Specific tumor probe region design method and device and probe for target region capture high-throughput sequencing

A technology of target region capture and design method, applied in the field of tumor probe design, can solve the problems of lack of pertinence, high cost, and inability to conduct large-scale research on liver cancer patients in gene chip design, reducing sequencing time and cost, and shortening detection cycle. , the effect of reducing the sequencing range

Active Publication Date: 2019-05-14
BGI TECH SOLUTIONS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

There are certain defects in this detection. The design of the gene chip is not targeted, and the cost is relatively high. It is impossible to conduct large-scale research on liver cancer patients.

Method used

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  • Specific tumor probe region design method and device and probe for target region capture high-throughput sequencing
  • Specific tumor probe region design method and device and probe for target region capture high-throughput sequencing
  • Specific tumor probe region design method and device and probe for target region capture high-throughput sequencing

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Effect test

Embodiment 1

[0066] According to the embodiment of the present invention, the whole exome data of 192 patients with liver cancer in the TCGA database were selected to evaluate a group of probes of the present invention, and the results showed that 107 patients (55%) had severe mutations in this region, and at the same time It was found that in the designed specific liver cancer chip region (LIVCAN_REG), the average 1Kb region contained at least one severe mutation, and a 211Kb region was randomly selected on the human genome for random data simulation, and the results showed that the randomly selected region averaged 1Kb Only about 0.0123 mutations related to liver cancer are contained, so it can be clearly seen that the chip region designed by the present invention is related to liver cancer, and the specificity of the chip is verified. At the same time, it shows that the probe (LIVCAN_SEQ) designed by the present invention has a very high detection rate of at least a part of the liver can...

Embodiment 2

[0068] According to the method for determining the nucleic acid sequence of the gene coding region of the sample to be tested according to the present invention, in this embodiment, a chip (chip508) data containing 508 gene coding regions is used for verification. chip508 covers currently known and various types of Cancer-related and reported mutated genes, as well as some genes related to chemotherapy and targeted drugs. Through the combination of target sequence capture technology, high-throughput sequencing and biological information analysis, 508 genes in the collected DNA samples of blood and cancer tissues were detected, and then the liver cancer-specific region (LIVCAN_REG) obtained in the present invention was analyzed. Analysis, to obtain the mutation information of the corresponding gene, and horizontally compare the obtained mutation region with the designed specific liver cancer region to verify the specificity of the design of the present invention.

[0069] Among...

Embodiment 3

[0210] According to the method for determining the nucleic acid sequence of the gene coding region of the sample to be tested according to the present invention, in this embodiment, a chip (chip508) containing 508 gene coding regions is also used for verification. Through sequence capture technology, high-throughput sequencing, and methods combined with bioinformatics analysis, 508 genes were detected in blood cell DNA samples and cancer tissue samples collected from 3 liver cancer patients, and then the liver cancer specificity obtained in the present invention The region is analyzed to obtain the mutation information of the corresponding gene, and the obtained mutation region is horizontally compared with the designed specific liver cancer region (LIVCAN_REG) to verify the specificity of the designed LIVCAN_REG region of the present invention.

[0211] Among them, the sample to be tested is the patient information as shown in Table 10:

[0212] Table 10

[0213] pa...

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Abstract

The invention discloses a specificity tumor probe area designing method for acquiring high-throughput sequencing in a target area, a device and a probe. The method comprises steps of calculating a gene and mutation related to a to-be-designed tumor in a first tumor mutation database, looking for a CDS area having the highest mutation frequency and designating the area as a first area, verifying the first area via tumor patient data stored in a second tumor mutation database, maximizing a sample frequency to achieve an area containing the most patients and designing the area as a second area, and calculating sample frequency and a RI value, further optimizing the sample area to achieve a third area. The RI value represents an average mutation number contained in each 1kb. By the use of the method, research is only required for the target area, so sequencing range can be greatly reduced and sequencing cost and time can be reduced; detection period can be obviously reduced; and cost can be lowered, so the specificity tumor probe area designing method for acquiring high-throughput sequencing in the target area is more suitable for clinical application.

Description

technical field [0001] The present invention relates to the technical field of tumor probe design, in particular to a specific tumor probe region design method and device for target region capture high-throughput sequencing and a probe. Background technique [0002] According to the new edition of the "World Cancer Report" released by the World Health Organization (WHO) on February 4, 2014, the number of new cancer patients is about 14 million each year, and it is expected to increase to 19 million in 2025 and 22 million in 2030. Grow to 24 million in 2035. Among them, the number of cancer cases in China in 2012 was 3.065 million, accounting for about one-fifth of the global cases. The number of cancer deaths was 2.205 million, accounting for about a quarter of the global cancer deaths. In the next 20 years, the incidence and death of cancer in my country will continue to rise. According to the forecast of the International Agency for Research on Cancer, if no effective m...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B25/20G16B50/00C12Q1/68C12N15/11
CPCC12Q1/6886C12Q2600/156G16B25/00G16B50/00
Inventor 孙岩程征宇方晓东魏晓明石泉于竞林木飞
Owner BGI TECH SOLUTIONS
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