraction concentration is required to be not less than 12ng / μL, and the extraction volume is not less than 6.6μL ;

[0036] 3): Using Affymetrix CNV FFPE Assay Kit processes the DNA solution extracted in step 2), after annealing (Anneal), gap filling (Gap Fill), first-stage polymerase chain reaction (1st PCR), second-stage polymerase chain reaction (2nd PCR), digestion (Hae III Di...

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Abstract

The invention discloses an HRD score calculation method based on chip detection. The HRD score calculation method comprises the specific operation steps: 1, establishing a genome heterozygosity deletion LOH calculation method; 2, establishing a calculation method of the telomere allele imbalance TAI; 3, establishing a calculation method of large chip end migration LST; 4, establishing an HRD calculation method. The invention provides a genome heterozygosity deletion LOH calculation method, a telomere allelic imbalance TAI calculation method, a large fragment end migration LST calculation method and an HRD calculation method, which can perform HRD score calculation on paraffin samples, and can evaluate HRD of tumor tissues by combining data of an Affymetrix OncoScan CNV FFPE gene chip withan HRD evaluation method; and the homologous recombination defect state of the detected tumor sample can be more accurately judged through the HRD score.

Description

technical field [0001] The invention relates to the field of tumor gene detection, in particular to an HRD score calculation method based on chip detection. Background technique [0002] Affymetrix's OncoScan CNV FFPE gene chip uses Molecular Inversion Probe (MIP) technology, which can identify copy number changes and loss of heterozygosity (LOH). The analysis uses MIP probes to capture more than 220,000 SNPs, which are evenly distributed In the whole genome, and with the increased probe density in about 900 cancer genes, the sample size only needs 80ng FFPE DNA, which can complete the detection of the copy number of the whole genome and the loss of heterozygosity (LOH) of ≤10Mb in the genome, focusing on Oncogenes can be detected by high-resolution (50-125kb) copy number, detecting copy number changes in as little as 25% of abnormal cells, and the copy number linear range is 50+ copies, due to the gene chip price of Affymetrix OncoScan CNV FFPE Inexpensive testing is fast ...

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Application Information

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IPC IPC(8): G16B30/00C12Q1/6886
CPCG16B30/00C12Q1/6886C12Q2600/156
Inventor 马杰石超郑金祥魏冰胡延平任鹏飞应建明张翠云夏庆欣李红乐
Owner HENAN CANCER HOSPITAL
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