Evaluation method and device for homologous recombination repair defect and storage medium

Abstract

The invention discloses a homologous recombination repair defect assessment method and device and a storage medium. The method comprises the following steps: acquiring low-depth whole genome sequencing data of a to-be-detected sample, removing linkers, comparing to a reference genome, and filtering PCR repetitive sequences; performing quality control and pollution data filtration on the data, and then performing CNV analysis by using ACE software to obtain a total CNA spectrum; calculating an LST value according to the total CNA spectrum, and correcting the LST value by adopting a WGD condition; and judging whether the HRD is positive or negative according to the BRCA genotype and the corrected LST value. According to the method, low-depth whole-genome sequencing data is utilized to calculate an LST value, and the LST value is corrected by adopting a WGD condition; other genomic scar markers such as LOH and TAI are not needed, the corrected LST value can be directly used for HRD state evaluation, and the effectiveness and accuracy of PARP inhibitor treatment prediction and prognosis are improved.

Description

technical field [0001] The present application relates to the technical field of homologous recombination repair defect evaluation, in particular to a homologous recombination repair defect evaluation method, device and storage medium. Background technique [0002] Homologous recombination repair (HRR) is the preferred repair method for DNA double strand break (DSB). Homologous recombination deficiency (HRD) usually refers to the HRR dysfunction state at the cellular level, which can be caused by many factors such as germline mutations or somatic mutations of HRR-related genes and epigenetic inactivation, and often exists in a variety of malignant tumors. Among tumors, it is particularly prominent in ovarian cancer, breast cancer, pancreatic ductal carcinoma, prostate cancer and other tumors. HRD will produce specific, quantifiable, and stable genomic changes, and the status and degree of tumor HRD can be predicted by establishing an evaluation system based on genomic featu...

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Problems solved by technology

However, gene chip capture sequencing has the problem of large data errors, and whole genome sequencing requires high sequencing depth

In addition, the foreign article ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing tried to use low-depth whole-genome data to calculate LST, but the performance of real clinical samples was poor, and there were high index scores and sensitivity for samples with whole-genome duplication. Low, low accuracy and other issues

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