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Kit and probe for measuring instability of genome and application of kit and probe

An instability and kit technology, which is applied in the determination/inspection of microorganisms, biochemical equipment and methods, etc., can solve the problem of analyzing the instability of the genome and other problems to be improved, and achieve the effect of saving production

Active Publication Date: 2021-04-16
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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  • Kit and probe for measuring instability of genome and application of kit and probe
  • Kit and probe for measuring instability of genome and application of kit and probe
  • Kit and probe for measuring instability of genome and application of kit and probe

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0286] Example 1—Copy number detection and purity correction module in the method of the present invention (GSA method)

[0287] In order to reflect the optimization made by the inventor for the detection of large-segment genotypes, the inventor selected 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.

[0288] 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 represen...

specific Embodiment example 2

[0330] Specific implementation case 2—a kit for comprehensive evaluation of genomic instability and homologous homogeneous gene repair gene mutation detection

[0331] (1) Sample selection

[0332] Randomly select 3 examples of commercialized cell line samples, and use the algorithm designed by the present invention and the test kit for the comprehensive evaluation of genome instability and homology and same group gene repair gene mutation detection to carry out embodiment verification.

[0333] sample name HCC1395 HCC1954 MDA-MB-436

[0334] (2) Sample fragmentation

[0335] 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 interruption instrument is precooled to 4°C, and the interruption parameters are:

[0336] Target Fragment Size (bp) ...

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Abstract

The invention provides a kit for measuring genome instability and application thereof, and a probe set contained in the kit is determined by the following steps: dividing a reference genome sequence into a plurality of first-level regions, wherein the first-level regions contain at least one known SNP site; performing SNP filtering on each of the plurality of primary regions; selecting a notch region; dividing the gap region into at least one secondary region based on an expected interval; for each of the at least one secondary region, respectively carrying out secondary high-frequency SNP search: carrying out extension treatment from the central point of the secondary region to two sides for at least one time, and after extending for a preset length for at least one time, searching for the SNP with the highest frequency in the obtained region, and determining a third-level region on the basis of taking the summary of the first-level high-frequency SNP and the second-level high-frequency SNP as the starting point SNP; and based on the third-level region, constructing a probe for specifically identifying the third-level region. By utilizing the method, the probe combination which can be effectively used for analyzing the instability of the genome can be effectively 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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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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