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A method and application for predicting homologous recombination deficiency in ovarian cancer based on genomic copy number variation biomarkers

A biomarker and copy number variation technology, applied in the field of biomedicine, achieves good accuracy, improves survival rate, and predicts stable effects

Active Publication Date: 2022-05-17
NANFANG HOSPITAL OF SOUTHERN MEDICAL UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

In conclusion, previous studies have suggested that there may be a correlation between CNVs and patients' HRD status, but little is known about which specific genomic loci of CNVs in tumors are directly associated with HRD

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  • A method and application for predicting homologous recombination deficiency in ovarian cancer based on genomic copy number variation biomarkers
  • A method and application for predicting homologous recombination deficiency in ovarian cancer based on genomic copy number variation biomarkers
  • A method and application for predicting homologous recombination deficiency in ovarian cancer based on genomic copy number variation biomarkers

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Embodiment 1

[0034] Application of a method for predicting homologous recombination deficiency in ovarian cancer based on copy number variation

[0035] The flow process of the present invention research is as Figure 5 As shown, in Example 1, 587 ovarian cancer patients from the TCGA-OV cohort were included in the study, and their clinical characteristics and DNA sequencing data were obtained from https: / / www.cancer.gov / tcga.

[0036] According to HRD-score (HRD score), 587 patients were divided into HRD group (HRD score ≥ 42) and non-HRD group (HRD score < 42), HRD score is loss of heterozygosity (Loss of heterozygosis, LOH), large Unweighted sum of Large-scale state Transition (LST) and Telomeric Allelic Imbalance (TAI).

[0037] GISTIC 2.0 was used to measure CNV profiles at the subchromosomal level of the tumor genome, and the segment files of the TCGA-OV cohort (recording the copy number of each locus in the genome) were used as input to GSITIC 2.0 to quantify the CNV status of chro...

Embodiment 2

[0047] Application of a copy number variation-based biomarker to predict pan-cancer homologous recombination deficiency

[0048] The DNA sequencing results of 10,635 patients with 33 cancer types from the TCGA pan-cancer cohort were analyzed to extend the predictive role of CNV for homologous recombination defects in ovarian cancer to other cancer types.

[0049] Calculate the average HRD score for each tumor to obtain the distribution of homologous recombination deficiency status in different tumors, found ovarian serous cystadenocarcinoma (OV), uterine carcinosarcoma (UCS), lung squamous cell carcinoma (LUSC), sarcoma (SARC) , Patients with esophageal cancer (ESCA). HRD scores were predominantly higher in patients with gastric adenocarcinoma (STAD), bladderurethral carcinoma (BLCA), breast cancer (BRCA), and lung adenocarcinoma (LUAD), whereas patients with thyroid cancer (THCA) and acute myelogenous leukemia (AML) had HRD scores lowest( image 3 A). This is consistent wi...

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Abstract

The invention relates to the field of biomedicine, in particular to a method and application for predicting homologous recombination deficiency in ovarian cancer based on biomarkers of genome copy number variation. The biomarker is a CNV based on any of chromosome segment 5q13.2, 8q24.2 or 19q12. The method for predicting the homologous recombination deficiency of ovarian cancer by the biomarkers is as follows: collecting surgical resection samples or tissue biopsy samples of ovarian cancer patients; performing DNA sequencing on the samples to obtain corresponding sequencing files; using GISTIC 2.0 to analyze the DNA sequencing files , to obtain the CNV map of the whole tumor genome; predict the HRD status of ovarian cancer based on the CNV of chromosome fragment 5q13.2, 8q24.2 or 19q12. The present invention provides the application of copy number variation CNV at the subchromosomal and gene levels in predicting homologous recombination defects in ovarian cancer patients, so as to screen potential beneficiaries of targeted therapy and bring more clinical benefits to HRD patients.

Description

technical field [0001] The invention relates to the field of biomedicine, in particular to a method and application for predicting homologous recombination deficiency in ovarian cancer based on biomarkers of genome copy number variation. Background technique [0002] Homologous recombination deficiency (HRD) is a common driver of tumorigenesis, leading to damage during DNA double-strand break repair and consequent genomic instability. Deficiency in homologous recombination is a common feature of many tumors, mainly seen in ovarian cancer. Meanwhile, as a therapeutic target, homologous recombination deficiency plays an important role in chemotherapy, targeted therapy and immunotherapy. Cytotoxic agents such as platinum analogues, topoisomerase I inhibitors, topoisomerase II inhibitors, and the antimetabolite gemcitabine have been shown to be effective against homologous recombination-deficient tumors. In contrast, PARP inhibitors show synthetic lethality when applied to cel...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6886C12Q1/6858C12N15/11
CPCC12Q1/6886C12Q1/6858C12Q2600/156C12Q2537/16C12Q2535/122
Inventor 董忠谊吴德华张萌王剑马思聪白雪谭家乐
Owner NANFANG HOSPITAL OF SOUTHERN MEDICAL UNIV
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