JP-7854805-B2 - Method for constructing a genomic scar model

Inventors

• 楊爽
• 董華
• 陳学俊
• 黄紅偉
• 鄭方克
• 鄭立謀

Assignees

• 厦門艾徳生物医薬科技股▲フン▼有限公司

Dates

Publication Date

20260507

Application Date

20201229

Priority Date

20200907

Claims (5)

1. A method for constructing a genomic scar model, The following steps: (1) Collect BRCAness -positive and BRCAness-negative samples and construct a training set; (2) Analyze the CNV status of the above training set and determine the type of CNV and the corresponding quantity; (3) Determine the BRCAness positive and BRCAness negative events of the training set; (4) Machine learning utilizes logistic regression to train the weights of CNV types based on the BRCAness type of the sample to construct a genomic scar model ; based on the BRCAness-positive and BRCAness-negative events of the training set, the weights of the different types of CNV determined in step (2) are trained and obtained; and then the weighted CNVs of the different types are accumulated to obtain a genomic scar model used for calculating the GSS; (5) Collect other known BRCAness-positive and BRCAness-negative samples to construct a test set, and obtain the type and corresponding quantity of CNV of the test set based on step (2); (6) Substitute the results obtained in step (5) into the genome scar model obtained in step (4) to calculate the GSS of the test set, and further validate the genome scar model based on the GSS score; A method for constructing a genomic scar model, characterized by including, The aforementioned genome scar model includes a training set and a test set. The BRCAness positivity includes: in any one of BRCA1/2, a pathogenic or probably pathogenic mutation occurs in one allele and loss of heterozygosity occurs in another allele; in any one of BRCA1/2, two pathogenic or probably pathogenic mutations occur; in one allele of BRCA1, loss of heterozygosity occurs and methylation occurs in the promoter region of another allele ; The aforementioned BRCAness positivity further includes related events in which other homologous recombination repair-related genes other than the BRCA1/2 genes cause genomic instability through mutation, loss of homozygosity, or silencing of the corresponding genes. The aforementioned BRCAness negativity means that the homologous recombination repair-related gene is wild-type, and furthermore, there is no loss of heterozygosity in the corresponding allele, or no methylation in its promoter region. The type of CNV in step (2) above is determined based on the length of the mutant fragment, the type of the mutant fragment, and the position of the mutant fragment on the genome. Here, the lengths of the mutant fragments are classified into short fragments of 5 to 10 M, medium fragments longer than 10 M and less than or equal to 15 M, and long fragments longer than 15 M. The types of mutant fragments are classified into categories including loss of heterozygosity, unbalanced amplification of mutant fragments, and balanced amplification of mutant fragments. A method for constructing a genomic scar model, wherein the genomic location of the mutated fragment is classified into types including the mutated fragment being located on the telomere side, the mutated fragment being located within the centromere region, and the mutated fragment being located outside the telomere side and within the centromere region.
2. The construction method according to claim 1 , characterized in that a measurement sample is calculated using a genome scar model, samples with a GSS score less than 0.5 are determined to be BRCAness-negative samples, and samples with a GSS score greater than 0.5 are determined to be BRCAness-positive samples.
3. Use of a genomic scar model constructed by the construction method described in claim 1 in enriching the HRR mutation-associated patient population.
4. Use of a genomic scar model constructed by the construction method described in claim 1 in enriching the platinum-sensitive patient population.
5. Use of a genomic scar model constructed by the construction method described in claim 1 in enriching the PARPi-sensitive patient population.

Description

This invention belongs to the field of genetic diagnostics and specifically relates to a method for constructing a genomic scar model. Homologous recombination repair (HRR) is a crucial repair mechanism for double-strand DNA damage and is commonly found in cells to accurately repair harmful breaks in double-strand DNA. HRR is a complex signaling pathway involving multiple steps, with the breast cancer susceptibility genes (BRCA1/2) being key homologous recombination function-related genes. Mutations in the BRCA genes, resulting in the loss of function of the BRCA1 and BRCA2 proteins, lead to HRR dysfunction. This is commonly known as homologous recombination deficiency (HRD), and HRD is widespread as a tumor driver event in breast cancer, ovarian cancer, prostate cancer, and pancreatic cancer. Tumors with BRCA1/2 mutations or expression abnormalities are typically sensitive to platinum-based drugs and poly[ADP-ribose] polymerase inhibitors (PARPi). Therefore, detecting BRCA1/2 gene mutations plays a crucial role in the clinical classification and medication guidance of this type of disease. However, as research progresses, the detection of BRCA gene mutations is increasingly unable to meet existing clinical needs. The concentration of patients with BRCA gene mutations in the treatment response group is decreasing, and some patients may be missed. For example, in triple-negative breast cancer, 20% of patients have BRCA gene mutations, but the overall response rate to platinum-based chemotherapy in this group is approximately 30%. Furthermore, in high-grade serous ovarian cancer, 30% of patients have BRCA gene mutations, but the overall response rate to PARPi in this group is approximately 50%. This indicates that some BRCA-negative patients respond to platinum-based chemotherapy or PARPi, and therefore, BRCA detection may miss some patients receiving treatment. The main reason for this omission is, firstly, that the detection of BRCA gene mutations is relatively limited. There are many HRR function-related genes, and BRCA1/2 are two of these with relatively high mutation frequencies. From an analysis of the principles of drug action, any HRR gene that can form a synthetic lethal effect with platinum-based drugs and PARPi is noteworthy (collectively referred to as BRCAness events). For example, the results of the PROfound trial showed that deletion of the HRR-related gene ATM is effective against prostate cancer with PARPi olaparib, and therefore, many clinical trials are gradually shifting from interest in BRCA to other HRR-related genes. Next, BRCA gene mutation detection cannot cover all types of genomic abnormalities that cause HRR dysfunction. In addition to gene mutations, methylation of the BRCA1 promoter region and loss of heterozygosity (LoH) within the BRCA gene region are also major causes of HRR dysfunction. Finally, the interpretation of results from BRCA gene mutation detection is complex and prone to omissions, making clinical application relatively difficult. Currently, many authoritative organizations, such as the American Society of Clinical Genetics and Genomics (ACMG) and the European Molecular Genetics Quality Network (EMQN), provide optimal guidelines for molecular genetic analysis of hereditary breast/ovarian cancer. The classification of BRCA mutations—pathogenic, probably pathogenic, significance unknown, probably benign, and benign—and the varying levels of evidence incorporated by different guidelines pose a significant obstacle to clinical application. Based on the above reasons, there is a very urgent need for novel clinical molecular markers that can easily quantitatively evaluate homologous recombination repair deficiencies in cells. Searching for molecular markers characteristic of downstream genomic mutations (including mutations, copy number variations (CNVs), and gene expression abnormalities) that induce HRR deficiency is a major research goal today. In 2009, Olafur et al. discovered that the characteristics of CNV mutations are closely related to BRCAness, and in 2012, Abkevich et al. discovered that the number of LoHs in the whole genome is significantly related to BRCAness events. In the same year, Popova et al. discovered that large-scale state transitions (LSTs) in the gene are associated with BRCA1/2 gene inactivation, and Birkbak et al. discovered that telomere allele imbalance (TAI) is associated with BRCAness events in triple-negative breast cancer and is significantly enriched in the platinum-sensitive group. In 2016, Myriad, Inc. in the United States quantitatively calculated the HRD score (HRD assessment) by aggregating the number of occurrences of LoH, LST, and TAI across the entire genome. This aggregated index can accurately predict BRCAness events and simultaneously effectively enrich the platinum-sensitive and PARPi-sensitive patient population. Compared to detecting the BRCA gene alone, the HRD assessment can screen 40% more potential patients. In addition