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Method and device for correcting homologous recombination repair defect score

A homologous recombination and defect technology, applied in the field of bioinformatics, can solve the problems of limited application, high sequencing data volume, inability to cover somatic cell mutations, etc., and achieve the effect of improving accuracy

Pending Publication Date: 2022-04-05
深圳吉因加医学检验实验室
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The shortcomings of WGS detection, such as the need for higher sequencing data and the inability to cover somatic mutations in the HRR signaling pathway, limit its clinical application

Method used

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  • Method and device for correcting homologous recombination repair defect score
  • Method and device for correcting homologous recombination repair defect score
  • Method and device for correcting homologous recombination repair defect score

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0092] The evaluation method of this embodiment mainly includes the following steps:

[0093] (1) Sequencing data files (bam format) generated after steps such as comparison, sorting, filtering, and labeling and repetition using sequencing off-machine data for tumor samples and paired blood cell samples;

[0094] (2) Use Mutect2 software to analyze the SNV of the tumor samples to be tested, and obtain the mutation set of the system SNV, including information such as mutation frequency and mutation site depth;

[0095] (3) Annotate the obtained system SNV;

[0096] (4) Use the cnvkit software to take the bam of the tumor sample to be tested and the paired sample as input, analyze and obtain the segment of the CNV mutation in the sample, and output the size of the segment, the number of probes contained in the segment, and the segment BAF value and other information;

[0097] (5) Use the ABSOLUTE software to analyze the purity and ploidy of the tumor samples to be tested, and ...

Embodiment 2

[0218] Embodiment 2 HRD accuracy evaluation

[0219] In this embodiment, the method in Example 1 (abbreviated as WES detection method) is used for evaluation.

[0220] (1) Consistency comparison with WGS detection

[0221] In this embodiment, 50 ovarian cancer FFPE samples (formalin-fixed and paraffin-embedded samples, Formalin-Fixed and Parrffin-Embedded, referred to as FFPE samples) were used, and the results detected by the WES detection method based on Example 1 were compared with Compared with the HRD values ​​obtained by WGS detection, the results are as follows figure 2 As shown, Spearman ρ=0.88, showing a good consistency.

[0222] (2) Consistency comparison with the standard

[0223] The present embodiment has detected 12 pairs of HRD standard items, by comparing with reference value, investigates the accuracy of this detection method, the result is as follows image 3 It shows that the HRD detection result of the detection method of this embodiment has a high co...

Embodiment 3

[0224] Embodiment 3HRD score and clinical curative effect

[0225] In this example, the method of Example 1 was used to detect the samples of 59 patients with high-grade serous ovarian cancer treated with platinum-based chemotherapy drugs for the first time, and the relationship between the first platinum curative effect data and HRD was calculated, including 45 patients with platinum-sensitive Data and 14 cases of platinum resistance data. Statistics see Figure 4 . from Figure 4 It can be seen that HRD-positive samples have a higher PFS than HRD-negative samples (Log rank p=0.04, HR=0.55). PFS refers to the progression-free survival period (progression-free survival). Time to disease progression or death from any cause.

[0226] Those skilled in the art can understand that all or part of the functions of the various methods in the foregoing implementation manners can be realized by means of hardware, or by means of computer programs. When all or part of the functions i...

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Abstract

The invention relates to a method and device for correcting a homologous recombination repair defect score, and the method comprises the following steps: a correction step: correcting the homologous recombination repair defect score according to the following formula: HRD score correction = LOH score + (1-alpha * WGD) * LST score + (1-beta * WGD) * TAI score, and obtaining the corrected homologous recombination repair defect score; hRD score correction refers to a corrected homologous recombination repair defect score, LOH score refers to a heterozygosity deficiency score, LST score refers to a large fragment migration score, TAI score refers to a telomere allele imbalance score, WGD refers to a whole genome replication information value, and alpha and beta refer to correction coefficients. By correcting the homologous recombination repair defect score, the accuracy of homologous recombination repair defect evaluation is effectively improved, and guidance is provided for medication of cancer patients.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a method and device for correcting homologous recombination repair defect scoring. Background technique [0002] Ovarian cancer is a common malignant tumor in the female reproductive system, and nearly 250,000 women are diagnosed with ovarian cancer every year in the world. With surgery and platinum- and taxane-based chemotherapy, the average 5-year survival rate is about 30% [1] . In recent years, a number of PARP inhibitors have been approved for marketing, effectively prolonging the progression-free survival (PFS) of ovarian cancer patients. The biomarkers of PARP inhibitors in ovarian cancer have been expanded from BRCA gene to homologous recombination deficiency (HRD), which means that the beneficiary population of ovarian cancer will expand from about 20% to more than 50%. Survival prognosis is of great help. [0003] Homologous recombination repair (HRR) is the preferred ...

Claims

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Application Information

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IPC IPC(8): G16B40/00
Inventor 易鑫付骁睿程海楠李彩琴潘潇郝时光孟璐杜新华易玉婷
Owner 深圳吉因加医学检验实验室
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