Gene scar for characterizing HRD homologous recombination repair defects and identification method

Abstract

The invention relates to a gene scar for characterizing HRD homologous recombination repair defects and an identification method. The identification method comprises the following steps of step 1, performing whole genome sequencing to obtain gene original data; step 2, establishing a chromosome information matrix X (X1, X2, X3... Xn); step 3, performing data quality control; step 4, performing sequence comparison; step 5, deleting repeated reads; step 6, extracting an LRP file through signals copied by two genomes. step 7, comparing the number of high-quality non-reference bases with the number of the high-quality bases to extract a BAF file; step 8, generating fragmented LRP and BAF files for preprocessing to obtain an A allele copy number nA and a B allele copy number nB; step 9, obtaining a telomere allele imbalance TAI score through the nA and the nB; step 10, obtaining a large-scale transition LST score according to the length of each site; step 11, obtaining a heterozygosity deletion LOH score through judgment of the nA and the nB of each SNP site; and step 12, performing statistical calculation to obtain an HRD score and preforming judgment.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a gene scar and an identification method for characterizing HRD homologous recombination repair defect. Background technique [0002] At present, the domestic patent "a genomic recombination fingerprint and its identification method for characterizing hHRD homologous recombination defect" focuses on the genomic recombination fingerprint of HRD, and the prediction efficiency for PARP inhibitors is not high. Foreign studies have shown that HRD can cause "genomic scarring" "Phenomenon referred to as genomic scars, including genomic heterozygosity loss, English is Loss of Heterozygosity, referred to as LOH, Telomere allele imbalance English is Telomeric Allelic Imbalance, referred to as TAI, large fragment migration, English is Large-scale state Transition, referred to as LST. Some studies have tested and scored LOH, TAI, LST, etc., and judged the scores to define BRC...

AI Technical Summary

Problems solved by technology

[0003] Therefore, the present invention provides a gene scar and an identification method for characterizing HRD homologous recombination repair defects to overcome the problems of relatively large errors and poor robustness in gene chip data in the prior art

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