Homologous recombination deficiency (HRD) detection method and reagent set thereof

A homologous recombination and state-of-the-art technology, applied in biochemical equipment and methods, genomics, proteomics, etc., can solve problems such as lethality

Pending Publication Date: 2022-02-25
ACT GENOMICS IP CO LTD
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Inhibition of PARP leads to synthetic lethality when HRR is absent

Method used

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  • Homologous recombination deficiency (HRD) detection method and reagent set thereof
  • Homologous recombination deficiency (HRD) detection method and reagent set thereof
  • Homologous recombination deficiency (HRD) detection method and reagent set thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0128] The stability test of embodiment 1LOH scoring algorithm

[0129] This study aimed to evaluate the stability of LOH scores derived by different algorithms.

[0130] 260,000 (260K), 150,000 (150K), 100,000 (100K), 50,000 (50K), 40,000 (40K), 3 Ten thousand (30K), twenty thousand (20K), ten thousand (10K), nine thousand (9K), eight thousand (8K), seven thousand (7K), six thousand (6K), five thousand (5K), four thousand ( 4K), 3 thousand (3K), 2 thousand (2K) or 1 thousand (1K) SNP loci were subjected to in silico downsampling. The aforementioned data were published in the high-throughput gene expression database GEO (Gene Expression Omnibus), and its GEO number is GSE39130 (Wang, Birkbak, et al., 2012). We first assigned chromosome arm information to each SNP site in the data set, and defined the allele frequency ranges for homozygous, heterozygous, and loss of heterozygous (LOH) SNP sites. This computational downsampling is performed by stratified sampling at the chrom...

Embodiment 2

[0134] Embodiment 2 Verification of LOH scoring algorithm

[0135] This study chose an algorithm for estimating the LOH score, which has a significant difference between the tumor group and the normal group when the number of SNP sites is different.

[0136] All samples used in the aforementioned studies were included in the analysis (Wang, Birkbak, et al., 2012). Tumor samples with BRCA2 LOH were classified as gene body high instability group (GI-H), in contrast to gene body low instability group (GI-L) tumor samples without BRCA2 LOH. Since cells with BRCA2 LOH exhibit gene body instability and exhibit high susceptibility to DNA damaging agents, the GI-H group in this study could represent the drug-sensitive group, while the GI-L group could represent the drug-resistant group Group. There were 12, 11 and 18 samples in GI-H group, GI-L group and normal group, respectively. The number of SNP sites is 260,000 (260K), 50,000 (50K), 10,000 (10K), 7,000 (7K), 5,000 (5K), 3,000 ...

Embodiment 3

[0138] Example 3 LOH scoring of samples with different tumor contents with or without consideration of chromosome arm imbalance factors

[0139] The aim of this study was to evaluate the effect of chromosome arm imbalance on the calculation of LOH scores.

[0140] A cancer cell line sample (NCL-H1395) with a copy number variation was mixed with a match-normal sample (match-normal sample) to simulate different tumor contents. The experimental procedure includes DNA extraction, sequence library construction and NGS sequencing, all of which are consistent with Example 5. The LOH scores of mixed samples with different tumor contents were estimated by three different algorithms. The first algorithm calculates the LOH score without considering the effect of chromosome arm imbalance (Equation 1). The second and third algorithms take into account the chromosome arm imbalance, which excludes SNPs located on the imbalanced chromosome arm (Equation 3). Unbalanced chromosome arms are c...

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Abstract

The invention provides a method, a system and a reagent set for evaluating the homologous recombination deficiency (HRD) state of an individual. The invention further provides a method, a system and a reagent set for determining therapy according to the HRD state of a human individual.

Description

technical field [0001] This application claims priority to US Provisional Application Serial No. 63 / 135,622, filed January 10, 2021, the entire contents of which are incorporated herein by reference. [0002] The present invention relates to a method, system and reagent set for assessing homologous recombination deficiency (HRD) status. Background technique [0003] Both poly(ADP-ribose) polymerases (PARPs) pathway and homologous recombination repair (HRR) pathway are involved in the repair of DNA damage. Inhibition of PARP may lead to the accumulation of unrepaired DNA single-strand breaks (single-strand breaks, SSBs) and paused replication forks (replication forks), resulting in the disintegration of replication forks and double-strand DNA breaks (double-strand DNA breaks, DSBs). In normal cells, double-stranded DNA breaks are repaired through the HRR pathway. Inhibition of PARP leads to synthetic lethality when HRR is absent. Today, PARP inhibitors have been developed...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6858C12Q1/6886G16B20/20G16B20/50
CPCC12Q1/6858C12Q1/6886G16B20/20G16B20/50C12Q2600/16C12Q2600/156C12Q2531/113C12Q2537/143C12Q2535/122C12Q2565/125C12Q1/6809C12Q2600/112C12Q2600/118C12Q2537/16C12Q2537/165
Inventor 王玮馥叶雅琪陈映嘉陈淑贞陈建宏陈冠萤谭文皓
Owner ACT GENOMICS IP CO LTD
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