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Method and device for correcting homologous recombination defect score and storage medium

A technology of homologous recombination and storage medium, applied in the fields of genomics, proteomics, instruments, etc., can solve the problems of low sensitivity and low accuracy, and achieve the effect of improving sensitivity and accuracy

Active Publication Date: 2022-02-18
北京吉因加医学检验实验室有限公司 +1
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Problems solved by technology

[0004] However, the existing homologous recombination defect scoring method cannot solve the problem of high scores of LST and TAI in tumor samples that have undergone whole-genome doubling (WGD, whole-genome doubling), and there is a problem of sensitivity due to the occurrence of WGD. Low, low accuracy and other defects

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  • Method and device for correcting homologous recombination defect score and storage medium
  • Method and device for correcting homologous recombination defect score and storage medium
  • Method and device for correcting homologous recombination defect score and storage medium

Examples

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Embodiment

[0079] This example corrects the method of homologous recombination defect score, including the following steps:

[0080] System CNV and System SNV Mutant Setting Procedure: Get the system CNV mutation and system SNV mutation to be tested.

[0081] This example uses GATK software to detect CNV mutation, combined with the sample CNV result, filter embryo CNV mutation, to obtain a system CNV mutation; use MUTECT2 software to detect SNV mutation, combined with the sample SNV result, filter embryo SNV mutation, to obtain system SNV mutation .

[0082] All genome Pienza WGD value acquisition steps: including the use of the obtained system CNV mutation and system SNV mutation, calculate the WGD value under the optimal model of the sample to be tested.

[0083] This example uses the filtered system CNV, SNV mutation point set as an input source software ABSOLUTE input, outputs WGD values, purity values, PLOIDY values ​​under multiple models to be tested, according to autonomous research ...

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Abstract

The invention discloses a method and device for correcting a homologous recombination defect score and a storage medium. The method comprises the following steps that: a system CNV and a system SNV of a to-be-detected sample are acquired; a WGD value, an original LOH score value, an original TAI score value and an original LST score value of the to-be-detected sample under an optimal model are calculated by utilizing system CNV and system SNV; and for the to-be-detected sample subjected to WGD, the corrected LST score value is equal to the product of (1-k1* WGD value) and the original LST score value, and the corrected TAI score value is equal to the product of (1-k2 * WGD value) and the original LST score value. According to the method and the device for correcting the homologous recombination defect score, the TAI and the LST are corrected by using the WGD value, so that the problem that TAI and LST scores of a whole genome multiplication sample are relatively high is solved, and the sensitivity and the accuracy of homologous recombination defect state evaluation are improved.

Description

Technical field [0001] The present application relates to the technical field of homologous recombinant defects, and in particular, to a method, apparatus, and storage medium for correcting homologous recombination defect scores. Background technique [0002] The research data shows that the incidence of ovarian cancer in women's compatriots will increase year by year, and mortality is also increasing; most ovarian cancer patients have found that 5 years of survival rate is less than 30%; therefore, ovarian cancer has become the most deadly malignant woman One of the tumors. However, with the approach of PARP inhibitors, a new hope for patients with ovarian cancer. After 2014, many PARP inhibitors were approved to be approved, which greatly improved the survival rate of patients with ovarian cancer and improved the benefits of survival. The biomarker of ovarian cancer PARP inhibitor expands from the BRCA gene to HRD (homologous recombination defect), meaning that the ovarian canc...

Claims

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Application Information

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IPC IPC(8): G16B20/50
CPCG16B20/50
Inventor 管彦芳李彩琴刘涛程海楠方欢
Owner 北京吉因加医学检验实验室有限公司
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