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Kits, probes and applications for measuring genomic instability

A technology of instability and kits, applied in the direction of microbial determination/inspection, biochemical equipment and methods, etc., can solve the problems that the analysis of genome instability needs to be improved

Active Publication Date: 2021-08-06
BGI GENOMICS CO LTD +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] However, the current means of analyzing genomic instability still needs to be improved

Method used

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  • Kits, probes and applications for measuring genomic instability
  • Kits, probes and applications for measuring genomic instability
  • Kits, probes and applications for measuring genomic instability

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0285] Example 1—Copy number detection and purity correction module in the method of the present invention (GSA method)

[0286] In order to reflect the optimization made by the inventor for the genotype detection of large fragments, the inventor selected the public software with better industry evaluation but no targeted optimization for comparison. PureCN is a relatively complete implementation of the ABSOLUTE algorithm, which is currently the mainstream method for purity correction based on copy number data. PureCN software updates are relatively active, and the inventor is currently using the stable version 1.8.1 for evaluation. In addition to the copy number calculation itself, the advantages and disadvantages of the method of the present invention and PureCN purity calculation are also an index in this comparison.

[0287]Here the inventors will show a scatter plot of BAF and LRR calculated for each capture interval. The paragraph division given by the software is repr...

specific Embodiment example 2

[0329] Specific implementation case 2—a kit for comprehensive evaluation of genomic instability and homologous homogeneous gene repair gene mutation detection

[0330] (1) Sample selection

[0331] Randomly select 3 samples of commercialized cell lines, and use the algorithm designed by the present invention and the kit for comprehensive evaluation of genomic instability and homologous homogeneous gene repair gene mutation detection to carry out the verification of the embodiment.

[0332] sample name HCC1395 HCC1954 MDA-MB-436

[0333] (2) Sample fragmentation

[0334] This kit is compatible with 100-400ng DNA samples, use nuclease-free ultrapure water (NF water) to make up its volume to 75μl. Transfer the liquid to the disruption tube and put it into the nucleic acid disruption instrument (Bioruptor pico). The interrupter is precooled to 4°C, and the interrupting parameters are:

[0335] Target Fragment Size (bp) Interrupt paramet...

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Abstract

The present invention proposes a kit for measuring genome instability and its application. The probe set contained in the kit is determined through the following steps: the reference genome sequence is divided into multiple first-level regions, and the first-level region contains at least one Known SNP sites; for each of a plurality of primary regions, SNP filtering is performed; gap regions are selected; based on expected intervals, the gap regions are divided into at least one secondary region; for each of at least one secondary region, respectively Perform secondary high-frequency SNP search: extend processing from the center point of the secondary region to both sides at least once; and after at least one extended predetermined length, search for the SNP with the highest frequency in the obtained region, based on the primary high-frequency SNP and the summary of the secondary high-frequency SNPs are used as the starting point SNP to determine the tertiary region; and based on the tertiary region, a probe for specifically recognizing the tertiary region is constructed. Using this method, a probe combination that can be effectively used to analyze genome instability can be efficiently obtained.

Description

technical field [0001] The present invention relates to kits, probes and applications for measuring genome instability. Background technique [0002] Most cancer cells are characterized by genomic instability, the tendency of the genome to change during cell division. Cancer is often caused by the inactivation of several genes that control cell division and tumor suppressor genes. Studies have shown that the integrity of the genome is closely monitored by multiple monitoring mechanisms, including DNA damage checkpoints, DNA repair mechanisms, and mitotic checkpoints. Defects in the regulation of any of these mechanisms often lead to genomic instability, predisposing cells to malignant transformation. For example, post-translational modifications of histone tails are closely related to the regulation of cell cycle and chromatin structure, and DNA methylation status is related to genome integrity. Genomic instability provides individuals with the advantage of a shorter cell...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6886
Inventor 焦阳陈冬菊宋程程蔡宇航李红梅孟培王春丽邵明辉石太平
Owner BGI GENOMICS CO LTD
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