Assay method, device, terminal device and computer readable storage medium for measuring genomic instability

A technology of instability and detection methods, applied in genomics, computer components, computing, etc., can solve the problems of genome instability that need to be improved

Active Publication Date: 2021-09-28
BGI GENOMICS CO LTD +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0006] However, the current analysis of genomic instability still needs to be improved

Method used

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  • Assay method, device, terminal device and computer readable storage medium for measuring genomic instability
  • Assay method, device, terminal device and computer readable storage medium for measuring genomic instability
  • Assay method, device, terminal device and computer readable storage medium for measuring genomic instability

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0230] Example 1—Copy number detection and purity correction module in the method of the present invention (GSA method)

[0231] 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.

[0232] Here the inventors will show a scatterplot of the calculated BAF and LRR for each capture region. The paragraph division given by the software is re...

specific Embodiment example 2

[0277] Specific implementation case 2—a kit for comprehensive evaluation of genomic instability and homologous homogeneous gene repair gene mutation detection (1) sample selection

[0278] Randomly select 3 samples of commercialized cell lines, and use the method and kit designed in the present invention to verify the examples.

[0279] Table 7

[0280] sample name HCC1395 HCC1954 MDA-MB-436

[0281] (2) Sample fragmentation

[0282] 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:

[0283] Table 8

[0284] Target Fragment Size (bp) Interrupt parameter number of cycles 200 Interrupt 30s / stop 30s 16

[0285] (3) End repair

[0286] 1) Take out the finishi...

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PUM

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Abstract

The invention provides a detection method for measuring genome instability, comprising: (1) obtaining sequencing data; (2) determining BAF values ​​and LRR values; (3) performing outlier removal; (4) at least one round of analysis segment processing; (5) merging of breakpoint sets; (6) merging of the second-level sorting segments; (7) filtering and cutting of the third-level sorting segments, (8) same distribution test; (9) determination BAF mean value, copy number mean value; (10) Carry out plane coordinate axis clustering and plotting to the BAF mean value, copy number mean percentage ordinal number of the four-level sorting fragments, so as to determine the tumor purity of the tumor sample in the test sample; (11) determine The ploidy correction factor of the sample to be tested; (12) performing BAF value correction and copy number correction; (13) determining the A genotype parameter value and the B genotype parameter value; (14) determining the variation type.

Description

technical field [0001] The invention belongs to the field of biotechnology, in particular, the invention relates to a detection method, equipment, terminal equipment and computer-readable storage medium 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 ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/10G16B20/30G16B20/20G06K9/62
Inventor 焦阳孟培王春丽陈冬菊蔡宇航邵明辉宋程程石太平
Owner BGI GENOMICS CO LTD
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