Gene set for liver cancer detection and detection and design method of panel of gene set

A liver cancer and gene technology is applied to the gene set for liver cancer detection and its panel detection design. The application of the gene set in the gene chip can solve the cumbersome process of information analysis method, the omission of important sites, and the single technical process, etc. problems, to achieve the effect of strong design controllability, low detection and analysis costs, and high overall coverage

Active Publication Date: 2018-11-06
ZHONGSHAN HOSPITAL FUDAN UNIV +1
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Problems solved by technology

The technology of diagnosing liver cancer by high-throughput sequencing of the genome in biological samples has made great progress, but the existing liver cancer detection has the following defects: 1. The detection content is single and the function is limited
At present, most panel designs are only aimed at drug guidelines, labels, and limited literature collection, and there are few comprehensive analyzes based on the results of large-scale sequencing platforms, public databases, and text mining techniques
3. At present, the technical process of panel design and synthesis method is single, and there are always areas that canno...

Method used

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  • Gene set for liver cancer detection and detection and design method of panel of gene set
  • Gene set for liver cancer detection and detection and design method of panel of gene set

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preparation example Construction

[0052] As a preferred embodiment, the preparation method of the gene panel of the present application mainly includes the following steps:

[0053] 1. Screening of liver cancer information and related genes. Including the collection of at least three aspects of liver cancer information and its related genes, the first aspect, the collection of liver cancer information and its related genes obtained from the sequencing of liver cancer patient samples in the local database; the second aspect, the collection of liver cancer information and its related genes disclosed in the public database. Genes; the third aspect is to collect liver cancer information and related genes disclosed in the literature; merge and remove redundancy from the liver cancer information and related genes collected in the three aspects, and determine the standard gene name through HGNCapproved Official Symbol to form a gene set ;

[0054] 2. Detection target area selection. Based on the gene set obtained i...

Embodiment 1

[0069] Example 1 Panel sequencing

[0070] 1) Sample collection

[0071] According to the collection standards of the "Chinese Standards for the Diagnosis and Treatment of Primary Liver Cancer", medical institutions collected samples from 110 liver cancer patients.

[0072] 2) Sample DNA extraction, library preparation

[0073] For individualized gene detection of liver cancer, liver cancer tumor FFPE is used as the experimental group for each sample, and the blood samples collected at the same time are used as the control group. Considering the influence of label joints, hybridization, and data volume utilization, the number of databases established is evaluated, and the number of databases established once is confirmed. 4 pairs of library samples are the best. Use FFPE Nucleic Acid Extraction Kit and Blood Cell Extraction Kit for sample extraction respectively, and use Qubit DNA Fluorescence Quantitator and Qubit dsDNA HS Assay kit for quantitative detection. The extractio...

Embodiment 2

[0087] Example 2 Data analysis after getting off the machine

[0088] The information analysis process is used for the paired sample analysis of the liver cancer project, taking the off-machine Fastq file of the sequencing platform (such as BGI-Seq500 in this example) as input, and obtaining The final mutation result and the basic statistical information of the data are displayed.

[0089] This protocol was used for the paired-sample analysis of the liver cancer project. For the fastq after the BGI-Seq500 is off the machine, it is first filtered by SOAPnuke to filter out the reads with a proportion of low-quality bases (≦10) greater than 50%, or a proportion of N (undetermined bases) greater than 10%. , and count relevant indicators before and after filtering, including initial data volume, effective data volume, CG content, N content, Q20, Q30, etc.; compare the clean fastq obtained after filtering to the human reference genome hg19, and this step is realized by paligner; A...

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Abstract

The invention discloses a preparation method of a liver cancer detection panel. The preparation method comprises the following steps: screening liver cancer information and related genes thereof, thusobtaining a gene set; selecting a gene target zone; designing a panel probe; synthesizing an RNA (Ribonucleic Acid) single-stranded probe, thus obtaining the gene detection panel. The gene detectionpanel designed by the invention can be used for diagnosis, typing and prognosis of liver cancer, has wide gene coverage degree and strong transferability and is suitable for newly-developed detectionplatforms.

Description

technical field [0001] The invention belongs to the field of gene detection, and in particular relates to a gene set for liver cancer detection and a panel detection design method thereof, and also relates to the application of the gene set in a gene chip. Background technique [0002] Liver cancer is one of the most common malignant tumors in clinical practice. According to statistics, there are about 740,000 new cases of liver cancer and 700,000 deaths from liver cancer every year worldwide, about half of which occur in China. Due to the high morbidity and mortality of liver cancer, liver cancer is paid special attention worldwide, and the incidence and mortality of liver cancer in my country are also increasing year by year. Liver cancer ranks second in the overall cause of death related to various malignant tumors. Seriously endangering human health, it has become a global and serious public health problem. The occurrence and development of liver cancer is a complex biol...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886
CPCC12Q1/6886
Inventor 周俭樊嘉安娜于竞杨欣荣阳作权王向东林木飞黄傲谢颖朱师达吴逵
Owner ZHONGSHAN HOSPITAL FUDAN UNIV
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