Specificity tumor probe area designing method for acquiring high-throughput sequencing in target area, device and probe

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

Active Publication Date: 2017-04-19
BGI TECH SOLUTIONS
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Problems solved by technology

There are certain defects in this detection. The design of the gene chip is not targeted, and the

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  • Specificity tumor probe area designing method for acquiring high-throughput sequencing in target area, device and probe
  • Specificity tumor probe area designing method for acquiring high-throughput sequencing in target area, device and probe
  • Specificity tumor probe area designing method for acquiring high-throughput sequencing in target area, device and probe

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Example Embodiment

[0065] Example 1

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

Example Embodiment

[0067] Example 2

[0068] According to the method for determining the nucleic acid sequence of the gene coding region of the sample to be tested, in this embodiment, a chip (chip508) data containing 508 gene coding regions is used for verification, and the chip508 covers currently known and various types of Cancer-related, 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 bioinformatics analysis, 508 genes in the collected blood and cancer tissue DNA samples were detected, and then the liver cancer-specific region (LIVCAN_REG) obtained by the present invention was detected. Analysis is performed to obtain the mutation information of the corresponding gene, and the obtained mutation region is horizontally compared with the designed specific liver cancer region to verify the specificity of the design of the present invention.

[0069] Among them,...

Example Embodiment

[0209] Example 3

[0210] According to the method for determining the nucleic acid sequence of the gene coding region of the sample to be tested of the present invention, in this embodiment, a chip (chip508) comprising 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 patients with liver cancer. 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] patient gender Inspection unit disease P2 Fema...

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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...

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Application Information

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IPC IPC(8): G06F19/20G06F19/28C12Q1/68C12N15/11
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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